Index – I

I (pyrosetta.rosetta.core.chemical.element.Elements attribute) (pyrosetta.rosetta.protocols.abinitio.abscript.StageID attribute) i (pyrosetta.rosetta.protocols.cluster.DataPoint property) I() (in module pyrosetta.rosetta.ObjexxFCL.format) i() (pyrosetta.rosetta.core.pose.rna.BasePairStep method) I() (pyrosetta.rosetta.numeric.Quaternion_double_t static method) (pyrosetta.rosetta.numeric.xyzMatrix_double_t static method) (pyrosetta.rosetta.numeric.xyzMatrix_float_t static method) (pyrosetta.rosetta.ObjexxFCL.FArray1_bool_t method) (pyrosetta.rosetta.ObjexxFCL.FArray1_char_t method) (pyrosetta.rosetta.ObjexxFCL.FArray1_double_t method) (pyrosetta.rosetta.ObjexxFCL.FArray1_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray1_int_t method) (pyrosetta.rosetta.ObjexxFCL.FArray1_ObjexxFCL_FArray1D_int_t method) (pyrosetta.rosetta.ObjexxFCL.FArray1_std_string_t method) (pyrosetta.rosetta.ObjexxFCL.FArray1_unsigned_long_t method) (pyrosetta.rosetta.ObjexxFCL.FArray1A_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray1A_int_t method) (pyrosetta.rosetta.ObjexxFCL.FArray1D_bool_t method) (pyrosetta.rosetta.ObjexxFCL.FArray1D_char_t method) (pyrosetta.rosetta.ObjexxFCL.FArray1D_double_t method) (pyrosetta.rosetta.ObjexxFCL.FArray1D_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray1D_int_t method) (pyrosetta.rosetta.ObjexxFCL.FArray1D_ObjexxFCL_FArray1D_int_t method) (pyrosetta.rosetta.ObjexxFCL.FArray1D_std_string_t method) (pyrosetta.rosetta.ObjexxFCL.FArray1D_unsigned_long_t method) i() (pyrosetta.rosetta.protocols.frag_picker.Contact method) I1() (pyrosetta.rosetta.ObjexxFCL.FArray1_bool_t method) (pyrosetta.rosetta.ObjexxFCL.FArray1_char_t method) (pyrosetta.rosetta.ObjexxFCL.FArray1_double_t method) (pyrosetta.rosetta.ObjexxFCL.FArray1_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray1_int_t method) (pyrosetta.rosetta.ObjexxFCL.FArray1_ObjexxFCL_FArray1D_int_t method) (pyrosetta.rosetta.ObjexxFCL.FArray1_std_string_t method) (pyrosetta.rosetta.ObjexxFCL.FArray1_unsigned_long_t method) (pyrosetta.rosetta.ObjexxFCL.FArray1A_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray1A_int_t method) (pyrosetta.rosetta.ObjexxFCL.FArray1D_bool_t method) (pyrosetta.rosetta.ObjexxFCL.FArray1D_char_t method) (pyrosetta.rosetta.ObjexxFCL.FArray1D_double_t method) (pyrosetta.rosetta.ObjexxFCL.FArray1D_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray1D_int_t method) (pyrosetta.rosetta.ObjexxFCL.FArray1D_ObjexxFCL_FArray1D_int_t method) (pyrosetta.rosetta.ObjexxFCL.FArray1D_std_string_t method) (pyrosetta.rosetta.ObjexxFCL.FArray1D_unsigned_long_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2_bool_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2_core_pack_dunbrack_BBDepNRChiSample_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2_core_pack_dunbrack_BBDepScoreInterpData_1_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2_core_pack_dunbrack_BBDepScoreInterpData_2_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2_core_pack_dunbrack_BBDepScoreInterpData_3_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2_core_pack_dunbrack_BBDepScoreInterpData_4_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2_core_pack_dunbrack_BBDepScoreInterpData_5_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2_core_pack_dunbrack_BBIndNRChiSample_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2_core_pack_dunbrack_PackedDunbrackRotamer_1_1_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2_core_pack_dunbrack_PackedDunbrackRotamer_1_2_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2_core_pack_dunbrack_PackedDunbrackRotamer_1_3_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2_core_pack_dunbrack_PackedDunbrackRotamer_1_4_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2_core_pack_dunbrack_PackedDunbrackRotamer_1_5_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2_core_pack_dunbrack_PackedDunbrackRotamer_2_1_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2_core_pack_dunbrack_PackedDunbrackRotamer_2_2_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2_core_pack_dunbrack_PackedDunbrackRotamer_2_3_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2_core_pack_dunbrack_PackedDunbrackRotamer_2_4_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2_core_pack_dunbrack_PackedDunbrackRotamer_2_5_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2_core_pack_dunbrack_PackedDunbrackRotamer_3_1_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2_core_pack_dunbrack_PackedDunbrackRotamer_3_2_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2_core_pack_dunbrack_PackedDunbrackRotamer_3_3_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2_core_pack_dunbrack_PackedDunbrackRotamer_3_4_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2_core_pack_dunbrack_PackedDunbrackRotamer_3_5_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2_core_pack_dunbrack_PackedDunbrackRotamer_4_1_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2_core_pack_dunbrack_PackedDunbrackRotamer_4_2_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2_core_pack_dunbrack_PackedDunbrackRotamer_4_3_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2_core_pack_dunbrack_PackedDunbrackRotamer_4_4_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2_core_pack_dunbrack_PackedDunbrackRotamer_4_5_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2_core_pack_dunbrack_PackedDunbrackRotamer_5_1_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2_core_pack_dunbrack_PackedDunbrackRotamer_5_2_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2_core_pack_dunbrack_PackedDunbrackRotamer_5_3_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2_core_pack_dunbrack_PackedDunbrackRotamer_5_4_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2_core_pack_dunbrack_PackedDunbrackRotamer_5_5_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2_double_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2_int_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2_numeric_xyzVector_double_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2_ObjexxFCL_FArray2D_float__star__t method) (pyrosetta.rosetta.ObjexxFCL.FArray2_ObjexxFCL_ubyte_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2_std_string_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2_unsigned_char_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2_unsigned_long_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2_utility_vector1_core_pack_dunbrack_cenrot_CentroidRotamerSampleData_std_allocator_core_pack_dunbrack_cenrot_CentroidRotamerSampleData_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2_utility_vector1_double_std_allocator_double_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2A_double_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2A_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_bool_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_core_pack_dunbrack_BBDepNRChiSample_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_core_pack_dunbrack_BBDepScoreInterpData_1_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_core_pack_dunbrack_BBDepScoreInterpData_2_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_core_pack_dunbrack_BBDepScoreInterpData_3_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_core_pack_dunbrack_BBDepScoreInterpData_4_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_core_pack_dunbrack_BBDepScoreInterpData_5_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_core_pack_dunbrack_BBIndNRChiSample_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_core_pack_dunbrack_PackedDunbrackRotamer_1_1_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_core_pack_dunbrack_PackedDunbrackRotamer_1_2_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_core_pack_dunbrack_PackedDunbrackRotamer_1_3_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_core_pack_dunbrack_PackedDunbrackRotamer_1_4_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_core_pack_dunbrack_PackedDunbrackRotamer_1_5_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_core_pack_dunbrack_PackedDunbrackRotamer_2_1_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_core_pack_dunbrack_PackedDunbrackRotamer_2_2_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_core_pack_dunbrack_PackedDunbrackRotamer_2_3_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_core_pack_dunbrack_PackedDunbrackRotamer_2_4_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_core_pack_dunbrack_PackedDunbrackRotamer_2_5_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_core_pack_dunbrack_PackedDunbrackRotamer_3_1_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_core_pack_dunbrack_PackedDunbrackRotamer_3_2_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_core_pack_dunbrack_PackedDunbrackRotamer_3_3_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_core_pack_dunbrack_PackedDunbrackRotamer_3_4_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_core_pack_dunbrack_PackedDunbrackRotamer_3_5_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_core_pack_dunbrack_PackedDunbrackRotamer_4_1_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_core_pack_dunbrack_PackedDunbrackRotamer_4_2_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_core_pack_dunbrack_PackedDunbrackRotamer_4_3_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_core_pack_dunbrack_PackedDunbrackRotamer_4_4_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_core_pack_dunbrack_PackedDunbrackRotamer_4_5_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_core_pack_dunbrack_PackedDunbrackRotamer_5_1_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_core_pack_dunbrack_PackedDunbrackRotamer_5_2_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_core_pack_dunbrack_PackedDunbrackRotamer_5_3_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_core_pack_dunbrack_PackedDunbrackRotamer_5_4_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_core_pack_dunbrack_PackedDunbrackRotamer_5_5_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_double_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_int_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_numeric_xyzVector_double_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_ObjexxFCL_FArray2D_float__star__t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_ObjexxFCL_ubyte_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_std_string_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_unsigned_char_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_unsigned_long_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_utility_vector1_core_pack_dunbrack_cenrot_CentroidRotamerSampleData_std_allocator_core_pack_dunbrack_cenrot_CentroidRotamerSampleData_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_utility_vector1_double_std_allocator_double_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2P_double_t method) (pyrosetta.rosetta.ObjexxFCL.FArray3_core_pack_dunbrack_BBDepScoreInterpData_1_t method) (pyrosetta.rosetta.ObjexxFCL.FArray3_core_pack_dunbrack_BBDepScoreInterpData_2_t method) (pyrosetta.rosetta.ObjexxFCL.FArray3_core_pack_dunbrack_BBDepScoreInterpData_3_t method) (pyrosetta.rosetta.ObjexxFCL.FArray3_core_pack_dunbrack_BBDepScoreInterpData_4_t method) (pyrosetta.rosetta.ObjexxFCL.FArray3_core_pack_dunbrack_BBDepScoreInterpData_5_t method) (pyrosetta.rosetta.ObjexxFCL.FArray3_double_t method) (pyrosetta.rosetta.ObjexxFCL.FArray3_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray3_int_t method) (pyrosetta.rosetta.ObjexxFCL.FArray3_std_complex_double_t method) (pyrosetta.rosetta.ObjexxFCL.FArray3_std_vector_unsigned_long_std_allocator_unsigned_long_t method) (pyrosetta.rosetta.ObjexxFCL.FArray3_unsigned_char_t method) (pyrosetta.rosetta.ObjexxFCL.FArray3_unsigned_long_t method) (pyrosetta.rosetta.ObjexxFCL.FArray3_utility_vector1_double_std_allocator_double_t method) (pyrosetta.rosetta.ObjexxFCL.FArray3_utility_vector1_numeric_xyzVector_double_std_allocator_numeric_xyzVector_double_t method) (pyrosetta.rosetta.ObjexxFCL.FArray3_utility_vector1_unsigned_int_std_allocator_unsigned_int_t method) (pyrosetta.rosetta.ObjexxFCL.FArray3A_double_t method) (pyrosetta.rosetta.ObjexxFCL.FArray3D_core_pack_dunbrack_BBDepScoreInterpData_1_t method) (pyrosetta.rosetta.ObjexxFCL.FArray3D_core_pack_dunbrack_BBDepScoreInterpData_2_t method) (pyrosetta.rosetta.ObjexxFCL.FArray3D_core_pack_dunbrack_BBDepScoreInterpData_3_t method) (pyrosetta.rosetta.ObjexxFCL.FArray3D_core_pack_dunbrack_BBDepScoreInterpData_4_t method) (pyrosetta.rosetta.ObjexxFCL.FArray3D_core_pack_dunbrack_BBDepScoreInterpData_5_t method) (pyrosetta.rosetta.ObjexxFCL.FArray3D_double_t method) (pyrosetta.rosetta.ObjexxFCL.FArray3D_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray3D_int_t method) (pyrosetta.rosetta.ObjexxFCL.FArray3D_std_complex_double_t method) (pyrosetta.rosetta.ObjexxFCL.FArray3D_std_vector_unsigned_long_std_allocator_unsigned_long_t method) (pyrosetta.rosetta.ObjexxFCL.FArray3D_unsigned_char_t method) (pyrosetta.rosetta.ObjexxFCL.FArray3D_unsigned_long_t method) (pyrosetta.rosetta.ObjexxFCL.FArray3D_utility_vector1_double_std_allocator_double_t method) (pyrosetta.rosetta.ObjexxFCL.FArray3D_utility_vector1_numeric_xyzVector_double_std_allocator_numeric_xyzVector_double_t method) (pyrosetta.rosetta.ObjexxFCL.FArray3D_utility_vector1_unsigned_int_std_allocator_unsigned_int_t method) (pyrosetta.rosetta.ObjexxFCL.FArray3P_double_t method) (pyrosetta.rosetta.ObjexxFCL.FArray4_double_t method) (pyrosetta.rosetta.ObjexxFCL.FArray4_int_t method) (pyrosetta.rosetta.ObjexxFCL.FArray4_unsigned_char_t method) (pyrosetta.rosetta.ObjexxFCL.FArray4D_double_t method) (pyrosetta.rosetta.ObjexxFCL.FArray4D_int_t method) (pyrosetta.rosetta.ObjexxFCL.FArray4D_unsigned_char_t method) (pyrosetta.rosetta.ObjexxFCL.FArray5_double_t method) (pyrosetta.rosetta.ObjexxFCL.FArray5_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray5_int_t method) (pyrosetta.rosetta.ObjexxFCL.FArray5D_double_t method) (pyrosetta.rosetta.ObjexxFCL.FArray5D_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray5D_int_t method) i2() (pyrosetta.rosetta.core.energy_methods.GoapRsdType method) I2() (pyrosetta.rosetta.ObjexxFCL.FArray2_bool_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2_core_pack_dunbrack_BBDepNRChiSample_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2_core_pack_dunbrack_BBDepScoreInterpData_1_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2_core_pack_dunbrack_BBDepScoreInterpData_2_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2_core_pack_dunbrack_BBDepScoreInterpData_3_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2_core_pack_dunbrack_BBDepScoreInterpData_4_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2_core_pack_dunbrack_BBDepScoreInterpData_5_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2_core_pack_dunbrack_BBIndNRChiSample_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2_core_pack_dunbrack_PackedDunbrackRotamer_1_1_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2_core_pack_dunbrack_PackedDunbrackRotamer_1_2_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2_core_pack_dunbrack_PackedDunbrackRotamer_1_3_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2_core_pack_dunbrack_PackedDunbrackRotamer_1_4_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2_core_pack_dunbrack_PackedDunbrackRotamer_1_5_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2_core_pack_dunbrack_PackedDunbrackRotamer_2_1_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2_core_pack_dunbrack_PackedDunbrackRotamer_2_2_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2_core_pack_dunbrack_PackedDunbrackRotamer_2_3_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2_core_pack_dunbrack_PackedDunbrackRotamer_2_4_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2_core_pack_dunbrack_PackedDunbrackRotamer_2_5_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2_core_pack_dunbrack_PackedDunbrackRotamer_3_1_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2_core_pack_dunbrack_PackedDunbrackRotamer_3_2_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2_core_pack_dunbrack_PackedDunbrackRotamer_3_3_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2_core_pack_dunbrack_PackedDunbrackRotamer_3_4_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2_core_pack_dunbrack_PackedDunbrackRotamer_3_5_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2_core_pack_dunbrack_PackedDunbrackRotamer_4_1_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2_core_pack_dunbrack_PackedDunbrackRotamer_4_2_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2_core_pack_dunbrack_PackedDunbrackRotamer_4_3_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2_core_pack_dunbrack_PackedDunbrackRotamer_4_4_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2_core_pack_dunbrack_PackedDunbrackRotamer_4_5_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2_core_pack_dunbrack_PackedDunbrackRotamer_5_1_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2_core_pack_dunbrack_PackedDunbrackRotamer_5_2_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2_core_pack_dunbrack_PackedDunbrackRotamer_5_3_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2_core_pack_dunbrack_PackedDunbrackRotamer_5_4_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2_core_pack_dunbrack_PackedDunbrackRotamer_5_5_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2_double_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2_int_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2_numeric_xyzVector_double_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2_ObjexxFCL_FArray2D_float__star__t method) (pyrosetta.rosetta.ObjexxFCL.FArray2_ObjexxFCL_ubyte_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2_std_string_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2_unsigned_char_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2_unsigned_long_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2_utility_vector1_core_pack_dunbrack_cenrot_CentroidRotamerSampleData_std_allocator_core_pack_dunbrack_cenrot_CentroidRotamerSampleData_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2_utility_vector1_double_std_allocator_double_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2A_double_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2A_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_bool_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_core_pack_dunbrack_BBDepNRChiSample_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_core_pack_dunbrack_BBDepScoreInterpData_1_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_core_pack_dunbrack_BBDepScoreInterpData_2_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_core_pack_dunbrack_BBDepScoreInterpData_3_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_core_pack_dunbrack_BBDepScoreInterpData_4_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_core_pack_dunbrack_BBDepScoreInterpData_5_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_core_pack_dunbrack_BBIndNRChiSample_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_core_pack_dunbrack_PackedDunbrackRotamer_1_1_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_core_pack_dunbrack_PackedDunbrackRotamer_1_2_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_core_pack_dunbrack_PackedDunbrackRotamer_1_3_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_core_pack_dunbrack_PackedDunbrackRotamer_1_4_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_core_pack_dunbrack_PackedDunbrackRotamer_1_5_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_core_pack_dunbrack_PackedDunbrackRotamer_2_1_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_core_pack_dunbrack_PackedDunbrackRotamer_2_2_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_core_pack_dunbrack_PackedDunbrackRotamer_2_3_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_core_pack_dunbrack_PackedDunbrackRotamer_2_4_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_core_pack_dunbrack_PackedDunbrackRotamer_2_5_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_core_pack_dunbrack_PackedDunbrackRotamer_3_1_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_core_pack_dunbrack_PackedDunbrackRotamer_3_2_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_core_pack_dunbrack_PackedDunbrackRotamer_3_3_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_core_pack_dunbrack_PackedDunbrackRotamer_3_4_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_core_pack_dunbrack_PackedDunbrackRotamer_3_5_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_core_pack_dunbrack_PackedDunbrackRotamer_4_1_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_core_pack_dunbrack_PackedDunbrackRotamer_4_2_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_core_pack_dunbrack_PackedDunbrackRotamer_4_3_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_core_pack_dunbrack_PackedDunbrackRotamer_4_4_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_core_pack_dunbrack_PackedDunbrackRotamer_4_5_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_core_pack_dunbrack_PackedDunbrackRotamer_5_1_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_core_pack_dunbrack_PackedDunbrackRotamer_5_2_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_core_pack_dunbrack_PackedDunbrackRotamer_5_3_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_core_pack_dunbrack_PackedDunbrackRotamer_5_4_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_core_pack_dunbrack_PackedDunbrackRotamer_5_5_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_double_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_int_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_numeric_xyzVector_double_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_ObjexxFCL_FArray2D_float__star__t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_ObjexxFCL_ubyte_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_std_string_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_unsigned_char_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_unsigned_long_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_utility_vector1_core_pack_dunbrack_cenrot_CentroidRotamerSampleData_std_allocator_core_pack_dunbrack_cenrot_CentroidRotamerSampleData_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_utility_vector1_double_std_allocator_double_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2P_double_t method) (pyrosetta.rosetta.ObjexxFCL.FArray3_core_pack_dunbrack_BBDepScoreInterpData_1_t method) (pyrosetta.rosetta.ObjexxFCL.FArray3_core_pack_dunbrack_BBDepScoreInterpData_2_t method) (pyrosetta.rosetta.ObjexxFCL.FArray3_core_pack_dunbrack_BBDepScoreInterpData_3_t method) (pyrosetta.rosetta.ObjexxFCL.FArray3_core_pack_dunbrack_BBDepScoreInterpData_4_t method) (pyrosetta.rosetta.ObjexxFCL.FArray3_core_pack_dunbrack_BBDepScoreInterpData_5_t method) (pyrosetta.rosetta.ObjexxFCL.FArray3_double_t method) (pyrosetta.rosetta.ObjexxFCL.FArray3_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray3_int_t method) (pyrosetta.rosetta.ObjexxFCL.FArray3_std_complex_double_t method) (pyrosetta.rosetta.ObjexxFCL.FArray3_std_vector_unsigned_long_std_allocator_unsigned_long_t method) (pyrosetta.rosetta.ObjexxFCL.FArray3_unsigned_char_t method) (pyrosetta.rosetta.ObjexxFCL.FArray3_unsigned_long_t method) (pyrosetta.rosetta.ObjexxFCL.FArray3_utility_vector1_double_std_allocator_double_t method) (pyrosetta.rosetta.ObjexxFCL.FArray3_utility_vector1_numeric_xyzVector_double_std_allocator_numeric_xyzVector_double_t method) (pyrosetta.rosetta.ObjexxFCL.FArray3_utility_vector1_unsigned_int_std_allocator_unsigned_int_t method) (pyrosetta.rosetta.ObjexxFCL.FArray3A_double_t method) (pyrosetta.rosetta.ObjexxFCL.FArray3D_core_pack_dunbrack_BBDepScoreInterpData_1_t method) (pyrosetta.rosetta.ObjexxFCL.FArray3D_core_pack_dunbrack_BBDepScoreInterpData_2_t method) (pyrosetta.rosetta.ObjexxFCL.FArray3D_core_pack_dunbrack_BBDepScoreInterpData_3_t method) (pyrosetta.rosetta.ObjexxFCL.FArray3D_core_pack_dunbrack_BBDepScoreInterpData_4_t method) (pyrosetta.rosetta.ObjexxFCL.FArray3D_core_pack_dunbrack_BBDepScoreInterpData_5_t method) (pyrosetta.rosetta.ObjexxFCL.FArray3D_double_t method) (pyrosetta.rosetta.ObjexxFCL.FArray3D_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray3D_int_t method) (pyrosetta.rosetta.ObjexxFCL.FArray3D_std_complex_double_t method) (pyrosetta.rosetta.ObjexxFCL.FArray3D_std_vector_unsigned_long_std_allocator_unsigned_long_t method) (pyrosetta.rosetta.ObjexxFCL.FArray3D_unsigned_char_t method) (pyrosetta.rosetta.ObjexxFCL.FArray3D_unsigned_long_t method) (pyrosetta.rosetta.ObjexxFCL.FArray3D_utility_vector1_double_std_allocator_double_t method) (pyrosetta.rosetta.ObjexxFCL.FArray3D_utility_vector1_numeric_xyzVector_double_std_allocator_numeric_xyzVector_double_t method) (pyrosetta.rosetta.ObjexxFCL.FArray3D_utility_vector1_unsigned_int_std_allocator_unsigned_int_t method) (pyrosetta.rosetta.ObjexxFCL.FArray3P_double_t method) (pyrosetta.rosetta.ObjexxFCL.FArray4_double_t method) (pyrosetta.rosetta.ObjexxFCL.FArray4_int_t method) (pyrosetta.rosetta.ObjexxFCL.FArray4_unsigned_char_t method) (pyrosetta.rosetta.ObjexxFCL.FArray4D_double_t method) (pyrosetta.rosetta.ObjexxFCL.FArray4D_int_t method) (pyrosetta.rosetta.ObjexxFCL.FArray4D_unsigned_char_t method) (pyrosetta.rosetta.ObjexxFCL.FArray5_double_t method) (pyrosetta.rosetta.ObjexxFCL.FArray5_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray5_int_t method) (pyrosetta.rosetta.ObjexxFCL.FArray5D_double_t method) (pyrosetta.rosetta.ObjexxFCL.FArray5D_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray5D_int_t method) i3() (pyrosetta.rosetta.core.energy_methods.GoapRsdType method) I3() (pyrosetta.rosetta.ObjexxFCL.FArray3_core_pack_dunbrack_BBDepScoreInterpData_1_t method) (pyrosetta.rosetta.ObjexxFCL.FArray3_core_pack_dunbrack_BBDepScoreInterpData_2_t method) (pyrosetta.rosetta.ObjexxFCL.FArray3_core_pack_dunbrack_BBDepScoreInterpData_3_t method) (pyrosetta.rosetta.ObjexxFCL.FArray3_core_pack_dunbrack_BBDepScoreInterpData_4_t method) (pyrosetta.rosetta.ObjexxFCL.FArray3_core_pack_dunbrack_BBDepScoreInterpData_5_t method) (pyrosetta.rosetta.ObjexxFCL.FArray3_double_t method) (pyrosetta.rosetta.ObjexxFCL.FArray3_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray3_int_t method) (pyrosetta.rosetta.ObjexxFCL.FArray3_std_complex_double_t method) (pyrosetta.rosetta.ObjexxFCL.FArray3_std_vector_unsigned_long_std_allocator_unsigned_long_t method) (pyrosetta.rosetta.ObjexxFCL.FArray3_unsigned_char_t method) (pyrosetta.rosetta.ObjexxFCL.FArray3_unsigned_long_t method) (pyrosetta.rosetta.ObjexxFCL.FArray3_utility_vector1_double_std_allocator_double_t method) (pyrosetta.rosetta.ObjexxFCL.FArray3_utility_vector1_numeric_xyzVector_double_std_allocator_numeric_xyzVector_double_t method) (pyrosetta.rosetta.ObjexxFCL.FArray3_utility_vector1_unsigned_int_std_allocator_unsigned_int_t method) (pyrosetta.rosetta.ObjexxFCL.FArray3A_double_t method) (pyrosetta.rosetta.ObjexxFCL.FArray3D_core_pack_dunbrack_BBDepScoreInterpData_1_t method) (pyrosetta.rosetta.ObjexxFCL.FArray3D_core_pack_dunbrack_BBDepScoreInterpData_2_t method) (pyrosetta.rosetta.ObjexxFCL.FArray3D_core_pack_dunbrack_BBDepScoreInterpData_3_t method) (pyrosetta.rosetta.ObjexxFCL.FArray3D_core_pack_dunbrack_BBDepScoreInterpData_4_t method) (pyrosetta.rosetta.ObjexxFCL.FArray3D_core_pack_dunbrack_BBDepScoreInterpData_5_t method) (pyrosetta.rosetta.ObjexxFCL.FArray3D_double_t method) (pyrosetta.rosetta.ObjexxFCL.FArray3D_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray3D_int_t method) (pyrosetta.rosetta.ObjexxFCL.FArray3D_std_complex_double_t method) (pyrosetta.rosetta.ObjexxFCL.FArray3D_std_vector_unsigned_long_std_allocator_unsigned_long_t method) (pyrosetta.rosetta.ObjexxFCL.FArray3D_unsigned_char_t method) (pyrosetta.rosetta.ObjexxFCL.FArray3D_unsigned_long_t method) (pyrosetta.rosetta.ObjexxFCL.FArray3D_utility_vector1_double_std_allocator_double_t method) (pyrosetta.rosetta.ObjexxFCL.FArray3D_utility_vector1_numeric_xyzVector_double_std_allocator_numeric_xyzVector_double_t method) (pyrosetta.rosetta.ObjexxFCL.FArray3D_utility_vector1_unsigned_int_std_allocator_unsigned_int_t method) (pyrosetta.rosetta.ObjexxFCL.FArray3P_double_t method) (pyrosetta.rosetta.ObjexxFCL.FArray4_double_t method) (pyrosetta.rosetta.ObjexxFCL.FArray4_int_t method) (pyrosetta.rosetta.ObjexxFCL.FArray4_unsigned_char_t method) (pyrosetta.rosetta.ObjexxFCL.FArray4D_double_t method) (pyrosetta.rosetta.ObjexxFCL.FArray4D_int_t method) (pyrosetta.rosetta.ObjexxFCL.FArray4D_unsigned_char_t method) (pyrosetta.rosetta.ObjexxFCL.FArray5_double_t method) (pyrosetta.rosetta.ObjexxFCL.FArray5_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray5_int_t method) (pyrosetta.rosetta.ObjexxFCL.FArray5D_double_t method) (pyrosetta.rosetta.ObjexxFCL.FArray5D_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray5D_int_t method) I4() (pyrosetta.rosetta.ObjexxFCL.FArray4_double_t method) (pyrosetta.rosetta.ObjexxFCL.FArray4_int_t method) (pyrosetta.rosetta.ObjexxFCL.FArray4_unsigned_char_t method) (pyrosetta.rosetta.ObjexxFCL.FArray4D_double_t method) (pyrosetta.rosetta.ObjexxFCL.FArray4D_int_t method) (pyrosetta.rosetta.ObjexxFCL.FArray4D_unsigned_char_t method) (pyrosetta.rosetta.ObjexxFCL.FArray5_double_t method) (pyrosetta.rosetta.ObjexxFCL.FArray5_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray5_int_t method) (pyrosetta.rosetta.ObjexxFCL.FArray5D_double_t method) (pyrosetta.rosetta.ObjexxFCL.FArray5D_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray5D_int_t method) I5() (pyrosetta.rosetta.ObjexxFCL.FArray5_double_t method) (pyrosetta.rosetta.ObjexxFCL.FArray5_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray5_int_t method) (pyrosetta.rosetta.ObjexxFCL.FArray5D_double_t method) (pyrosetta.rosetta.ObjexxFCL.FArray5D_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray5D_int_t method) i_next() (pyrosetta.rosetta.core.pose.rna.BasePairStep method) i_param (pyrosetta.rosetta.core.scoring.APBSConfig property) i_str (pyrosetta.rosetta.protocols.environment.claims.DOFElement property) i_to_a() (pyrosetta.rosetta.protocols.normalmode.NormalMode method) i_want_this_atom_to_move() (pyrosetta.rosetta.protocols.rna.movers.ErraserMinimizerMover method) IACHAR() (in module pyrosetta.rosetta.ObjexxFCL) iatom (pyrosetta.rosetta.core.pack.guidance_scoreterms.lk_dome.MyWaterHolder property) ibx (pyrosetta.rosetta.core.scoring.APBSResult property) iby (pyrosetta.rosetta.core.scoring.APBSResult property) ibz (pyrosetta.rosetta.core.scoring.APBSResult property) IC_RefineCCDStandard (pyrosetta.rosetta.protocols.loops.loop_mover.refine.LoopRefineInnerCycleName attribute) IC_RepackTrial (pyrosetta.rosetta.protocols.loops.loop_mover.refine.LoopRefineInnerCycleName attribute) IC_ShearMinCCDTrial (pyrosetta.rosetta.protocols.loops.loop_mover.refine.LoopRefineInnerCycleName attribute) IC_SmallMinCCDTrial (pyrosetta.rosetta.protocols.loops.loop_mover.refine.LoopRefineInnerCycleName attribute) ICHAR() (in module pyrosetta.rosetta.ObjexxFCL) iCode (pyrosetta.rosetta.core.io.AtomInformation property) (pyrosetta.rosetta.core.io.ModifiedResidueInformation property) (pyrosetta.rosetta.core.pose.PDBInfo.ResidueRecord property) icode (pyrosetta.rosetta.core.scoring.packstat.SimplePDB_Atom property) (pyrosetta.rosetta.protocols.antibody.design.PDBNumbering property) iCode (pyrosetta.rosetta.protocols.loops.LoopConfiguration attribute) iCode() (pyrosetta.rosetta.core.io.ResidueInformation method) icode() (pyrosetta.rosetta.core.pose.PDBInfo method) icode1 (pyrosetta.rosetta.core.io.CisPeptideInformation property) (pyrosetta.rosetta.core.io.HELIXInformation property) iCode1 (pyrosetta.rosetta.core.io.LinkInformation property) icode1 (pyrosetta.rosetta.core.io.SHEETInformation property) iCode1 (pyrosetta.rosetta.core.io.SSBondInformation property) icode2 (pyrosetta.rosetta.core.io.CisPeptideInformation property) (pyrosetta.rosetta.core.io.HELIXInformation property) iCode2 (pyrosetta.rosetta.core.io.LinkInformation property) icode2 (pyrosetta.rosetta.core.io.SHEETInformation property) iCode2 (pyrosetta.rosetta.core.io.SSBondInformation property) icoor() (pyrosetta.rosetta.core.chemical.Atom method) (pyrosetta.rosetta.core.chemical.MutableResidueConnection method) (pyrosetta.rosetta.core.chemical.MutableResidueType method) (pyrosetta.rosetta.core.chemical.Orbital method) (pyrosetta.rosetta.core.chemical.ResidueConnection method) (pyrosetta.rosetta.core.chemical.ResidueType method) (pyrosetta.rosetta.core.conformation.Residue method) ICoorAtomID (class in pyrosetta.rosetta.core.chemical) ICoordAtomIDType (class in pyrosetta.rosetta.core.chemical) ICoorOrbitalData (class in pyrosetta.rosetta.core.chemical.orbitals) icstream (class in pyrosetta.rosetta.utility.io) id (pyrosetta.rosetta.core.kinematics.inverse.AlignmentAtom property) (pyrosetta.rosetta.core.scoring.packstat.Sphere property) (pyrosetta.rosetta.protocols.environment.claims.DOFElement property) (pyrosetta.rosetta.protocols.features.Segment property) (pyrosetta.rosetta.protocols.features.TaskOperationFeatures.Taskop_id_name_factory_ property) (pyrosetta.rosetta.protocols.hbnet.HBondNetStruct property) (pyrosetta.rosetta.protocols.indexed_structure_store.StructureEntry property) ID (pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna.Cluster_Member property) id (pyrosetta.rosetta.protocols.stepwise.modeler.rna.Torsion_Info property) (pyrosetta.rosetta.protocols.toolbox.Node property) id() (pyrosetta.rosetta.core.environment.EnvCore method) (pyrosetta.rosetta.core.fragment.FragID method) (pyrosetta.rosetta.core.fragment.picking_old.vall.VallResidue method) (pyrosetta.rosetta.core.kinematics.tree.Atom method) (pyrosetta.rosetta.core.kinematics.tree.Atom_ method) (pyrosetta.rosetta.core.kinematics.tree.BondedAtom method) (pyrosetta.rosetta.core.kinematics.tree.JumpAtom method) (pyrosetta.rosetta.core.scoring.nmr.NMRDummySpinlabelAtom method) (pyrosetta.rosetta.core.scoring.nmr.VoxelGridPoint method) (pyrosetta.rosetta.core.scoring.nmr.VoxelGridPoint_AA method) (pyrosetta.rosetta.core.scoring.packstat.CavityBall method) (pyrosetta.rosetta.core.scoring.PDvertex method) (pyrosetta.rosetta.core.scoring.power_diagram.PDvertex method) (pyrosetta.rosetta.core.sequence.ChemicalShiftSequence method) (pyrosetta.rosetta.core.sequence.CompositeSequence method) (pyrosetta.rosetta.core.sequence.Sequence method) (pyrosetta.rosetta.core.sequence.SequenceCoupling method) (pyrosetta.rosetta.core.sequence.SequenceProfile method) (pyrosetta.rosetta.numeric.ClusteringTreeNode method) (pyrosetta.rosetta.protocols.constraint_generator.AtomPairConstraintGenerator method) (pyrosetta.rosetta.protocols.constraint_generator.ConstraintGenerator method) (pyrosetta.rosetta.protocols.constraint_generator.CoordinateConstraintGenerator method) (pyrosetta.rosetta.protocols.constraint_generator.DihedralConstraintGenerator method) (pyrosetta.rosetta.protocols.constraint_generator.DistanceConstraintGenerator method) (pyrosetta.rosetta.protocols.constraint_generator.HydrogenBondConstraintGenerator method) (pyrosetta.rosetta.protocols.constraint_generator.MembraneSpanConstraintGenerator method) (pyrosetta.rosetta.protocols.constraint_generator.MetalContactsConstraintGenerator method) (pyrosetta.rosetta.protocols.constraint_generator.ResidueTypeConstraintGenerator method) (pyrosetta.rosetta.protocols.constraint_generator.TerminiConstraintGenerator method) (pyrosetta.rosetta.protocols.denovo_design.architects.BetaSheetArchitect method) (pyrosetta.rosetta.protocols.denovo_design.architects.BlueprintArchitect method) (pyrosetta.rosetta.protocols.denovo_design.architects.CompoundArchitect method) (pyrosetta.rosetta.protocols.denovo_design.architects.DeNovoArchitect method) (pyrosetta.rosetta.protocols.denovo_design.architects.HelixArchitect method) (pyrosetta.rosetta.protocols.denovo_design.architects.MotifArchitect method) (pyrosetta.rosetta.protocols.denovo_design.architects.PoseArchitect method) (pyrosetta.rosetta.protocols.denovo_design.architects.StrandArchitect method) (pyrosetta.rosetta.protocols.denovo_design.architects.StructureArchitect method) (pyrosetta.rosetta.protocols.denovo_design.components.Segment method) (pyrosetta.rosetta.protocols.denovo_design.components.StructureData method) (pyrosetta.rosetta.protocols.denovo_design.connection.ConnectionArchitect method) (pyrosetta.rosetta.protocols.denovo_design.constraints.FileConstraintGenerator method) (pyrosetta.rosetta.protocols.denovo_design.movers.BuildDeNovoBackboneMover method) (pyrosetta.rosetta.protocols.denovo_design.movers.FoldArchitectMover method) (pyrosetta.rosetta.protocols.environment.Environment method) (pyrosetta.rosetta.protocols.environment.EXCN_Env_Security_Exception method) (pyrosetta.rosetta.protocols.fldsgn.SheetConstraintGenerator method) (pyrosetta.rosetta.protocols.fldsgn.SheetRemodelConstraintGenerator method) (pyrosetta.rosetta.protocols.fold_from_loops.constraint_generator.AutomaticSheetConstraintGenerator method) (pyrosetta.rosetta.protocols.fold_from_loops.constraint_generator.SegmentedAtomPairConstraintGenerator method) (pyrosetta.rosetta.protocols.forge.constraints.InverseRotamersRCG method) (pyrosetta.rosetta.protocols.forge.constraints.InvrotTreeRCG method) (pyrosetta.rosetta.protocols.forge.constraints.NtoCConstraintGenerator method) (pyrosetta.rosetta.protocols.forge.remodel.GenericRemodelConstraintGenerator method) (pyrosetta.rosetta.protocols.forge.remodel.RemodelConstraintGenerator method) (pyrosetta.rosetta.protocols.forge.remodel.ResidueVicinityRCG method) (pyrosetta.rosetta.protocols.frag_picker.VallResidue method) (pyrosetta.rosetta.protocols.jd2.archive.Batch method) (pyrosetta.rosetta.protocols.loophash.WorkUnit_LoopHash method) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_bbGauss method) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_CombinePose method) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_FragInsert method) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_KicCloser method) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_LoopHash method) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_MD method) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_NormalMode method) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_PartialAbinitio method) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_RamaPerturber method) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_Relax method) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_Sampler method) (pyrosetta.rosetta.protocols.nmr.pcs.AtomGridPoint method) (pyrosetta.rosetta.protocols.optimize_weights.OptEVariableExpression method) (pyrosetta.rosetta.protocols.relax.WorkUnit_BatchRelax method) (pyrosetta.rosetta.protocols.relax.WorkUnit_BatchRelax_and_PostRescore method) (pyrosetta.rosetta.protocols.stepwise.sampler.copy_dofs.CopyDofStepWiseSampler method) (pyrosetta.rosetta.protocols.stepwise.sampler.copy_dofs.ResidueAlternativeStepWiseSampler method) (pyrosetta.rosetta.protocols.stepwise.sampler.copy_dofs.ResidueAlternativeStepWiseSamplerComb method) (pyrosetta.rosetta.protocols.stepwise.sampler.copy_dofs.ResidueListStepWiseSampler method) (pyrosetta.rosetta.protocols.stepwise.sampler.input_streams.InputStreamStepWiseSampler method) (pyrosetta.rosetta.protocols.stepwise.sampler.jump.JumpStepWiseSampler method) (pyrosetta.rosetta.protocols.stepwise.sampler.protein.ProteinBetaAntiParallelStepWiseSampler method) (pyrosetta.rosetta.protocols.stepwise.sampler.protein.ProteinFragmentStepWiseSampler method) (pyrosetta.rosetta.protocols.stepwise.sampler.protein.ProteinMainChainStepWiseSampler method) (pyrosetta.rosetta.protocols.stepwise.sampler.rigid_body.RigidBodyStepWiseSampler method) (pyrosetta.rosetta.protocols.stepwise.sampler.rna.RNA_ChiStepWiseSampler method) (pyrosetta.rosetta.protocols.stepwise.sampler.rna.RNA_KinematicCloser method) (pyrosetta.rosetta.protocols.stepwise.sampler.rna.RNA_NucleosideStepWiseSampler method) (pyrosetta.rosetta.protocols.stepwise.sampler.rna.RNA_SugarStepWiseSampler method) (pyrosetta.rosetta.protocols.stepwise.sampler.rna.RNA_SuiteStepWiseSampler method) (pyrosetta.rosetta.protocols.stepwise.sampler.StepWiseSamplerOneDOF method) (pyrosetta.rosetta.protocols.stepwise.sampler.StepWiseSamplerOneTorsion method) (pyrosetta.rosetta.protocols.stepwise.sampler.StepWiseSamplerOneValue method) (pyrosetta.rosetta.protocols.stepwise.sampler.StepWiseSamplerOneValueComb method) (pyrosetta.rosetta.protocols.stepwise.sampler.StepWiseSamplerRingConformer method) (pyrosetta.rosetta.protocols.stepwise.sampler.StepWiseSamplerSized method) (pyrosetta.rosetta.protocols.stepwise.sampler.StepWiseSamplerSizedAny method) (pyrosetta.rosetta.protocols.stepwise.sampler.StepWiseSamplerSizedComb method) (pyrosetta.rosetta.protocols.trRosetta_protocols.constraint_generators.trRosettaConstraintGenerator method) (pyrosetta.rosetta.protocols.wum.DatabaseEntryWorkUnit method) (pyrosetta.rosetta.protocols.wum.WorkUnit_MoverWrapper method) (pyrosetta.rosetta.protocols.wum.WorkUnit_SilentStructStore method) (pyrosetta.rosetta.protocols.wum.WorkUnit_Wait method) (pyrosetta.rosetta.protocols.wum.WorkUnitBase method) (pyrosetta.rosetta.utility.keys.AutoKey_utility_options_Option_utility_keys_Key_utility_keys_NoClient_t method) (pyrosetta.rosetta.utility.keys.Key method) (pyrosetta.rosetta.utility.keys.VariantKey_utility_options_OptionKey_t method) (pyrosetta.rosetta.utility.options.AnyOptionKey method) (pyrosetta.rosetta.utility.options.AnyVectorOptionKey method) (pyrosetta.rosetta.utility.options.BooleanOption method) (pyrosetta.rosetta.utility.options.BooleanOptionKey method) (pyrosetta.rosetta.utility.options.BooleanVectorOption method) (pyrosetta.rosetta.utility.options.BooleanVectorOptionKey method) (pyrosetta.rosetta.utility.options.FileOption method) (pyrosetta.rosetta.utility.options.FileOptionKey method) (pyrosetta.rosetta.utility.options.FileVectorOption method) (pyrosetta.rosetta.utility.options.FileVectorOptionKey method) (pyrosetta.rosetta.utility.options.IntegerOption method) (pyrosetta.rosetta.utility.options.IntegerOptionKey method) (pyrosetta.rosetta.utility.options.IntegerVectorOption method) (pyrosetta.rosetta.utility.options.IntegerVectorOptionKey method) (pyrosetta.rosetta.utility.options.Option method) (pyrosetta.rosetta.utility.options.OptionKey method) (pyrosetta.rosetta.utility.options.PathOption method) (pyrosetta.rosetta.utility.options.PathOptionKey method) (pyrosetta.rosetta.utility.options.PathVectorOption method) (pyrosetta.rosetta.utility.options.PathVectorOptionKey method) (pyrosetta.rosetta.utility.options.RealOption method) (pyrosetta.rosetta.utility.options.RealOptionKey method) (pyrosetta.rosetta.utility.options.RealVectorOption method) (pyrosetta.rosetta.utility.options.RealVectorOptionKey method) (pyrosetta.rosetta.utility.options.ResidueChainVectorOption method) (pyrosetta.rosetta.utility.options.ResidueChainVectorOptionKey method) (pyrosetta.rosetta.utility.options.ScalarOption method) (pyrosetta.rosetta.utility.options.ScalarOption_T_utility_options_BooleanOptionKey_bool_t method) (pyrosetta.rosetta.utility.options.ScalarOption_T_utility_options_FileOptionKey_utility_file_FileName_t method) (pyrosetta.rosetta.utility.options.ScalarOption_T_utility_options_IntegerOptionKey_int_t method) (pyrosetta.rosetta.utility.options.ScalarOption_T_utility_options_PathOptionKey_utility_file_PathName_t method) (pyrosetta.rosetta.utility.options.ScalarOption_T_utility_options_RealOptionKey_double_t method) (pyrosetta.rosetta.utility.options.ScalarOption_T_utility_options_StringOptionKey_std_string_t method) (pyrosetta.rosetta.utility.options.ScalarOptionKey method) (pyrosetta.rosetta.utility.options.StringOption method) (pyrosetta.rosetta.utility.options.StringOptionKey method) (pyrosetta.rosetta.utility.options.StringVectorOption method) (pyrosetta.rosetta.utility.options.StringVectorOptionKey method) (pyrosetta.rosetta.utility.options.VariantOption_utility_options_ScalarOption_t method) (pyrosetta.rosetta.utility.options.VariantOption_utility_options_VectorOption_t method) (pyrosetta.rosetta.utility.options.VectorOption method) (pyrosetta.rosetta.utility.options.VectorOption_T_utility_options_BooleanVectorOptionKey_bool_t method) (pyrosetta.rosetta.utility.options.VectorOption_T_utility_options_FileVectorOptionKey_utility_file_FileName_t method) (pyrosetta.rosetta.utility.options.VectorOption_T_utility_options_IntegerVectorOptionKey_int_t method) (pyrosetta.rosetta.utility.options.VectorOption_T_utility_options_PathVectorOptionKey_utility_file_PathName_t method) (pyrosetta.rosetta.utility.options.VectorOption_T_utility_options_RealVectorOptionKey_double_t method) (pyrosetta.rosetta.utility.options.VectorOption_T_utility_options_ResidueChainVectorOptionKey_int_t method) (pyrosetta.rosetta.utility.options.VectorOption_T_utility_options_StringVectorOptionKey_std_string_t method) (pyrosetta.rosetta.utility.options.VectorOptionKey method) (pyrosetta.tests.bindings.core.test_pose.TestPoseIO method) (pyrosetta.tests.bindings.core.test_pose.TestPoseResidueAccessor method) (pyrosetta.tests.bindings.core.test_pose.TestPoseResidueLabelAccessor method) (pyrosetta.tests.bindings.core.test_pose.TestPoseScoresAccessor method) (pyrosetta.tests.bindings.core.test_pose.TestPosesToSilent method) (pyrosetta.tests.distributed.test_dask_worker.TestDaskArgs method) id_ (pyrosetta.rosetta.core.scoring.packstat.CavityBall property) (pyrosetta.rosetta.core.scoring.saxs.FormFactor property) (pyrosetta.rosetta.protocols.loophash.WorkUnit_LoopHash.WU_Header property) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_bbGauss.WU_Header property) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_CombinePose.WU_Header property) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_FragInsert.WU_Header property) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_KicCloser.WU_Header property) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_LoopHash.WU_Header property) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_MD.WU_Header property) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_NormalMode.WU_Header property) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_PartialAbinitio.WU_Header property) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_RamaPerturber.WU_Header property) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_Relax.WU_Header property) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_Sampler.WU_Header property) (pyrosetta.rosetta.protocols.relax.WorkUnit_BatchRelax.WU_Header property) (pyrosetta.rosetta.protocols.relax.WorkUnit_BatchRelax_and_PostRescore.WU_Header property) (pyrosetta.rosetta.protocols.wum.DatabaseEntryWorkUnit.WU_Header property) (pyrosetta.rosetta.protocols.wum.WorkUnit_MoverWrapper.WU_Header property) (pyrosetta.rosetta.protocols.wum.WorkUnit_SilentStructStore.WU_Header property) (pyrosetta.rosetta.protocols.wum.WorkUnit_Wait.WU_Header property) (pyrosetta.rosetta.protocols.wum.WorkUnitBase.WU_Header property) id_for_current_rotamer() (pyrosetta.rosetta.core.pack.rotamer_set.RotamerSet method) (pyrosetta.rosetta.core.pack.rotamer_set.RotamerSet_ method) (pyrosetta.rosetta.core.pack.rotamer_set.RotamerSubset method) (pyrosetta.rosetta.core.pack.rotamer_set.symmetry.SymmetricRotamerSet_ method) (pyrosetta.rosetta.protocols.flexpack.rotamer_set.FlexbbRotamerSet method) id_for_resnum() (pyrosetta.rosetta.protocols.stepwise.sampler.copy_dofs.ResidueAlternativeStepWiseSamplerComb method) id_to_index() (pyrosetta.rosetta.core.scoring.packing.PoseBalls method) (pyrosetta.rosetta.core.scoring.packing.PoseBallsLite method) idate() (in module pyrosetta.rosetta.ObjexxFCL) idCode() (pyrosetta.rosetta.core.io.HeaderInformation method) ideal_bond_length_set() (pyrosetta.rosetta.core.chemical.ChemicalManager method) ideal_contacts_num (pyrosetta.rosetta.protocols.sewing.data_storage.LigandDescription property) ideal_contacts_str (pyrosetta.rosetta.protocols.sewing.data_storage.LigandDescription property) ideal_val() (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.GeomSampleInfo method) ideal_xyz() (pyrosetta.rosetta.core.chemical.Atom method) (pyrosetta.rosetta.core.chemical.Orbital method) (pyrosetta.rosetta.core.chemical.ResidueType method) IdealAbegoGenerator (class in pyrosetta.rosetta.protocols.denovo_design.components) IdealBondLengthSet (class in pyrosetta.rosetta.core.chemical) IdealContact (class in pyrosetta.rosetta.protocols.sewing.hashing) idealize() (pyrosetta.rosetta.protocols.relax.RangeRelaxMover method) idealize_combined_pose() (in module pyrosetta.rosetta.protocols.grafting) idealize_glycan_residues() (pyrosetta.rosetta.protocols.carbohydrates.GlycanSampler method) idealize_hydrogens() (in module pyrosetta.rosetta.core.conformation) idealize_insert() (pyrosetta.rosetta.protocols.grafting.AnchoredGraftMover method) (pyrosetta.rosetta.protocols.grafting.CCDEndsGraftMover method) idealize_last_n_glycans_in_pose() (in module pyrosetta.rosetta.core.pose.carbohydrates) idealize_loop() (in module pyrosetta.rosetta.protocols.loops) idealize_position() (in module pyrosetta.rosetta.core.conformation) idealize_proline_nvs() (pyrosetta.rosetta.core.energy_methods.CartesianBondedEnergy method) idealize_sidechains() (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.JumpRotamerSidechainMover method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.PerturbChiSidechainMover method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.PerturbRotamerSidechainMover method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SidechainMCMover method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SidechainMover method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SidechainMoverBase method) IdealizeAnomericHydrogens (class in pyrosetta.rosetta.protocols.carbohydrates) IdealizeAnomericHydrogensCreator (class in pyrosetta.rosetta.protocols.carbohydrates) IdealizeHelicesMover (class in pyrosetta.rosetta.protocols.rbsegment_relax) IdealizeHelicesMoverCreator (class in pyrosetta.rosetta.protocols.rbsegment_relax) IdealizeMover (class in pyrosetta.rosetta.protocols.idealize) IdealizeMoverCreator (class in pyrosetta.rosetta.protocols.idealize) IdealizeNonPhiPsi (class in pyrosetta.rosetta.protocols.kinematic_closure.perturbers) IdealizeRamaEnergy() (pyrosetta.rosetta.core.scoring.Ramachandran2B method) IdealParameters (class in pyrosetta.rosetta.protocols.kinematic_closure) IdealParametersDatabase (class in pyrosetta.rosetta.core.energy_methods) identical_info_consistency_check() (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.EnzCstTemplateRes method) identifier() (pyrosetta.rosetta.utility.keys.AutoKey_utility_options_Option_utility_keys_Key_utility_keys_NoClient_t method) (pyrosetta.rosetta.utility.keys.Key method) (pyrosetta.rosetta.utility.keys.VariantKey_utility_options_OptionKey_t method) (pyrosetta.rosetta.utility.options.AnyOptionKey method) (pyrosetta.rosetta.utility.options.AnyVectorOptionKey method) (pyrosetta.rosetta.utility.options.BooleanOption method) (pyrosetta.rosetta.utility.options.BooleanOptionKey method) (pyrosetta.rosetta.utility.options.BooleanVectorOption method) (pyrosetta.rosetta.utility.options.BooleanVectorOptionKey method) (pyrosetta.rosetta.utility.options.FileOption method) (pyrosetta.rosetta.utility.options.FileOptionKey method) (pyrosetta.rosetta.utility.options.FileVectorOption method) (pyrosetta.rosetta.utility.options.FileVectorOptionKey method) (pyrosetta.rosetta.utility.options.IntegerOption method) (pyrosetta.rosetta.utility.options.IntegerOptionKey method) (pyrosetta.rosetta.utility.options.IntegerVectorOption method) (pyrosetta.rosetta.utility.options.IntegerVectorOptionKey method) (pyrosetta.rosetta.utility.options.Option method) (pyrosetta.rosetta.utility.options.OptionKey method) (pyrosetta.rosetta.utility.options.PathOption method) (pyrosetta.rosetta.utility.options.PathOptionKey method) (pyrosetta.rosetta.utility.options.PathVectorOption method) (pyrosetta.rosetta.utility.options.PathVectorOptionKey method) (pyrosetta.rosetta.utility.options.RealOption method) (pyrosetta.rosetta.utility.options.RealOptionKey method) (pyrosetta.rosetta.utility.options.RealVectorOption method) (pyrosetta.rosetta.utility.options.RealVectorOptionKey method) (pyrosetta.rosetta.utility.options.ResidueChainVectorOption method) (pyrosetta.rosetta.utility.options.ResidueChainVectorOptionKey method) (pyrosetta.rosetta.utility.options.ScalarOption method) (pyrosetta.rosetta.utility.options.ScalarOption_T_utility_options_BooleanOptionKey_bool_t method) (pyrosetta.rosetta.utility.options.ScalarOption_T_utility_options_FileOptionKey_utility_file_FileName_t method) (pyrosetta.rosetta.utility.options.ScalarOption_T_utility_options_IntegerOptionKey_int_t method) (pyrosetta.rosetta.utility.options.ScalarOption_T_utility_options_PathOptionKey_utility_file_PathName_t method) (pyrosetta.rosetta.utility.options.ScalarOption_T_utility_options_RealOptionKey_double_t method) (pyrosetta.rosetta.utility.options.ScalarOption_T_utility_options_StringOptionKey_std_string_t method) (pyrosetta.rosetta.utility.options.ScalarOptionKey method) (pyrosetta.rosetta.utility.options.StringOption method) (pyrosetta.rosetta.utility.options.StringOptionKey method) (pyrosetta.rosetta.utility.options.StringVectorOption method) (pyrosetta.rosetta.utility.options.StringVectorOptionKey method) (pyrosetta.rosetta.utility.options.VariantOption_utility_options_ScalarOption_t method) (pyrosetta.rosetta.utility.options.VariantOption_utility_options_VectorOption_t method) (pyrosetta.rosetta.utility.options.VectorOption method) (pyrosetta.rosetta.utility.options.VectorOption_T_utility_options_BooleanVectorOptionKey_bool_t method) (pyrosetta.rosetta.utility.options.VectorOption_T_utility_options_FileVectorOptionKey_utility_file_FileName_t method) (pyrosetta.rosetta.utility.options.VectorOption_T_utility_options_IntegerVectorOptionKey_int_t method) (pyrosetta.rosetta.utility.options.VectorOption_T_utility_options_PathVectorOptionKey_utility_file_PathName_t method) (pyrosetta.rosetta.utility.options.VectorOption_T_utility_options_RealVectorOptionKey_double_t method) (pyrosetta.rosetta.utility.options.VectorOption_T_utility_options_ResidueChainVectorOptionKey_int_t method) (pyrosetta.rosetta.utility.options.VectorOption_T_utility_options_StringVectorOptionKey_std_string_t method) (pyrosetta.rosetta.utility.options.VectorOptionKey method) identify_and_set_cdr_cluster() (pyrosetta.rosetta.protocols.antibody.clusters.CDRClusterSet method) identify_hbonds_1way() (in module pyrosetta.rosetta.core.scoring.hbonds) identify_hbonds_1way_AHdist() (in module pyrosetta.rosetta.core.scoring.hbonds) identify_hbonds_1way_membrane() (in module pyrosetta.rosetta.core.scoring.hbonds) identify_intra_res_hbonds() (in module pyrosetta.rosetta.core.scoring.hbonds) identify_motif_build_positions() (pyrosetta.rosetta.protocols.motifs.LigandMotifSearch method) (pyrosetta.rosetta.protocols.motifs.MotifSearch method) identify_motif_BuildPositions() (pyrosetta.rosetta.protocols.motifs.LigandMotifSearch method) (pyrosetta.rosetta.protocols.motifs.MotifSearch method) identify_possible_binders() (pyrosetta.rosetta.protocols.sewing.hashing.LigandBindingResPlacer method) identify_sheet_id_by_residue_end() (in module pyrosetta.rosetta.protocols.features.strand_assembly) identify_ss_blocks_vec() (in module pyrosetta.rosetta.core.select.residue_selector) (in module pyrosetta.rosetta.protocols.pose_sewing) identities() (pyrosetta.rosetta.core.sequence.SequenceAlignment method) (pyrosetta.rosetta.protocols.task_operations.RestrictIdentitiesOperation method) identity (pyrosetta.rosetta.protocols.antibody.grafting.SCS_BlastResult property) identity() (pyrosetta.rosetta.core.chemical.AtomRefMapping_unsigned_long_void__star__t method) (pyrosetta.rosetta.core.chemical.AtomRefMapping_void__star__unsigned_long_t method) (pyrosetta.rosetta.core.chemical.AtomRefMapping_void__star__void__star__t method) (pyrosetta.rosetta.core.id.SequenceMapping static method) (pyrosetta.rosetta.core.sequence.DerivedSequenceMapping static method) (pyrosetta.rosetta.numeric.Py_xyzTransform_double static method) (pyrosetta.rosetta.numeric.Quaternion_double_t static method) (pyrosetta.rosetta.numeric.xyzMatrix_double_t static method) (pyrosetta.rosetta.numeric.xyzMatrix_float_t static method) (pyrosetta.rosetta.numeric.xyzTransform_double_t static method) (pyrosetta.rosetta.numeric.xyzTransform_float_t static method) identity_matrix() (pyrosetta.rosetta.protocols.forge.remodel.RemodelGlobalFrame method) (pyrosetta.rosetta.protocols.simple_filters.RepeatParameterFilter method) identity_pass_through() (pyrosetta.rosetta.core.chemical.RefConvert_std_string_t static method) (pyrosetta.rosetta.core.chemical.RefConvert_unsigned_long_t static method) (pyrosetta.rosetta.core.chemical.RefConvert_void__star__t static method) identity_transform() (pyrosetta.rosetta.core.kinematics.Jump method) (pyrosetta.rosetta.core.kinematics.RT method) IdentityEval (class in pyrosetta.rosetta.core.fragment.picking_old.vall.eval) IdentityEvent (class in pyrosetta.rosetta.core.conformation.signals) IdentityEvent.Tag (class in pyrosetta.rosetta.core.conformation.signals) IdentityFunc (class in pyrosetta.rosetta.core.scoring.func) idle() (pyrosetta.rosetta.protocols.abinitio.HedgeArchive method) (pyrosetta.rosetta.protocols.abinitio.IterativeAbrelax method) (pyrosetta.rosetta.protocols.abinitio.IterativeBase method) (pyrosetta.rosetta.protocols.abinitio.IterativeCentroid method) (pyrosetta.rosetta.protocols.abinitio.IterativeFullatom method) (pyrosetta.rosetta.protocols.jd2.archive.AbstractArchiveBase method) (pyrosetta.rosetta.protocols.jd2.archive.ArchiveBase method) (pyrosetta.rosetta.protocols.jd2.archive.EvaluatedArchive method) (pyrosetta.rosetta.protocols.jd2.archive.NormalizedEvaluatedArchive method) (pyrosetta.rosetta.protocols.jd2.archive.VarianceStatisticsArchive method) idx (pyrosetta.rosetta.protocols.simple_moves.AtomHashNode property) idx2cart() (pyrosetta.rosetta.core.scoring.electron_density.ElectronDensity method) idx_to_euler() (pyrosetta.rosetta.numeric.fourier.SHT method) idx_to_rot() (pyrosetta.rosetta.numeric.fourier.SHT method) if_late_scoring_for_zeros() (pyrosetta.rosetta.protocols.frag_picker.scores.FragmentScoreManager method) (pyrosetta.rosetta.protocols.frag_picker.scores.PValuedFragmentScoreManager method) ifc() (pyrosetta.rosetta.protocols.kinmatch.BruteFunGroupTK method) (pyrosetta.rosetta.protocols.kinmatch.FunGroupTK method) (pyrosetta.rosetta.protocols.kinmatch.KinFunGroupTK method) ifft3() (in module pyrosetta.rosetta.numeric.fourier) ifft3_dynamic() (in module pyrosetta.rosetta.numeric.fourier) IfMover (class in pyrosetta.rosetta.protocols.moves) IfMoverCreator (class in pyrosetta.rosetta.protocols.moves) ifstream (class in pyrosetta.rosetta.std) ifstream.sentry (class in pyrosetta.rosetta.std) IfThenFilter (class in pyrosetta.rosetta.protocols.filters) IfThenFilterCreator (class in pyrosetta.rosetta.protocols.filters) ig() (pyrosetta.rosetta.protocols.multistate_design.PackingState method) (pyrosetta.rosetta.protocols.pack_daemon.PackDaemon method) ig_threads_to_request() (pyrosetta.rosetta.core.pack.task.PackerTask method) (pyrosetta.rosetta.core.pack.task.PackerTask_ method) IGEdgeReweightContainer (class in pyrosetta.rosetta.core.pack.task) IGEdgeReweighter (class in pyrosetta.rosetta.core.pack.task) IGEdgeReweights() (pyrosetta.rosetta.core.pack.task.PackerTask method) (pyrosetta.rosetta.core.pack.task.PackerTask_ method) IGInterfaceEdgeUpweighter (class in pyrosetta.rosetta.protocols.toolbox) IGLigandDesignEdgeUpweighter (class in pyrosetta.rosetta.protocols.toolbox) IGNORE (pyrosetta.rosetta.core.select.residue_selector.slice_enums.OutOfBoundsMode attribute) ignore() (pyrosetta.rosetta.protocols.comparative_modeling.IgnoreSubsetConstraintSet method) (pyrosetta.rosetta.std.ifstream method) (pyrosetta.rosetta.std.iostream method) (pyrosetta.rosetta.std.istream method) (pyrosetta.rosetta.std.istringstream method) (pyrosetta.rosetta.std.stringstream method) (pyrosetta.rosetta.std.wistream method) (pyrosetta.rosetta.utility.io.icstream method) (pyrosetta.rosetta.utility.io.irstream method) (pyrosetta.rosetta.utility.io.izstream method) ignore_assignments() (pyrosetta.rosetta.protocols.noesy_assign.PeakFileFormat method) (pyrosetta.rosetta.protocols.noesy_assign.PeakFileFormat_Base method) (pyrosetta.rosetta.protocols.noesy_assign.PeakFileFormat_Sparky method) (pyrosetta.rosetta.protocols.noesy_assign.PeakFileFormat_xeasy method) (pyrosetta.rosetta.protocols.noesy_assign.PeakFileFormat_xpk method) ignore_atom_named_H() (pyrosetta.rosetta.core.chemical.ResidueTypeFinder method) ignore_cmdline_enzdes_cstfile() (pyrosetta.rosetta.protocols.denovo_design.components.VLBProtected method) (pyrosetta.rosetta.protocols.forge.components.VarLengthBuild method) ignore_default_task() (pyrosetta.rosetta.protocols.antibody.snugdock.SnugDock method) (pyrosetta.rosetta.protocols.docking.DockingEnsemblePrepackProtocol method) (pyrosetta.rosetta.protocols.docking.DockingHighRes method) (pyrosetta.rosetta.protocols.docking.DockingHighResLegacy method) (pyrosetta.rosetta.protocols.docking.DockingPrepackProtocol method) (pyrosetta.rosetta.protocols.docking.DockMCMProtocol method) (pyrosetta.rosetta.protocols.docking.DockMinMover method) (pyrosetta.rosetta.protocols.docking.InterfaceSidechainMinMover method) (pyrosetta.rosetta.protocols.docking.SidechainMinMover method) ignore_h_collisions() (pyrosetta.rosetta.protocols.match.downstream.LigandConformerBuilder method) (pyrosetta.rosetta.protocols.match.downstream.RigidLigandBuilder method) (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.LigandConformer method) ignore_light_chain() (pyrosetta.rosetta.protocols.antibody.AntibodyDatabaseManager method) ignore_list() (pyrosetta.rosetta.protocols.comparative_modeling.IgnoreSubsetConstraintSet method) ignore_loops() (pyrosetta.rosetta.protocols.fldsgn.NcontactsCalculator method) ignore_negative_intensity() (pyrosetta.rosetta.protocols.noesy_assign.PeakFileFormat method) (pyrosetta.rosetta.protocols.noesy_assign.PeakFileFormat_Base method) (pyrosetta.rosetta.protocols.noesy_assign.PeakFileFormat_Sparky method) (pyrosetta.rosetta.protocols.noesy_assign.PeakFileFormat_xeasy method) (pyrosetta.rosetta.protocols.noesy_assign.PeakFileFormat_xpk method) ignore_oxt() (pyrosetta.rosetta.core.scoring.lDDT_Calculator method) ignore_pikaa_natro() (pyrosetta.rosetta.protocols.flxbb.LayerDesignOperation method) ignore_radius() (pyrosetta.rosetta.core.scoring.sc.ElectrostaticComplementarityCalculator method) (pyrosetta.rosetta.core.simple_metrics.composite_metrics.ElectrostaticComplementarityMetric method) ignore_residue() (pyrosetta.rosetta.protocols.comparative_modeling.IgnoreSubsetConstraintSet method) ignore_residues_in_csts() (pyrosetta.rosetta.protocols.idealize.IdealizeMover method) ignore_resonancefile_intensities_ (pyrosetta.rosetta.protocols.noesy_assign.PeakAssignmentParameters property) ignore_resonancefile_tolerances_ (pyrosetta.rosetta.protocols.noesy_assign.PeakAssignmentParameters property) ignore_same_sheet() (pyrosetta.rosetta.protocols.fldsgn.NcontactsCalculator method) ignore_same_sselement() (pyrosetta.rosetta.protocols.fldsgn.NcontactsCalculator method) ignore_secstruct() (pyrosetta.rosetta.core.import_pose.options.RNA_DeNovoProtocolOptions method) (pyrosetta.rosetta.core.import_pose.options.RNA_FragmentMonteCarloOptions method) ignore_sugars() (pyrosetta.rosetta.core.import_pose.ImportPoseOptions method) (pyrosetta.rosetta.core.io.StructFileReaderOptions method) (pyrosetta.rosetta.core.io.StructFileRepOptions method) ignore_template() (in module pyrosetta.rosetta.protocols.tcr) ignore_unconnected_upper() (pyrosetta.rosetta.core.select.residue_selector.PhiSelector method) ignore_unrecognized_res() (pyrosetta.rosetta.core.import_pose.ImportPoseOptions method) (pyrosetta.rosetta.core.io.StructFileReaderOptions method) (pyrosetta.rosetta.core.io.StructFileRepOptions method) ignore_waters() (pyrosetta.rosetta.core.import_pose.ImportPoseOptions method) (pyrosetta.rosetta.core.io.StructFileReaderOptions method) (pyrosetta.rosetta.core.io.StructFileRepOptions method) ignore_zero_byte() (pyrosetta.rosetta.protocols.simple_filters.FileExistFilter method) ignore_zero_occupancy() (pyrosetta.rosetta.core.import_pose.ImportPoseOptions method) (pyrosetta.rosetta.core.io.StructFileReaderOptions method) (pyrosetta.rosetta.core.io.StructFileRepOptions method) ignored() (pyrosetta.rosetta.protocols.denovo_design.components.CompoundPerturber method) (pyrosetta.rosetta.protocols.denovo_design.components.ConnectionPerturber method) (pyrosetta.rosetta.protocols.denovo_design.components.HelixPerturber method) (pyrosetta.rosetta.protocols.denovo_design.components.NullPerturber method) (pyrosetta.rosetta.protocols.denovo_design.components.StructureDataPerturber method) ignorefinished() (pyrosetta.rosetta.protocols.jobdist.AtomTreeDiffJobDistributor method) (pyrosetta.rosetta.protocols.jobdist.BaseJobDistributor method) (pyrosetta.rosetta.protocols.jobdist.PlainPdbJobDistributor method) (pyrosetta.rosetta.protocols.jobdist.PlainRawJobDistributor method) (pyrosetta.rosetta.protocols.jobdist.PlainSilentFileJobDistributor method) IgnoreSubsetConstraintSet (class in pyrosetta.rosetta.protocols.comparative_modeling) iha_cut() (pyrosetta.rosetta.protocols.mpi_refinement.MultiObjective method) iha_penalty_mode() (pyrosetta.rosetta.protocols.mpi_refinement.MultiObjective method) iha_penalty_slope() (pyrosetta.rosetta.protocols.mpi_refinement.MultiObjective method) II (pyrosetta.rosetta.protocols.abinitio.abscript.StageID attribute) IIIa (pyrosetta.rosetta.protocols.abinitio.abscript.StageID attribute) IIIb (pyrosetta.rosetta.protocols.abinitio.abscript.StageID attribute) imbue() (pyrosetta.rosetta.std.ios_base method) imbue_event (pyrosetta.rosetta.std.ios_base attribute) (pyrosetta.rosetta.std.ios_base.event attribute) IMGT_Scheme (pyrosetta.rosetta.protocols.antibody.AntibodyNumberingSchemeEnum attribute) implicit_lipids() (pyrosetta.rosetta.core.conformation.membrane.MembraneInfo method) ImplicitFastClashCheck (class in pyrosetta.rosetta.protocols.scoring) ImplicitLipidInfo (class in pyrosetta.rosetta.core.conformation.membrane) implies (pyrosetta.rosetta.core.chemical.carbohydrates.SugarModificationsNomenclatureTableRow property) import() (pyrosetta.rosetta.core.kinematics.MoveMap method) import_false() (pyrosetta.rosetta.core.kinematics.MoveMap method) import_ID (pyrosetta.rosetta.core.pose.rna.VDW_RepScreenInfo property) import_pose_from_silent_file() (in module pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna) import_tags() (pyrosetta.rosetta.protocols.rosetta_scripts.RosettaScriptsParser method) import_true() (pyrosetta.rosetta.core.kinematics.MoveMap method) ImportPoseOptions (class in pyrosetta.rosetta.core.import_pose) ImportUnboundRotamersOperation (class in pyrosetta.rosetta.protocols.task_operations) ImportUnboundRotamersOperationCreator (class in pyrosetta.rosetta.protocols.task_operations) impose_constraints() (pyrosetta.rosetta.protocols.idealize.IdealizeMover method) improper_parameters() (pyrosetta.rosetta.core.energy_methods.ResidueCartBondedParameters method) In (pyrosetta.rosetta.core.chemical.element.Elements attribute) in (pyrosetta.rosetta.core.conformation.membrane.Orientation attribute) in_a_submotif() (pyrosetta.rosetta.core.pose.full_model_info.FullModelInfo method) in_a_submotif_seed() (pyrosetta.rosetta.core.pose.full_model_info.FullModelInfo method) in_avail() (pyrosetta.rosetta.std.filebuf method) (pyrosetta.rosetta.std.streambuf method) (pyrosetta.rosetta.std.stringbuf method) (pyrosetta.rosetta.std.wstreambuf method) (pyrosetta.rosetta.utility.io.mpi_stream.basic_mpi_streambuf_char_std_char_traits_char_std_allocator_char_unsigned_char_std_allocator_unsigned_char_t method) in_bin_i() (pyrosetta.rosetta.core.scoring.bin_transitions.BinTransitionData method) in_bin_iplus1() (pyrosetta.rosetta.core.scoring.bin_transitions.BinTransitionData method) in_blacklist() (pyrosetta.rosetta.protocols.loophash.WorkUnit_LoopHash method) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_bbGauss method) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_CombinePose method) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_FragInsert method) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_KicCloser method) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_LoopHash method) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_MD method) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_NormalMode method) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_PartialAbinitio method) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_RamaPerturber method) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_Relax method) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_Sampler method) (pyrosetta.rosetta.protocols.relax.WorkUnit_BatchRelax method) (pyrosetta.rosetta.protocols.relax.WorkUnit_BatchRelax_and_PostRescore method) (pyrosetta.rosetta.protocols.wum.DatabaseEntryWorkUnit method) (pyrosetta.rosetta.protocols.wum.WorkUnit_MoverWrapper method) (pyrosetta.rosetta.protocols.wum.WorkUnit_SilentStructStore method) (pyrosetta.rosetta.protocols.wum.WorkUnit_Wait method) (pyrosetta.rosetta.protocols.wum.WorkUnitBase method) in_charge() (pyrosetta.rosetta.protocols.loops.GuardedLoopsFromFile method) in_context() (pyrosetta.rosetta.protocols.fold_from_loops.filters.ScorePoseSegmentFromResidueSelectorFilter method) in_fullatom() (pyrosetta.rosetta.core.io.silent.SilentFileOptions method) in_helix() (pyrosetta.rosetta.core.pose.rna.RNA_SecStruct method) in_list (pyrosetta.rosetta.protocols.toolbox.Node property) in_map_from_reference() (pyrosetta.rosetta.core.pose.toolbox.AtomID_Mapper method) in_membrane() (pyrosetta.rosetta.core.conformation.membrane.MembraneInfo method) in_membrane_atom() (pyrosetta.rosetta.core.conformation.membrane.MembraneInfo method) in_ngbat_sphere() (in module pyrosetta.rosetta.protocols.neighbor) in_nrg_graph() (in module pyrosetta.rosetta.protocols.neighbor) in_paired_strands() (pyrosetta.rosetta.core.scoring.dssp.Dssp method) in_range_CCD_torsion (pyrosetta.rosetta.protocols.stepwise.modeler.rna.StepWiseRNA_CountStruct property) in_root_partition (pyrosetta.rosetta.core.pose.rna.VDW_RepScreenInfo property) in_same_helix() (pyrosetta.rosetta.core.pose.rna.RNA_SecStruct method) in_silent_score_prefix() (pyrosetta.rosetta.core.io.silent.SilentFileOptions method) in_silent_scores_wanted() (pyrosetta.rosetta.core.io.silent.SilentFileOptions method) in_silent_scores_wanted_set() (pyrosetta.rosetta.core.io.silent.SilentFileOptions method) in_silent_struct_type() (pyrosetta.rosetta.core.io.silent.SilentFileOptions method) in_silent_struct_type_set() (pyrosetta.rosetta.core.io.silent.SilentFileOptions method) in_span() (pyrosetta.rosetta.core.conformation.membrane.SpanningTopology method) in_use() (pyrosetta.rosetta.cppdb.backend.driver method) (pyrosetta.rosetta.cppdb.backend.loadable_driver method) inactive() (pyrosetta.rosetta.utility.Bound_bool_t method) (pyrosetta.rosetta.utility.Bound_double_t method) (pyrosetta.rosetta.utility.Bound_int_t method) (pyrosetta.rosetta.utility.Bound_std_string_t method) (pyrosetta.rosetta.utility.Bound_utility_file_FileName_t method) (pyrosetta.rosetta.utility.Bound_utility_file_PathName_t method) (pyrosetta.rosetta.utility.keys.SmallKeyVector_utility_options_AnyOptionKey_utility_options_VariantOption_utility_options_ScalarOption_t method) (pyrosetta.rosetta.utility.keys.SmallKeyVector_utility_options_AnyVectorOptionKey_utility_options_VariantOption_utility_options_VectorOption_t method) (pyrosetta.rosetta.utility.keys.SmallKeyVector_utility_options_BooleanOptionKey_utility_options_BooleanOption_t method) (pyrosetta.rosetta.utility.keys.SmallKeyVector_utility_options_BooleanVectorOptionKey_utility_options_BooleanVectorOption_t method) (pyrosetta.rosetta.utility.keys.SmallKeyVector_utility_options_FileOptionKey_utility_options_FileOption_t method) (pyrosetta.rosetta.utility.keys.SmallKeyVector_utility_options_FileVectorOptionKey_utility_options_FileVectorOption_t method) (pyrosetta.rosetta.utility.keys.SmallKeyVector_utility_options_IntegerOptionKey_utility_options_IntegerOption_t method) (pyrosetta.rosetta.utility.keys.SmallKeyVector_utility_options_IntegerVectorOptionKey_utility_options_IntegerVectorOption_t method) (pyrosetta.rosetta.utility.keys.SmallKeyVector_utility_options_OptionKey_utility_options_OptionTypes_t method) (pyrosetta.rosetta.utility.keys.SmallKeyVector_utility_options_PathOptionKey_utility_options_PathOption_t method) (pyrosetta.rosetta.utility.keys.SmallKeyVector_utility_options_PathVectorOptionKey_utility_options_PathVectorOption_t method) (pyrosetta.rosetta.utility.keys.SmallKeyVector_utility_options_RealOptionKey_utility_options_RealOption_t method) (pyrosetta.rosetta.utility.keys.SmallKeyVector_utility_options_RealVectorOptionKey_utility_options_RealVectorOption_t method) (pyrosetta.rosetta.utility.keys.SmallKeyVector_utility_options_ResidueChainVectorOptionKey_utility_options_ResidueChainVectorOption_t method) (pyrosetta.rosetta.utility.keys.SmallKeyVector_utility_options_StringOptionKey_utility_options_StringOption_t method) (pyrosetta.rosetta.utility.keys.SmallKeyVector_utility_options_StringVectorOptionKey_utility_options_StringVectorOption_t method) inbound() (pyrosetta.rosetta.protocols.loophash.MPI_LoopHashRefine method) (pyrosetta.rosetta.protocols.loophash.MPI_LoopHashRefine_Emperor method) (pyrosetta.rosetta.protocols.loophash.MPI_LoopHashRefine_Master method) (pyrosetta.rosetta.protocols.mpi_refinement.MPI_Refine_Emperor method) (pyrosetta.rosetta.protocols.mpi_refinement.MPI_Refine_Master method) (pyrosetta.rosetta.protocols.mpi_refinement.MPI_Refinement method) (pyrosetta.rosetta.protocols.wum.MPI_WorkUnitManager method) (pyrosetta.rosetta.protocols.wum.MPI_WorkUnitManager_Slave method) (pyrosetta.rosetta.protocols.wum.WorkUnitManager method) incl_nonopt() (pyrosetta.rosetta.protocols.design_opt.GreedyOptMutationMover method) (pyrosetta.rosetta.protocols.matdes.MatDesGreedyOptMutationMover method) include_all_water() (pyrosetta.rosetta.protocols.task_operations.RestrictToInterfaceVectorOperation method) include_arg() (pyrosetta.rosetta.protocols.design_opt.Supercharge method) include_asp() (pyrosetta.rosetta.protocols.design_opt.Supercharge method) include_citation_info() (pyrosetta.rosetta.utility.tag.XMLSchemaDefinition method) include_current() (pyrosetta.rosetta.core.pack.task.operation.OptH method) (pyrosetta.rosetta.core.pack.task.PackerTask method) (pyrosetta.rosetta.core.pack.task.PackerTask_ method) (pyrosetta.rosetta.core.pack.task.ResidueLevelTask method) (pyrosetta.rosetta.core.pack.task.ResidueLevelTask_ method) include_distance_during_fast_cluster_ (pyrosetta.rosetta.protocols.electron_density.DensityGridSearchOptions property) include_eggshell_points_based_on_known_ligand() (pyrosetta.rosetta.protocols.pockets.NonPlaidFingerprint method) include_glu() (pyrosetta.rosetta.protocols.design_opt.Supercharge method) include_gly() (pyrosetta.rosetta.core.pack.task.operation.RestrictYSDesign method) include_lys() (pyrosetta.rosetta.protocols.design_opt.Supercharge method) include_native_aa() (pyrosetta.rosetta.protocols.task_operations.ConservativeDesignOperation method) (pyrosetta.rosetta.protocols.task_operations.MutationSetDesignOperation method) include_native_restype() (pyrosetta.rosetta.protocols.task_operations.ResidueProbDesignOperation method) include_neighbors() (pyrosetta.rosetta.protocols.simple_task_operations.RestrictToLoopsAndNeighbors method) include_only_center_clusters() (pyrosetta.rosetta.protocols.antibody.CDRSetOptions method) include_only_clusters() (pyrosetta.rosetta.protocols.antibody.CDRSetOptions method) include_only_clusters_add() (pyrosetta.rosetta.protocols.antibody.CDRSetOptions method) include_only_clusters_clear() (pyrosetta.rosetta.protocols.antibody.CDRSetOptions method) include_only_current_cluster() (pyrosetta.rosetta.protocols.antibody.CDRSetOptions method) include_only_end_stage1_ (pyrosetta.rosetta.protocols.scoring.methods.pcs2.PcsGridSearchParameter property) include_only_end_stage2_ (pyrosetta.rosetta.protocols.scoring.methods.pcs2.PcsGridSearchParameter property) include_only_end_stage3_ (pyrosetta.rosetta.protocols.scoring.methods.pcs2.PcsGridSearchParameter property) include_only_end_stage4_ (pyrosetta.rosetta.protocols.scoring.methods.pcs2.PcsGridSearchParameter property) include_only_germlines() (pyrosetta.rosetta.protocols.antibody.CDRSetOptions method) include_only_germlines_add() (pyrosetta.rosetta.protocols.antibody.CDRSetOptions method) include_only_germlines_clear() (pyrosetta.rosetta.protocols.antibody.CDRSetOptions method) include_only_pdbs() (pyrosetta.rosetta.protocols.antibody.CDRSetOptions method) include_only_pdbs_add() (pyrosetta.rosetta.protocols.antibody.CDRSetOptions method) include_only_pdbs_clear() (pyrosetta.rosetta.protocols.antibody.CDRSetOptions method) include_only_species() (pyrosetta.rosetta.protocols.antibody.CDRSetOptions method) include_only_species_add() (pyrosetta.rosetta.protocols.antibody.CDRSetOptions method) include_only_species_clear() (pyrosetta.rosetta.protocols.antibody.CDRSetOptions method) include_only_start_stage1_ (pyrosetta.rosetta.protocols.scoring.methods.pcs2.PcsGridSearchParameter property) include_only_start_stage2_ (pyrosetta.rosetta.protocols.scoring.methods.pcs2.PcsGridSearchParameter property) include_only_start_stage3_ (pyrosetta.rosetta.protocols.scoring.methods.pcs2.PcsGridSearchParameter property) include_only_start_stage4_ (pyrosetta.rosetta.protocols.scoring.methods.pcs2.PcsGridSearchParameter property) include_resid() (pyrosetta.rosetta.core.pack.task.operation.RestrictYSDesign method) include_residue() (pyrosetta.rosetta.core.pack.task.operation.PreventRepacking method) (pyrosetta.rosetta.core.pack.task.operation.RestrictAbsentCanonicalAAS method) (pyrosetta.rosetta.core.pack.task.operation.RestrictResidueToRepacking method) (pyrosetta.rosetta.protocols.task_operations.ConservativeDesignOperation method) (pyrosetta.rosetta.protocols.task_operations.DesignAroundOperation method) include_residues() (pyrosetta.rosetta.protocols.hybridization.FragmentBiasAssigner method) include_trp() (pyrosetta.rosetta.protocols.task_operations.LimitAromaChi2_RotamerSetOperation method) (pyrosetta.rosetta.protocols.task_operations.LimitAromaChi2Operation method) include_virtual_side_chain() (pyrosetta.rosetta.core.pack.task.ResidueLevelTask method) (pyrosetta.rosetta.core.pack.task.ResidueLevelTask_ method) IncludeCurrent (class in pyrosetta.rosetta.core.pack.task.operation) IncludeCurrentCreator (class in pyrosetta.rosetta.core.pack.task.operation) IncludeCurrentRLT (class in pyrosetta.rosetta.core.pack.task.operation) IncludeCurrentRLTCreator (class in pyrosetta.rosetta.core.pack.task.operation) Inclusive (pyrosetta.rosetta.protocols.features.RelevantResiduesMode.T attribute) incoming_edge_list_begin() (pyrosetta.rosetta.protocols.jd3.JobDirectedNode method) (pyrosetta.rosetta.utility.graph.DirectedNode method) incoming_edge_list_end() (pyrosetta.rosetta.protocols.jd3.JobDirectedNode method) (pyrosetta.rosetta.utility.graph.DirectedNode method) incoming_message_queue_is_empty() (pyrosetta.rosetta.utility.SimulateMPI static method) incomplete() (pyrosetta.rosetta.core.chemical.ResConnID method) incorporate_motifs() (pyrosetta.rosetta.protocols.motifs.IRCollection method) (pyrosetta.rosetta.protocols.motifs.LigandMotifSearch method) (pyrosetta.rosetta.protocols.motifs.MotifSearch method) increase_count() (pyrosetta.rosetta.numeric.histograms.TwoDHistogram_unsigned_long_long_t method) increase_multi_cool_annealer_history_size() (pyrosetta.rosetta.core.pack.task.PackerTask method) (pyrosetta.rosetta.core.pack.task.PackerTask_ method) increase_packer_residue_radius() (pyrosetta.rosetta.core.pack.rotamer_set.AddResiduesRotamerSetOperation method) (pyrosetta.rosetta.core.pack.rotamer_set.DeleteAllRotamerSetOperation method) (pyrosetta.rosetta.core.pack.rotamer_set.RotamerSetOperation method) (pyrosetta.rosetta.core.pack.rotamer_set.UnboundRotamersOperation method) (pyrosetta.rosetta.protocols.hotspot_hashing.SearchPatternRotSetOp method) (pyrosetta.rosetta.protocols.matdes.MotifHitsRotamersOperation method) (pyrosetta.rosetta.protocols.splice.SampleRotamersFromPDB_RotamerSetOperation method) (pyrosetta.rosetta.protocols.task_operations.LimitAromaChi2_RotamerSetOperation method) (pyrosetta.rosetta.protocols.toolbox.rotamer_set_operations.AddGood2BPairEnergyRotamers method) (pyrosetta.rosetta.protocols.toolbox.rotamer_set_operations.RigidBodyMoveBaseRSO method) (pyrosetta.rosetta.protocols.toolbox.rotamer_set_operations.RigidBodyMoveRSO method) (pyrosetta.rosetta.protocols.toolbox.rotamer_set_operations.SpecialRotamerRSO method) increase_range_to_ignore_ss_element() (pyrosetta.rosetta.protocols.pose_creation.MergePDBatOverlapMover method) (pyrosetta.rosetta.protocols.pose_creation.MergePDBMover method) increasing() (pyrosetta.rosetta.protocols.loops.Loop method) increment_accepted_hbond_count_for_group() (pyrosetta.rosetta.core.pack.guidance_scoreterms.buried_unsat_penalty.graph.BuriedUnsatPenaltyNode method) increment_both() (pyrosetta.rosetta.core.pack.interaction_graph.RotamerDots method) increment_both_and_cache() (pyrosetta.rosetta.core.pack.interaction_graph.RotamerDots method) increment_client_rank() (pyrosetta.rosetta.protocols.jd2.archive.MPIArchiveJobDistributor method) (pyrosetta.rosetta.protocols.jd2.MPIFileBufJobDistributor method) (pyrosetta.rosetta.protocols.jd2.MPIMultiCommJobDistributor method) increment_count() (pyrosetta.rosetta.core.pack.interaction_graph.RotamerDotsCache method) (pyrosetta.rosetta.protocols.stepwise.legacy.screener.ProteinAtrRepScreener method) (pyrosetta.rosetta.protocols.stepwise.legacy.screener.RNA_AtrRepScreener method) (pyrosetta.rosetta.protocols.stepwise.legacy.screener.SimplePoseSelection method) (pyrosetta.rosetta.protocols.stepwise.legacy.screener.SimpleRMSD_Screener method) (pyrosetta.rosetta.protocols.stepwise.screener.AlignRMSD_Screener method) (pyrosetta.rosetta.protocols.stepwise.screener.AnchorSugarScreener method) (pyrosetta.rosetta.protocols.stepwise.screener.BaseBinMapUpdater method) (pyrosetta.rosetta.protocols.stepwise.screener.BaseCentroidScreener method) (pyrosetta.rosetta.protocols.stepwise.screener.BulgeApplier method) (pyrosetta.rosetta.protocols.stepwise.screener.CentroidDistanceScreener method) (pyrosetta.rosetta.protocols.stepwise.screener.FastForwardToNextResidueAlternative method) (pyrosetta.rosetta.protocols.stepwise.screener.FastForwardToNextRigidBody method) (pyrosetta.rosetta.protocols.stepwise.screener.IntegrationTestBreaker method) (pyrosetta.rosetta.protocols.stepwise.screener.O2PrimeScreener method) (pyrosetta.rosetta.protocols.stepwise.screener.PackScreener method) (pyrosetta.rosetta.protocols.stepwise.screener.PartitionContactScreener method) (pyrosetta.rosetta.protocols.stepwise.screener.PhosphateScreener method) (pyrosetta.rosetta.protocols.stepwise.screener.PoseSelectionScreener method) (pyrosetta.rosetta.protocols.stepwise.screener.ProteinCCD_ClosureScreener method) (pyrosetta.rosetta.protocols.stepwise.screener.ResidueContactScreener method) (pyrosetta.rosetta.protocols.stepwise.screener.RNA_ChainClosableGeometryResidueBasedScreener method) (pyrosetta.rosetta.protocols.stepwise.screener.RNA_ChainClosableGeometryScreener method) (pyrosetta.rosetta.protocols.stepwise.screener.RNA_ChainClosableGeometryStubBasedScreener method) (pyrosetta.rosetta.protocols.stepwise.screener.RNA_ChainClosureScreener method) (pyrosetta.rosetta.protocols.stepwise.screener.SampleApplier method) (pyrosetta.rosetta.protocols.stepwise.screener.Scorer method) (pyrosetta.rosetta.protocols.stepwise.screener.StepWiseResiduePairScreener method) (pyrosetta.rosetta.protocols.stepwise.screener.StepWiseScreener method) (pyrosetta.rosetta.protocols.stepwise.screener.StubApplier method) (pyrosetta.rosetta.protocols.stepwise.screener.StubDistanceScreener method) (pyrosetta.rosetta.protocols.stepwise.screener.SugarInstantiator method) (pyrosetta.rosetta.protocols.stepwise.screener.TagDefinition method) (pyrosetta.rosetta.protocols.stepwise.screener.VDW_BinScreener method) increment_count_nodes_in_flexseg() (pyrosetta.rosetta.protocols.flexpack.interaction_graph.FlexbbInteractionGraph method) (pyrosetta.rosetta.protocols.flexpack.interaction_graph.MinimalistFlexbbInteractionGraph method) (pyrosetta.rosetta.protocols.flexpack.interaction_graph.OTFFlexbbInteractionGraph method) (pyrosetta.rosetta.protocols.flexpack.interaction_graph.PrecomputedFlexbbInteractionGraph method) increment_counts() (pyrosetta.rosetta.core.pack.guidance_scoreterms.buried_unsat_penalty.graph.BuriedUnsatPenaltyNode method) increment_cur_indices() (pyrosetta.rosetta.protocols.helical_bundle.BackboneGridSamplerHelper method) (pyrosetta.rosetta.protocols.helical_bundle.BundleGridSamplerHelper method) increment_current_job_index() (pyrosetta.rosetta.protocols.jd3.JobTracker method) increment_donated_hbond_count_for_group() (pyrosetta.rosetta.core.pack.guidance_scoreterms.buried_unsat_penalty.graph.BuriedUnsatPenaltyNode method) increment_edge_list_iterator() (pyrosetta.rosetta.core.pack.hbonds.HBondGraphInitializerIG method) (pyrosetta.rosetta.core.pack.interaction_graph.DensePDInteractionGraph method) (pyrosetta.rosetta.core.pack.interaction_graph.DoubleDensePDInteractionGraph method) (pyrosetta.rosetta.core.pack.interaction_graph.DoubleLazyInteractionGraph method) (pyrosetta.rosetta.core.pack.interaction_graph.FASTERInteractionGraph method) (pyrosetta.rosetta.core.pack.interaction_graph.FixedBBInteractionGraph method) (pyrosetta.rosetta.core.pack.interaction_graph.InteractionGraphBase method) (pyrosetta.rosetta.core.pack.interaction_graph.LazyInteractionGraph method) (pyrosetta.rosetta.core.pack.interaction_graph.LinearMemoryInteractionGraph method) (pyrosetta.rosetta.core.pack.interaction_graph.OnTheFlyInteractionGraph method) (pyrosetta.rosetta.core.pack.interaction_graph.PDInteractionGraph method) (pyrosetta.rosetta.core.pack.interaction_graph.PrecomputedPairEnergiesInteractionGraph method) (pyrosetta.rosetta.core.pack.interaction_graph.SymmLinearMemoryInteractionGraph method) (pyrosetta.rosetta.core.pack.interaction_graph.SymmMinimalistInteractionGraph method) (pyrosetta.rosetta.core.pack.interaction_graph.SymmOnTheFlyInteractionGraph method) (pyrosetta.rosetta.protocols.flexpack.interaction_graph.FlexbbInteractionGraph method) (pyrosetta.rosetta.protocols.flexpack.interaction_graph.MinimalistFlexbbInteractionGraph method) (pyrosetta.rosetta.protocols.flexpack.interaction_graph.OTFFlexbbInteractionGraph method) (pyrosetta.rosetta.protocols.flexpack.interaction_graph.PrecomputedFlexbbInteractionGraph method) increment_energy_coords() (pyrosetta.rosetta.core.chemical.mainchain_potential.MainchainScoreTable method) increment_from_cached() (pyrosetta.rosetta.core.pack.interaction_graph.RotamerDots method) increment_hbond_energy() (in module pyrosetta.rosetta.core.scoring.hbonds) increment_helix_count() (pyrosetta.rosetta.protocols.helical_bundle.BundleGridSampler method) increment_histogram_bin() (pyrosetta.rosetta.core.scoring.orbitals.OrbitalsStatistics method) increment_npd_hbond_energy() (in module pyrosetta.rosetta.core.scoring.hbonds) increment_nread_limit() (pyrosetta.rosetta.utility.io.FileContentsMap method) increment_reference_pose_mapping_after_seqpos() (pyrosetta.rosetta.core.pose.Pose method) (pyrosetta.rosetta.core.pose.reference_pose.ReferencePose method) (pyrosetta.rosetta.core.pose.reference_pose.ReferencePoseSet method) increment_self_overlap() (pyrosetta.rosetta.core.pack.interaction_graph.RotamerDots method) (pyrosetta.rosetta.protocols.vardist_solaccess.VarSolDRotamerDots method) increment_this_and_cache() (pyrosetta.rosetta.core.pack.interaction_graph.RotamerDots method) increment_unique_id() (pyrosetta.rosetta.protocols.motifs.IRCollection method) incremente_n_multi_data() (pyrosetta.rosetta.protocols.scoring.methods.pcs2.PcsEnergyParameterManager method) (pyrosetta.rosetta.protocols.scoring.methods.pcs2.PcsGridSearchParameterManager method) ind() (pyrosetta.rosetta.core.scoring.hbonds.HBDerivAssigner method) ind_remodel_tcr_cdr_loops() (in module pyrosetta.rosetta.protocols.tcr) indegree() (pyrosetta.rosetta.protocols.jd3.JobDirectedNode method) (pyrosetta.rosetta.utility.graph.DirectedNode method) indel_motif() (in module pyrosetta.rosetta.protocols.evolution.AlignmentCleanerTools) indel_motif_radius() (pyrosetta.rosetta.protocols.evolution.AlignmentAAFinder method) (pyrosetta.rosetta.protocols.evolution.AlignmentGapInserter method) indel_motif_seq_id() (in module pyrosetta.rosetta.protocols.evolution.AlignmentCleanerTools) IndelOptimizationMover (class in pyrosetta.rosetta.protocols.indel) indent_w_spaces() (in module pyrosetta.rosetta.utility.tag) independent_cycles() (pyrosetta.rosetta.protocols.forge.remodel.RemodelLoopMover method) independent_residues() (pyrosetta.rosetta.core.conformation.symmetry.SymmetryInfo method) IndependentBBTorsionSRFD (class in pyrosetta.rosetta.core.fragment) IndependentLoopMover (class in pyrosetta.rosetta.protocols.loops.loop_mover) Index (class in pyrosetta.rosetta.basic.database.schema_generator) index (pyrosetta.rosetta.core.scoring.motif.MotifHit property) (pyrosetta.rosetta.protocols.cartesian.CartesianAtom property) (pyrosetta.rosetta.protocols.forge.remodel.LineObject property) (pyrosetta.rosetta.protocols.loophash.LeapIndex property) (pyrosetta.rosetta.protocols.mpi_refinement.MethodParams property) (pyrosetta.rosetta.protocols.protein_interface_design.movers.SecretionOptimizationMover.tm_region property) (pyrosetta.rosetta.protocols.simple_filters.SecretionPredictionFilter.tm_region property) (pyrosetta.rosetta.utility.graph.DS_Node property) index() (in module pyrosetta.rosetta.ObjexxFCL) (pyrosetta.CD method) (pyrosetta.rosetta.core.chemical.ResidueConnection method) (pyrosetta.rosetta.core.chemical.sdf.MolFileIOAtom method) (pyrosetta.rosetta.core.chemical.sdf.MolFileIOBond method) (pyrosetta.rosetta.core.fragment.picking_old.vall.VallSection method) (pyrosetta.rosetta.core.scoring.hbonds.HBond method) (pyrosetta.rosetta.cppdb.result method) (pyrosetta.rosetta.ObjexxFCL.FArray1_bool_t method) (pyrosetta.rosetta.ObjexxFCL.FArray1_char_t method) (pyrosetta.rosetta.ObjexxFCL.FArray1_double_t method) (pyrosetta.rosetta.ObjexxFCL.FArray1_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray1_int_t method) (pyrosetta.rosetta.ObjexxFCL.FArray1_ObjexxFCL_FArray1D_int_t method) (pyrosetta.rosetta.ObjexxFCL.FArray1_std_string_t method) (pyrosetta.rosetta.ObjexxFCL.FArray1_unsigned_long_t method) (pyrosetta.rosetta.ObjexxFCL.FArray1A_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray1A_int_t method) (pyrosetta.rosetta.ObjexxFCL.FArray1D_bool_t method) (pyrosetta.rosetta.ObjexxFCL.FArray1D_char_t method) (pyrosetta.rosetta.ObjexxFCL.FArray1D_double_t method) (pyrosetta.rosetta.ObjexxFCL.FArray1D_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray1D_int_t method) (pyrosetta.rosetta.ObjexxFCL.FArray1D_ObjexxFCL_FArray1D_int_t method) (pyrosetta.rosetta.ObjexxFCL.FArray1D_std_string_t method) (pyrosetta.rosetta.ObjexxFCL.FArray1D_unsigned_long_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2_bool_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2_core_pack_dunbrack_BBDepNRChiSample_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2_core_pack_dunbrack_BBDepScoreInterpData_1_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2_core_pack_dunbrack_BBDepScoreInterpData_2_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2_core_pack_dunbrack_BBDepScoreInterpData_3_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2_core_pack_dunbrack_BBDepScoreInterpData_4_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2_core_pack_dunbrack_BBDepScoreInterpData_5_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2_core_pack_dunbrack_BBIndNRChiSample_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2_core_pack_dunbrack_PackedDunbrackRotamer_1_1_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2_core_pack_dunbrack_PackedDunbrackRotamer_1_2_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2_core_pack_dunbrack_PackedDunbrackRotamer_1_3_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2_core_pack_dunbrack_PackedDunbrackRotamer_1_4_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2_core_pack_dunbrack_PackedDunbrackRotamer_1_5_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2_core_pack_dunbrack_PackedDunbrackRotamer_2_1_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2_core_pack_dunbrack_PackedDunbrackRotamer_2_2_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2_core_pack_dunbrack_PackedDunbrackRotamer_2_3_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2_core_pack_dunbrack_PackedDunbrackRotamer_2_4_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2_core_pack_dunbrack_PackedDunbrackRotamer_2_5_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2_core_pack_dunbrack_PackedDunbrackRotamer_3_1_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2_core_pack_dunbrack_PackedDunbrackRotamer_3_2_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2_core_pack_dunbrack_PackedDunbrackRotamer_3_3_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2_core_pack_dunbrack_PackedDunbrackRotamer_3_4_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2_core_pack_dunbrack_PackedDunbrackRotamer_3_5_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2_core_pack_dunbrack_PackedDunbrackRotamer_4_1_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2_core_pack_dunbrack_PackedDunbrackRotamer_4_2_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2_core_pack_dunbrack_PackedDunbrackRotamer_4_3_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2_core_pack_dunbrack_PackedDunbrackRotamer_4_4_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2_core_pack_dunbrack_PackedDunbrackRotamer_4_5_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2_core_pack_dunbrack_PackedDunbrackRotamer_5_1_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2_core_pack_dunbrack_PackedDunbrackRotamer_5_2_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2_core_pack_dunbrack_PackedDunbrackRotamer_5_3_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2_core_pack_dunbrack_PackedDunbrackRotamer_5_4_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2_core_pack_dunbrack_PackedDunbrackRotamer_5_5_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2_double_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2_int_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2_numeric_xyzVector_double_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2_ObjexxFCL_FArray2D_float__star__t method) (pyrosetta.rosetta.ObjexxFCL.FArray2_ObjexxFCL_ubyte_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2_std_string_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2_unsigned_char_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2_unsigned_long_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2_utility_vector1_core_pack_dunbrack_cenrot_CentroidRotamerSampleData_std_allocator_core_pack_dunbrack_cenrot_CentroidRotamerSampleData_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2_utility_vector1_double_std_allocator_double_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2A_double_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2A_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_bool_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_core_pack_dunbrack_BBDepNRChiSample_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_core_pack_dunbrack_BBDepScoreInterpData_1_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_core_pack_dunbrack_BBDepScoreInterpData_2_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_core_pack_dunbrack_BBDepScoreInterpData_3_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_core_pack_dunbrack_BBDepScoreInterpData_4_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_core_pack_dunbrack_BBDepScoreInterpData_5_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_core_pack_dunbrack_BBIndNRChiSample_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_core_pack_dunbrack_PackedDunbrackRotamer_1_1_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_core_pack_dunbrack_PackedDunbrackRotamer_1_2_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_core_pack_dunbrack_PackedDunbrackRotamer_1_3_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_core_pack_dunbrack_PackedDunbrackRotamer_1_4_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_core_pack_dunbrack_PackedDunbrackRotamer_1_5_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_core_pack_dunbrack_PackedDunbrackRotamer_2_1_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_core_pack_dunbrack_PackedDunbrackRotamer_2_2_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_core_pack_dunbrack_PackedDunbrackRotamer_2_3_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_core_pack_dunbrack_PackedDunbrackRotamer_2_4_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_core_pack_dunbrack_PackedDunbrackRotamer_2_5_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_core_pack_dunbrack_PackedDunbrackRotamer_3_1_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_core_pack_dunbrack_PackedDunbrackRotamer_3_2_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_core_pack_dunbrack_PackedDunbrackRotamer_3_3_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_core_pack_dunbrack_PackedDunbrackRotamer_3_4_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_core_pack_dunbrack_PackedDunbrackRotamer_3_5_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_core_pack_dunbrack_PackedDunbrackRotamer_4_1_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_core_pack_dunbrack_PackedDunbrackRotamer_4_2_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_core_pack_dunbrack_PackedDunbrackRotamer_4_3_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_core_pack_dunbrack_PackedDunbrackRotamer_4_4_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_core_pack_dunbrack_PackedDunbrackRotamer_4_5_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_core_pack_dunbrack_PackedDunbrackRotamer_5_1_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_core_pack_dunbrack_PackedDunbrackRotamer_5_2_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_core_pack_dunbrack_PackedDunbrackRotamer_5_3_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_core_pack_dunbrack_PackedDunbrackRotamer_5_4_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_core_pack_dunbrack_PackedDunbrackRotamer_5_5_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_double_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_int_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_numeric_xyzVector_double_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_ObjexxFCL_FArray2D_float__star__t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_ObjexxFCL_ubyte_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_std_string_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_unsigned_char_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_unsigned_long_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_utility_vector1_core_pack_dunbrack_cenrot_CentroidRotamerSampleData_std_allocator_core_pack_dunbrack_cenrot_CentroidRotamerSampleData_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_utility_vector1_double_std_allocator_double_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2P_double_t method) (pyrosetta.rosetta.ObjexxFCL.FArray3_core_pack_dunbrack_BBDepScoreInterpData_1_t method) (pyrosetta.rosetta.ObjexxFCL.FArray3_core_pack_dunbrack_BBDepScoreInterpData_2_t method) (pyrosetta.rosetta.ObjexxFCL.FArray3_core_pack_dunbrack_BBDepScoreInterpData_3_t method) (pyrosetta.rosetta.ObjexxFCL.FArray3_core_pack_dunbrack_BBDepScoreInterpData_4_t method) (pyrosetta.rosetta.ObjexxFCL.FArray3_core_pack_dunbrack_BBDepScoreInterpData_5_t method) (pyrosetta.rosetta.ObjexxFCL.FArray3_double_t method) (pyrosetta.rosetta.ObjexxFCL.FArray3_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray3_int_t method) (pyrosetta.rosetta.ObjexxFCL.FArray3_std_complex_double_t method) (pyrosetta.rosetta.ObjexxFCL.FArray3_std_vector_unsigned_long_std_allocator_unsigned_long_t method) (pyrosetta.rosetta.ObjexxFCL.FArray3_unsigned_char_t method) (pyrosetta.rosetta.ObjexxFCL.FArray3_unsigned_long_t method) (pyrosetta.rosetta.ObjexxFCL.FArray3_utility_vector1_double_std_allocator_double_t method) (pyrosetta.rosetta.ObjexxFCL.FArray3_utility_vector1_numeric_xyzVector_double_std_allocator_numeric_xyzVector_double_t method) (pyrosetta.rosetta.ObjexxFCL.FArray3_utility_vector1_unsigned_int_std_allocator_unsigned_int_t method) (pyrosetta.rosetta.ObjexxFCL.FArray3A_double_t method) (pyrosetta.rosetta.ObjexxFCL.FArray3D_core_pack_dunbrack_BBDepScoreInterpData_1_t method) (pyrosetta.rosetta.ObjexxFCL.FArray3D_core_pack_dunbrack_BBDepScoreInterpData_2_t method) (pyrosetta.rosetta.ObjexxFCL.FArray3D_core_pack_dunbrack_BBDepScoreInterpData_3_t method) (pyrosetta.rosetta.ObjexxFCL.FArray3D_core_pack_dunbrack_BBDepScoreInterpData_4_t method) (pyrosetta.rosetta.ObjexxFCL.FArray3D_core_pack_dunbrack_BBDepScoreInterpData_5_t method) (pyrosetta.rosetta.ObjexxFCL.FArray3D_double_t method) (pyrosetta.rosetta.ObjexxFCL.FArray3D_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray3D_int_t method) (pyrosetta.rosetta.ObjexxFCL.FArray3D_std_complex_double_t method) (pyrosetta.rosetta.ObjexxFCL.FArray3D_std_vector_unsigned_long_std_allocator_unsigned_long_t method) (pyrosetta.rosetta.ObjexxFCL.FArray3D_unsigned_char_t method) (pyrosetta.rosetta.ObjexxFCL.FArray3D_unsigned_long_t method) (pyrosetta.rosetta.ObjexxFCL.FArray3D_utility_vector1_double_std_allocator_double_t method) (pyrosetta.rosetta.ObjexxFCL.FArray3D_utility_vector1_numeric_xyzVector_double_std_allocator_numeric_xyzVector_double_t method) (pyrosetta.rosetta.ObjexxFCL.FArray3D_utility_vector1_unsigned_int_std_allocator_unsigned_int_t method) (pyrosetta.rosetta.ObjexxFCL.FArray3P_double_t method) (pyrosetta.rosetta.ObjexxFCL.FArray4_double_t method) (pyrosetta.rosetta.ObjexxFCL.FArray4_int_t method) (pyrosetta.rosetta.ObjexxFCL.FArray4_unsigned_char_t method) (pyrosetta.rosetta.ObjexxFCL.FArray4D_double_t method) (pyrosetta.rosetta.ObjexxFCL.FArray4D_int_t method) (pyrosetta.rosetta.ObjexxFCL.FArray4D_unsigned_char_t method) (pyrosetta.rosetta.ObjexxFCL.FArray5_double_t method) (pyrosetta.rosetta.ObjexxFCL.FArray5_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray5_int_t method) (pyrosetta.rosetta.ObjexxFCL.FArray5D_double_t method) (pyrosetta.rosetta.ObjexxFCL.FArray5D_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray5D_int_t method) (pyrosetta.rosetta.protocols.denovo_design.components.EnumeratedVectorSelector_utility_vector1_std_shared_ptr_const_protocols_denovo_design_components_Segment_std_allocator_std_shared_ptr_const_protocols_denovo_design_components_Segment_t method) (pyrosetta.rosetta.protocols.denovo_design.components.VectorSelector_utility_vector1_std_shared_ptr_const_protocols_denovo_design_components_Segment_std_allocator_std_shared_ptr_const_protocols_denovo_design_components_Segment_t method) (pyrosetta.rosetta.protocols.enzdes.EnzdesFlexibleRegion method) (pyrosetta.rosetta.protocols.genetic_algorithm.EntityElement method) (pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.Pharmacophore method) (pyrosetta.rosetta.protocols.match.upstream.OriginalBackboneBuildPoint method) (pyrosetta.rosetta.protocols.match.upstream.ProteinBackboneBuildPoint method) (pyrosetta.rosetta.protocols.match.upstream.ScaffoldBuildPoint method) (pyrosetta.rosetta.protocols.mean_field.AAMatrix method) (pyrosetta.rosetta.protocols.mean_field.jagged_array_double_std_allocator_double_t method) (pyrosetta.rosetta.protocols.mean_field.jagged_array_protocols_mean_field_AAProb_std_allocator_protocols_mean_field_AAProb_t method) (pyrosetta.rosetta.protocols.mean_field.jagged_array_protocols_mean_field_RotProb_std_allocator_protocols_mean_field_RotProb_t method) (pyrosetta.rosetta.protocols.mean_field.RotMatrix method) (pyrosetta.rosetta.protocols.multistate_design.PosType method) (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.MatchConstraintFileInfo method) (pyrosetta.rosetta.utility.deep_copy_vector1_std_shared_ptr_core_chemical_Orbital_t method) (pyrosetta.rosetta.utility.keys.SmallKeyVector_utility_options_AnyOptionKey_utility_options_VariantOption_utility_options_ScalarOption_t method) (pyrosetta.rosetta.utility.keys.SmallKeyVector_utility_options_AnyVectorOptionKey_utility_options_VariantOption_utility_options_VectorOption_t method) (pyrosetta.rosetta.utility.keys.SmallKeyVector_utility_options_BooleanOptionKey_utility_options_BooleanOption_t method) (pyrosetta.rosetta.utility.keys.SmallKeyVector_utility_options_BooleanVectorOptionKey_utility_options_BooleanVectorOption_t method) (pyrosetta.rosetta.utility.keys.SmallKeyVector_utility_options_FileOptionKey_utility_options_FileOption_t method) (pyrosetta.rosetta.utility.keys.SmallKeyVector_utility_options_FileVectorOptionKey_utility_options_FileVectorOption_t method) (pyrosetta.rosetta.utility.keys.SmallKeyVector_utility_options_IntegerOptionKey_utility_options_IntegerOption_t method) (pyrosetta.rosetta.utility.keys.SmallKeyVector_utility_options_IntegerVectorOptionKey_utility_options_IntegerVectorOption_t method) (pyrosetta.rosetta.utility.keys.SmallKeyVector_utility_options_OptionKey_utility_options_OptionTypes_t method) (pyrosetta.rosetta.utility.keys.SmallKeyVector_utility_options_PathOptionKey_utility_options_PathOption_t method) (pyrosetta.rosetta.utility.keys.SmallKeyVector_utility_options_PathVectorOptionKey_utility_options_PathVectorOption_t method) (pyrosetta.rosetta.utility.keys.SmallKeyVector_utility_options_RealOptionKey_utility_options_RealOption_t method) (pyrosetta.rosetta.utility.keys.SmallKeyVector_utility_options_RealVectorOptionKey_utility_options_RealVectorOption_t method) (pyrosetta.rosetta.utility.keys.SmallKeyVector_utility_options_ResidueChainVectorOptionKey_utility_options_ResidueChainVectorOption_t method) (pyrosetta.rosetta.utility.keys.SmallKeyVector_utility_options_StringOptionKey_utility_options_StringOption_t method) (pyrosetta.rosetta.utility.keys.SmallKeyVector_utility_options_StringVectorOptionKey_utility_options_StringVectorOption_t method) (pyrosetta.rosetta.utility.LexicographicalIterator method) (pyrosetta.rosetta.utility.libsvm.Svm_node_rosetta method) (pyrosetta.rosetta.utility.SimulateMPIMessage method) index1 (pyrosetta.rosetta.protocols.cartesian.MD_Angle property) (pyrosetta.rosetta.protocols.cartesian.MD_Bond property) (pyrosetta.rosetta.protocols.cartesian.MD_HarmonicDihedral property) index2 (pyrosetta.rosetta.protocols.cartesian.MD_Angle property) (pyrosetta.rosetta.protocols.cartesian.MD_Bond property) (pyrosetta.rosetta.protocols.cartesian.MD_HarmonicDihedral property) index2symbol() (pyrosetta.rosetta.core.sequence.ABEGOManager method) (pyrosetta.rosetta.core.sequence.SSManager method) index2symbolString() (pyrosetta.rosetta.core.sequence.SSManager method) index3 (pyrosetta.rosetta.protocols.cartesian.MD_Angle property) (pyrosetta.rosetta.protocols.cartesian.MD_HarmonicDihedral property) index4 (pyrosetta.rosetta.protocols.cartesian.MD_HarmonicDihedral property) index_ (pyrosetta.rosetta.core.pack.dunbrack.ProbSortClass property) index_match (pyrosetta.rosetta.protocols.indexed_structure_store.BackboneStub property) index_of_entity() (pyrosetta.rosetta.protocols.pack_daemon.TopEntitySet method) index_of_next_message() (pyrosetta.rosetta.utility.SimulateMPI static method) index_to_id() (pyrosetta.rosetta.core.scoring.packing.PoseBalls method) (pyrosetta.rosetta.core.scoring.packing.PoseBallsLite method) index_to_vd() (pyrosetta.rosetta.core.chemical.rdkit.RDMolToRestype method) (pyrosetta.rosetta.core.chemical.rdkit.RestypeToRDMol method) indexed_coordinate_array_broadcast_rmsd() (in module pyrosetta.rosetta.numeric.alignment) IndexRange (class in pyrosetta.rosetta.ObjexxFCL) indicate_required_context_graphs() (pyrosetta.rosetta.core.energy_methods.AACompositionEnergy method) (pyrosetta.rosetta.core.energy_methods.AARepeatEnergy method) (pyrosetta.rosetta.core.energy_methods.Abego method) (pyrosetta.rosetta.core.energy_methods.ArgCationPiEnergy method) (pyrosetta.rosetta.core.energy_methods.AromaticBackboneRestraintEnergy method) (pyrosetta.rosetta.core.energy_methods.AspartimidePenaltyEnergy method) (pyrosetta.rosetta.core.energy_methods.BranchEnergy method) (pyrosetta.rosetta.core.energy_methods.Burial_v2Energy method) (pyrosetta.rosetta.core.energy_methods.BurialEnergy method) (pyrosetta.rosetta.core.energy_methods.CartesianBondedEnergy method) (pyrosetta.rosetta.core.energy_methods.CCS_IMMSEnergy method) (pyrosetta.rosetta.core.energy_methods.CenHBEnergy method) (pyrosetta.rosetta.core.energy_methods.CenPairEnergy method) (pyrosetta.rosetta.core.energy_methods.CenPairMotifDegreeEnergy method) (pyrosetta.rosetta.core.energy_methods.CenPairMotifEnergy method) (pyrosetta.rosetta.core.energy_methods.CenRotEnvEnergy method) (pyrosetta.rosetta.core.energy_methods.CenRotPairEnergy method) (pyrosetta.rosetta.core.energy_methods.CentroidDisulfideEnergy method) (pyrosetta.rosetta.core.energy_methods.ChainbreakEnergy method) (pyrosetta.rosetta.core.energy_methods.ChemicalShiftAnisotropyEnergy method) (pyrosetta.rosetta.core.energy_methods.ContactOrderEnergy method) (pyrosetta.rosetta.core.energy_methods.ContextDependentGeometricSolEnergy method) (pyrosetta.rosetta.core.energy_methods.ContextIndependentGeometricSolEnergy method) (pyrosetta.rosetta.core.energy_methods.CovalentLabelingEnergy method) (pyrosetta.rosetta.core.energy_methods.CovalentLabelingFAEnergy method) (pyrosetta.rosetta.core.energy_methods.CustomAtomPairEnergy method) (pyrosetta.rosetta.core.energy_methods.D2H_SA_Energy method) (pyrosetta.rosetta.core.energy_methods.DEEREnergy method) (pyrosetta.rosetta.core.energy_methods.DEPC_MS_Energy method) (pyrosetta.rosetta.core.energy_methods.dfire.DFIRE_Energy method) (pyrosetta.rosetta.core.energy_methods.DipolarCouplingEnergy method) (pyrosetta.rosetta.core.energy_methods.DirectReadoutEnergy method) (pyrosetta.rosetta.core.energy_methods.DistanceChainbreakEnergy method) (pyrosetta.rosetta.core.energy_methods.DisulfideMatchingEnergy method) (pyrosetta.rosetta.core.energy_methods.DNA_BaseEnergy method) (pyrosetta.rosetta.core.energy_methods.DNA_DihedralEnergy method) (pyrosetta.rosetta.core.energy_methods.DNA_EnvPairEnergy method) (pyrosetta.rosetta.core.energy_methods.DNA_ReferenceEnergy method) (pyrosetta.rosetta.core.energy_methods.DNAChiEnergy method) (pyrosetta.rosetta.core.energy_methods.DNATorsionEnergy method) (pyrosetta.rosetta.core.energy_methods.DumpTrajectoryEnergy method) (pyrosetta.rosetta.core.energy_methods.ElecDensAllAtomCenEnergy method) (pyrosetta.rosetta.core.energy_methods.ElecDensAtomwiseEnergy method) (pyrosetta.rosetta.core.energy_methods.ElecDensCenEnergy method) (pyrosetta.rosetta.core.energy_methods.ElecDensEnergy method) (pyrosetta.rosetta.core.energy_methods.EnvEnergy method) (pyrosetta.rosetta.core.energy_methods.EnvSmoothEnergy method) (pyrosetta.rosetta.core.energy_methods.ExactOccludedHbondSolEnergy method) (pyrosetta.rosetta.core.energy_methods.FA_ElecEnergyAroAll method) (pyrosetta.rosetta.core.energy_methods.FA_ElecEnergyAroAro method) (pyrosetta.rosetta.core.energy_methods.FA_GrpElecEnergy method) (pyrosetta.rosetta.core.energy_methods.Fa_MbenvEnergy method) (pyrosetta.rosetta.core.energy_methods.Fa_MbsolvEnergy method) (pyrosetta.rosetta.core.energy_methods.FACTSEnergy method) (pyrosetta.rosetta.core.energy_methods.FaMPAsymEzCBEnergy method) (pyrosetta.rosetta.core.energy_methods.FaMPAsymEzCGEnergy method) (pyrosetta.rosetta.core.energy_methods.FaMPEnvEnergy method) (pyrosetta.rosetta.core.energy_methods.FaMPEnvSmoothEnergy method) (pyrosetta.rosetta.core.energy_methods.FaMPSolvEnergy method) (pyrosetta.rosetta.core.energy_methods.FastDensEnergy method) (pyrosetta.rosetta.core.energy_methods.FastSAXSEnergy method) (pyrosetta.rosetta.core.energy_methods.FiberDiffractionEnergy method) (pyrosetta.rosetta.core.energy_methods.FiberDiffractionEnergyDens method) (pyrosetta.rosetta.core.energy_methods.FreeDOF_Energy method) (pyrosetta.rosetta.core.energy_methods.FullatomDisulfideEnergy method) (pyrosetta.rosetta.core.energy_methods.GaussianOverlapEnergy method) (pyrosetta.rosetta.core.energy_methods.GenBornEnergy method) (pyrosetta.rosetta.core.energy_methods.GenericBondedEnergy method) (pyrosetta.rosetta.core.energy_methods.GoapEnergy method) (pyrosetta.rosetta.core.energy_methods.HackAroEnergy method) (pyrosetta.rosetta.core.energy_methods.HolesEnergy method) (pyrosetta.rosetta.core.energy_methods.HRF_MSLabelingEnergy method) (pyrosetta.rosetta.core.energy_methods.HRFDynamicsEnergy method) (pyrosetta.rosetta.core.energy_methods.HybridVDW_Energy method) (pyrosetta.rosetta.core.energy_methods.HydroxylTorsionEnergy method) (pyrosetta.rosetta.core.energy_methods.IntermolEnergy method) (pyrosetta.rosetta.core.energy_methods.LinearBranchEnergy method) (pyrosetta.rosetta.core.energy_methods.LinearChainbreakEnergy method) (pyrosetta.rosetta.core.energy_methods.LK_hack method) (pyrosetta.rosetta.core.energy_methods.LK_PolarNonPolarEnergy method) (pyrosetta.rosetta.core.energy_methods.LoopCloseEnergy method) (pyrosetta.rosetta.core.energy_methods.MembraneCbetaEnergy method) (pyrosetta.rosetta.core.energy_methods.MembraneCenPairEnergy method) (pyrosetta.rosetta.core.energy_methods.MembraneEnvEnergy method) (pyrosetta.rosetta.core.energy_methods.MembraneEnvPenalties method) (pyrosetta.rosetta.core.energy_methods.MembraneEnvSmoothEnergy method) (pyrosetta.rosetta.core.energy_methods.MembraneLipo method) (pyrosetta.rosetta.core.energy_methods.MgEnergy method) (pyrosetta.rosetta.core.energy_methods.MHCEpitopeEnergy method) (pyrosetta.rosetta.core.energy_methods.MissingEnergy method) (pyrosetta.rosetta.core.energy_methods.MotifDockEnergy method) (pyrosetta.rosetta.core.energy_methods.MPCbetaEnergy method) (pyrosetta.rosetta.core.energy_methods.MPEnvEnergy method) (pyrosetta.rosetta.core.energy_methods.MPHelicalityEnergy method) (pyrosetta.rosetta.core.energy_methods.MPPairEnergy method) (pyrosetta.rosetta.core.energy_methods.MPResidueLipophilicityEnergy method) (pyrosetta.rosetta.core.energy_methods.MPSpanAngleEnergy method) (pyrosetta.rosetta.core.energy_methods.MPSpanInsertionEnergy method) (pyrosetta.rosetta.core.energy_methods.MultipoleElecEnergy method) (pyrosetta.rosetta.core.energy_methods.NetChargeEnergy method) (pyrosetta.rosetta.core.energy_methods.NPDHBondEnergy method) (pyrosetta.rosetta.core.energy_methods.OccludedHbondSolEnergy method) (pyrosetta.rosetta.core.energy_methods.OccludedHbondSolEnergy_onebody method) (pyrosetta.rosetta.core.energy_methods.OmegaTetherEnergy method) (pyrosetta.rosetta.core.energy_methods.OtherPoseEnergy method) (pyrosetta.rosetta.core.energy_methods.P_AA_Energy method) (pyrosetta.rosetta.core.energy_methods.P_AA_pp_Energy method) (pyrosetta.rosetta.core.energy_methods.P_AA_ss_Energy method) (pyrosetta.rosetta.core.energy_methods.PackStatEnergy method) (pyrosetta.rosetta.core.energy_methods.PairEnergy method) (pyrosetta.rosetta.core.energy_methods.PeptideBondEnergy method) (pyrosetta.rosetta.core.energy_methods.pHEnergy method) (pyrosetta.rosetta.core.energy_methods.PointWaterEnergy method) (pyrosetta.rosetta.core.energy_methods.PoissonBoltzmannEnergy method) (pyrosetta.rosetta.core.energy_methods.ProClosureEnergy method) (pyrosetta.rosetta.core.energy_methods.ProQ_Energy method) (pyrosetta.rosetta.core.energy_methods.RamachandranEnergy method) (pyrosetta.rosetta.core.energy_methods.RamachandranEnergy2B method) (pyrosetta.rosetta.core.energy_methods.RamaPreProEnergy method) (pyrosetta.rosetta.core.energy_methods.ReferenceEnergy method) (pyrosetta.rosetta.core.energy_methods.ReferenceEnergyNoncanonical method) (pyrosetta.rosetta.core.energy_methods.ResidualDipolarCouplingEnergy method) (pyrosetta.rosetta.core.energy_methods.ResidualDipolarCouplingEnergy_Rohl method) (pyrosetta.rosetta.core.energy_methods.RG_Energy_Fast method) (pyrosetta.rosetta.core.energy_methods.RG_Energy_RNA method) (pyrosetta.rosetta.core.energy_methods.RG_LocalEnergy method) (pyrosetta.rosetta.core.energy_methods.RingClosureEnergy method) (pyrosetta.rosetta.core.energy_methods.RMS_Energy method) (pyrosetta.rosetta.core.energy_methods.RNA_BulgeEnergy method) (pyrosetta.rosetta.core.energy_methods.RNA_ChemicalMappingEnergy method) (pyrosetta.rosetta.core.energy_methods.RNA_ChemicalShiftEnergy method) (pyrosetta.rosetta.core.energy_methods.RNA_CoarseDistEnergy method) (pyrosetta.rosetta.core.energy_methods.RNA_DataBackboneEnergy method) (pyrosetta.rosetta.core.energy_methods.RNA_FA_ElecEnergy method) (pyrosetta.rosetta.core.energy_methods.RNA_FullAtomStackingEnergy method) (pyrosetta.rosetta.core.energy_methods.RNA_FullAtomVDW_BasePhosphate method) (pyrosetta.rosetta.core.energy_methods.RNA_JR_SuiteEnergy method) (pyrosetta.rosetta.core.energy_methods.RNA_LJ_BaseEnergy method) (pyrosetta.rosetta.core.energy_methods.RNA_MgPointEnergy method) (pyrosetta.rosetta.core.energy_methods.RNA_PairwiseLowResolutionEnergy method) (pyrosetta.rosetta.core.energy_methods.RNA_PartitionEnergy method) (pyrosetta.rosetta.core.energy_methods.RNA_StubCoordinateEnergy method) (pyrosetta.rosetta.core.energy_methods.RNA_SugarCloseEnergy method) (pyrosetta.rosetta.core.energy_methods.RNA_SuiteEnergy method) (pyrosetta.rosetta.core.energy_methods.RNA_TorsionEnergy method) (pyrosetta.rosetta.core.energy_methods.RNA_VDW_Energy method) (pyrosetta.rosetta.core.energy_methods.RNP_LowResEnergy method) (pyrosetta.rosetta.core.energy_methods.RNP_LowResPairDistEnergy method) (pyrosetta.rosetta.core.energy_methods.RNP_LowResStackEnergy method) (pyrosetta.rosetta.core.energy_methods.SA_Energy method) (pyrosetta.rosetta.core.energy_methods.SASAEnergy method) (pyrosetta.rosetta.core.energy_methods.SAXSEnergy method) (pyrosetta.rosetta.core.energy_methods.SAXSEnergyCEN method) (pyrosetta.rosetta.core.energy_methods.SAXSEnergyFA method) (pyrosetta.rosetta.core.energy_methods.SecondaryStructureEnergy method) (pyrosetta.rosetta.core.energy_methods.SequenceDependentRefEnergy method) (pyrosetta.rosetta.core.energy_methods.SmoothCenPairEnergy method) (pyrosetta.rosetta.core.energy_methods.SmoothEnvEnergy method) (pyrosetta.rosetta.core.energy_methods.SplitUnfoldedTwoBodyEnergy method) (pyrosetta.rosetta.core.energy_methods.SSElementMotifContactEnergy method) (pyrosetta.rosetta.core.energy_methods.StackElecEnergy method) (pyrosetta.rosetta.core.energy_methods.SuckerEnergy method) (pyrosetta.rosetta.core.energy_methods.SugarBackboneEnergy method) (pyrosetta.rosetta.core.energy_methods.SurfEnergy method) (pyrosetta.rosetta.core.energy_methods.SurfVolEnergy method) (pyrosetta.rosetta.core.energy_methods.SymmetricLigandEnergy method) (pyrosetta.rosetta.core.energy_methods.TNA_SuiteEnergy method) (pyrosetta.rosetta.core.energy_methods.UnfoldedStateEnergy method) (pyrosetta.rosetta.core.energy_methods.VdWTinkerEnergy method) (pyrosetta.rosetta.core.energy_methods.WaterAdductHBondEnergy method) (pyrosetta.rosetta.core.energy_methods.WaterAdductIntraEnergy method) (pyrosetta.rosetta.core.energy_methods.WaterSpecificEnergy method) (pyrosetta.rosetta.core.energy_methods.XtalMLEnergy method) (pyrosetta.rosetta.core.energy_methods.YHHPlanarityEnergy method) (pyrosetta.rosetta.core.pack.dunbrack.cenrot.CenRotDunEnergy method) (pyrosetta.rosetta.core.pack.dunbrack.DunbrackEnergy method) (pyrosetta.rosetta.core.pack.guidance_scoreterms.approximate_buried_unsat_penalty.ApproximateBuriedUnsatPenalty method) (pyrosetta.rosetta.core.pack.guidance_scoreterms.buried_unsat_penalty.BuriedUnsatPenalty method) (pyrosetta.rosetta.core.pack.guidance_scoreterms.hbnet_energy.HBNetEnergy method) (pyrosetta.rosetta.core.pack.guidance_scoreterms.lk_dome.LK_DomePackEnergy method) (pyrosetta.rosetta.core.pack.guidance_scoreterms.sap.SapConstraintEnergy method) (pyrosetta.rosetta.core.pack.guidance_scoreterms.voids_penalty_energy.VoidsPenaltyEnergy method) (pyrosetta.rosetta.core.pack.interaction_graph.HPatchEnergy method) (pyrosetta.rosetta.core.pack.interaction_graph.SurfaceEnergy method) (pyrosetta.rosetta.core.scoring.carbon_hbonds.CarbonHBondEnergy method) (pyrosetta.rosetta.core.scoring.constraints.ConstraintsEnergy method) (pyrosetta.rosetta.core.scoring.custom_pair_distance.FullatomCustomPairDistanceEnergy method) (pyrosetta.rosetta.core.scoring.DockingScoreFunction method) (pyrosetta.rosetta.core.scoring.elec.FA_ElecEnergy method) (pyrosetta.rosetta.core.scoring.etable.AnalyticEtableEnergy method) (pyrosetta.rosetta.core.scoring.etable.BaseEtableEnergy_core_scoring_etable_AnalyticEtableEnergy_t method) (pyrosetta.rosetta.core.scoring.etable.BaseEtableEnergy_core_scoring_etable_TableLookupEtableEnergy_t method) (pyrosetta.rosetta.core.scoring.etable.TableLookupEtableEnergy method) (pyrosetta.rosetta.core.scoring.hbonds.HBondEnergy method) (pyrosetta.rosetta.core.scoring.interface_.DDPscore method) (pyrosetta.rosetta.core.scoring.lkball.LK_BallEnergy method) (pyrosetta.rosetta.core.scoring.lkball.LK_DomeEnergy method) (pyrosetta.rosetta.core.scoring.membrane.MPNonHelixPenalty method) (pyrosetta.rosetta.core.scoring.membrane.MPTerminiPenalty method) (pyrosetta.rosetta.core.scoring.membrane.MPTMProjPenalty method) (pyrosetta.rosetta.core.scoring.methods.ContextDependentLRTwoBodyEnergy method) (pyrosetta.rosetta.core.scoring.methods.ContextDependentOneBodyEnergy method) (pyrosetta.rosetta.core.scoring.methods.ContextDependentTwoBodyEnergy method) (pyrosetta.rosetta.core.scoring.methods.ContextIndependentLRTwoBodyEnergy method) (pyrosetta.rosetta.core.scoring.methods.ContextIndependentOneBodyEnergy method) (pyrosetta.rosetta.core.scoring.methods.ContextIndependentTwoBodyEnergy method) (pyrosetta.rosetta.core.scoring.methods.EnergyMethod method) (pyrosetta.rosetta.core.scoring.methods.LongRangeTwoBodyEnergy method) (pyrosetta.rosetta.core.scoring.methods.MMBondAngleEnergy method) (pyrosetta.rosetta.core.scoring.methods.MMBondLengthEnergy method) (pyrosetta.rosetta.core.scoring.methods.MMLJEnergyInter method) (pyrosetta.rosetta.core.scoring.methods.MMLJEnergyIntra method) (pyrosetta.rosetta.core.scoring.methods.MMTorsionEnergy method) (pyrosetta.rosetta.core.scoring.methods.NMerPSSMEnergy method) (pyrosetta.rosetta.core.scoring.methods.NMerRefEnergy method) (pyrosetta.rosetta.core.scoring.methods.NMerSVMEnergy method) (pyrosetta.rosetta.core.scoring.methods.OneBodyEnergy method) (pyrosetta.rosetta.core.scoring.methods.ShortRangeTwoBodyEnergy method) (pyrosetta.rosetta.core.scoring.methods.TwoBodyEnergy method) (pyrosetta.rosetta.core.scoring.methods.WholeStructureEnergy method) (pyrosetta.rosetta.core.scoring.MinScoreScoreFunction method) (pyrosetta.rosetta.core.scoring.nv.NVscore method) (pyrosetta.rosetta.core.scoring.orbitals.OrbitalsScore method) (pyrosetta.rosetta.core.scoring.packing.HolesEnergyRes method) (pyrosetta.rosetta.core.scoring.rna.chemical_shift.RNA_ChemicalShiftPotential method) (pyrosetta.rosetta.core.scoring.rna.RNA_LowResolutionPotential method) (pyrosetta.rosetta.core.scoring.ScoreFunction method) (pyrosetta.rosetta.core.scoring.sym_e.symEnergy method) (pyrosetta.rosetta.core.scoring.symmetry.SymmetricScoreFunction method) (pyrosetta.rosetta.core.scoring.vdwaals.VDW_Energy method) (pyrosetta.rosetta.protocols.fldsgn.potentials.AACompositionEnergy method) (pyrosetta.rosetta.protocols.fldsgn.potentials.sspot.NatbiasSecondaryStructureEnergy method) (pyrosetta.rosetta.protocols.flexpack.OtherContextScoreFunction method) (pyrosetta.rosetta.protocols.membrane.scoring.FaWaterToBilayerEnergy method) (pyrosetta.rosetta.protocols.nmr.pcs.PCSEnergy method) (pyrosetta.rosetta.protocols.nmr.pre.PREEnergy method) (pyrosetta.rosetta.protocols.nmr.rdc.RDCEnergy method) (pyrosetta.rosetta.protocols.rna.AlignmentEnergy method) (pyrosetta.rosetta.protocols.scoring.methods.EnsembleEnergy method) (pyrosetta.rosetta.protocols.scoring.methods.InterchainEnvEnergy method) (pyrosetta.rosetta.protocols.scoring.methods.InterchainPairEnergy method) (pyrosetta.rosetta.protocols.scoring.methods.pcs.PCS_Energy method) (pyrosetta.rosetta.protocols.scoring.methods.pcs2.PcsEnergy method) (pyrosetta.rosetta.protocols.scoring.methods.pcsTs1.PCS_Energy_Ts1 method) (pyrosetta.rosetta.protocols.scoring.methods.pcsTs2.PCS_Energy_Ts2 method) (pyrosetta.rosetta.protocols.scoring.methods.pcsTs3.PCS_Energy_Ts3 method) (pyrosetta.rosetta.protocols.scoring.methods.pcsTs4.PCS_Energy_Ts4 method) (pyrosetta.rosetta.protocols.scoring.methods.ResidualDipolarCouplingEnergyRigidSegments method) (pyrosetta.rosetta.protocols.scoring.methods.saxs.PDDFEnergy method) (pyrosetta.rosetta.protocols.scoring.methods.SpecialRotamerEnergy method) (pyrosetta.rosetta.protocols.scoring.methods.TargetClashEnergy method) (pyrosetta.rosetta.protocols.scoring.VDW_GridEnergy method) indices() (pyrosetta.rosetta.core.pack.task.operation.ResidueIndexIs method) (pyrosetta.rosetta.core.pack.task.operation.ResidueIndexIsnt method) (pyrosetta.rosetta.core.pack.task.operation.ResiduePDBIndexIs method) (pyrosetta.rosetta.core.pack.task.operation.ResiduePDBIndexIsnt method) (pyrosetta.rosetta.core.scoring.epr_deer.DEERDataCache method) (pyrosetta.rosetta.protocols.features.BatchFeatures method) (pyrosetta.rosetta.protocols.features.ProtocolFeatures method) indices1() (in module pyrosetta.rosetta.utility) individual_hbonds() (pyrosetta.rosetta.protocols.simple_filters.TaskAwareScoreTypeFilter method) (pyrosetta.rosetta.protocols.task_operations.SelectByDeltaScoreOperation method) individual_helix_calculator() (pyrosetta.rosetta.protocols.helical_bundle.PerturbBundle method) individual_helix_calculator_cop() (pyrosetta.rosetta.protocols.helical_bundle.PerturbBundle method) individual_scale_stage1_ (pyrosetta.rosetta.protocols.scoring.methods.pcs2.PcsGridSearchParameter property) individual_scale_stage2_ (pyrosetta.rosetta.protocols.scoring.methods.pcs2.PcsGridSearchParameter property) individual_scale_stage3_ (pyrosetta.rosetta.protocols.scoring.methods.pcs2.PcsGridSearchParameter property) individual_scale_stage4_ (pyrosetta.rosetta.protocols.scoring.methods.pcs2.PcsGridSearchParameter property) individual_weights_ (pyrosetta.rosetta.protocols.scoring.methods.pcs2.PcsGridSearchParameter property) induce_polarizable_dipoles() (pyrosetta.rosetta.core.scoring.MultipoleElecPotential method) induced_dipole() (pyrosetta.rosetta.core.scoring.MultipoleElecResidueInfo method) induced_rf_dipole() (pyrosetta.rosetta.core.scoring.MultipoleElecResidueInfo method) infile() (pyrosetta.rosetta.protocols.recces.options.RECCES_Options method) Info (pyrosetta.rosetta.basic.MemTracer property) (pyrosetta.rosetta.basic.MemTracerImpl property) (pyrosetta.rosetta.basic.Tracer property) (pyrosetta.rosetta.basic.TracerImpl property) info (pyrosetta.rosetta.numeric.nls.lm_status_struct property) info() (pyrosetta.rosetta.core.scoring.DockingScoreFunction method) (pyrosetta.rosetta.core.scoring.MinScoreScoreFunction method) (pyrosetta.rosetta.core.scoring.ScoreFunction method) (pyrosetta.rosetta.core.scoring.symmetry.SymmetricScoreFunction method) (pyrosetta.rosetta.protocols.aa_composition.AddCompositionConstraintMover method) (pyrosetta.rosetta.protocols.aa_composition.AddHelixSequenceConstraintsMover method) (pyrosetta.rosetta.protocols.aa_composition.AddMHCEpitopeConstraintMover method) (pyrosetta.rosetta.protocols.aa_composition.AddNetChargeConstraintMover method) (pyrosetta.rosetta.protocols.aa_composition.ClearCompositionConstraintsMover method) (pyrosetta.rosetta.protocols.abinitio.AbrelaxMover method) (pyrosetta.rosetta.protocols.abinitio.abscript.AbscriptLoopCloserCM method) (pyrosetta.rosetta.protocols.abinitio.abscript.AbscriptMover method) (pyrosetta.rosetta.protocols.abinitio.abscript.AbscriptStageMover method) (pyrosetta.rosetta.protocols.abinitio.abscript.ConstraintPreparer method) (pyrosetta.rosetta.protocols.abinitio.abscript.FragmentCM method) (pyrosetta.rosetta.protocols.abinitio.abscript.FragmentJumpCM method) (pyrosetta.rosetta.protocols.abinitio.abscript.RigidChunkCM method) (pyrosetta.rosetta.protocols.abinitio.abscript.StagePreparer method) (pyrosetta.rosetta.protocols.abinitio.abscript.StructPerturberCM method) (pyrosetta.rosetta.protocols.abinitio.ClassicAbinitio method) (pyrosetta.rosetta.protocols.abinitio.ConstraintFragmentSampler method) (pyrosetta.rosetta.protocols.abinitio.DomainAssembly method) (pyrosetta.rosetta.protocols.abinitio.DoubleLayerKinematicAbinitio method) (pyrosetta.rosetta.protocols.abinitio.FoldConstraints method) (pyrosetta.rosetta.protocols.abinitio.FragmentSampler method) (pyrosetta.rosetta.protocols.abinitio.JumpingFoldConstraintsWrapper method) (pyrosetta.rosetta.protocols.abinitio.KinematicAbinitio method) (pyrosetta.rosetta.protocols.abinitio.KinematicTaskControl method) (pyrosetta.rosetta.protocols.abinitio.LoopJumpFoldCst method) (pyrosetta.rosetta.protocols.abinitio.MembraneAbinitio method) (pyrosetta.rosetta.protocols.abinitio.Protocol method) (pyrosetta.rosetta.protocols.abinitio.ResolutionSwitcher method) (pyrosetta.rosetta.protocols.analysis.GlycanInfoMover method) (pyrosetta.rosetta.protocols.analysis.InterfaceAnalyzerMover method) (pyrosetta.rosetta.protocols.analysis.LoopAnalyzerMover method) (pyrosetta.rosetta.protocols.analysis.PackStatMover method) (pyrosetta.rosetta.protocols.analysis.simple_metrics.RunSimpleMetricsMover method) (pyrosetta.rosetta.protocols.anchored_design.AnchoredDesignMover method) (pyrosetta.rosetta.protocols.anchored_design.AnchoredPerturbMover method) (pyrosetta.rosetta.protocols.anchored_design.AnchoredRefineMover method) (pyrosetta.rosetta.protocols.antibody.AntibodyCDRGrafter method) (pyrosetta.rosetta.protocols.antibody.AntibodyModelerProtocol method) (pyrosetta.rosetta.protocols.antibody.AntibodyNumberingConverterMover method) (pyrosetta.rosetta.protocols.antibody.CDRsMinPackMin method) (pyrosetta.rosetta.protocols.antibody.CloseOneCDRLoop method) (pyrosetta.rosetta.protocols.antibody.constraints.CDRDihedralConstraintMover method) (pyrosetta.rosetta.protocols.antibody.constraints.ParatopeEpitopeSiteConstraintMover method) (pyrosetta.rosetta.protocols.antibody.constraints.ParatopeSiteConstraintMover method) (pyrosetta.rosetta.protocols.antibody.design.AntibodyDesignMover method) (pyrosetta.rosetta.protocols.antibody.design.MutateFrameworkForCluster method) (pyrosetta.rosetta.protocols.antibody.GraftCDRLoopsProtocol method) (pyrosetta.rosetta.protocols.antibody.GraftedStemOptimizer method) (pyrosetta.rosetta.protocols.antibody.GraftOneCDRLoop method) (pyrosetta.rosetta.protocols.antibody.H3CterInsert method) (pyrosetta.rosetta.protocols.antibody.H3PerturbCCD method) (pyrosetta.rosetta.protocols.antibody.H3RefineCCD method) (pyrosetta.rosetta.protocols.antibody.LHRepulsiveRamp method) (pyrosetta.rosetta.protocols.antibody.LHRepulsiveRampLegacy method) (pyrosetta.rosetta.protocols.antibody.LHSnugFitLegacy method) (pyrosetta.rosetta.protocols.antibody.RefineBetaBarrel method) (pyrosetta.rosetta.protocols.antibody.snugdock.SnugDock method) (pyrosetta.rosetta.protocols.antibody.snugdock.SnugDockProtocol method) (pyrosetta.rosetta.protocols.antibody_legacy.AntibodyModeler method) (pyrosetta.rosetta.protocols.antibody_legacy.CDRH3Modeler method) (pyrosetta.rosetta.protocols.antibody_legacy.CloseOneMover method) (pyrosetta.rosetta.protocols.antibody_legacy.GraftMover method) (pyrosetta.rosetta.protocols.antibody_legacy.GraftOneMover method) (pyrosetta.rosetta.protocols.antibody_legacy.LoopRlxMover method) (pyrosetta.rosetta.protocols.backbone_moves.local_backbone_mover.LocalBackboneMover method) (pyrosetta.rosetta.protocols.backbone_moves.RandomizeBBByRamaPrePro method) (pyrosetta.rosetta.protocols.backrub.BackrubMover method) (pyrosetta.rosetta.protocols.backrub.BackrubProtocol method) (pyrosetta.rosetta.protocols.backrub.BackrubSidechainMover method) (pyrosetta.rosetta.protocols.calc_taskop_movers.ConsensusDesignMover method) (pyrosetta.rosetta.protocols.calc_taskop_movers.CreateSequenceMotifMover method) (pyrosetta.rosetta.protocols.calc_taskop_movers.DesignRepackMover method) (pyrosetta.rosetta.protocols.calc_taskop_movers.ForceDisulfidesMover method) (pyrosetta.rosetta.protocols.canonical_sampling.AsyncMPITemperingBase method) (pyrosetta.rosetta.protocols.canonical_sampling.BiasEnergy method) (pyrosetta.rosetta.protocols.canonical_sampling.CanonicalSamplingMover method) (pyrosetta.rosetta.protocols.canonical_sampling.DbTrajectoryRecorder method) (pyrosetta.rosetta.protocols.canonical_sampling.FixedTemperatureController method) (pyrosetta.rosetta.protocols.canonical_sampling.HamiltonianExchange method) (pyrosetta.rosetta.protocols.canonical_sampling.MetricRecorder method) (pyrosetta.rosetta.protocols.canonical_sampling.MetropolisHastingsMover method) (pyrosetta.rosetta.protocols.canonical_sampling.ParallelTempering method) (pyrosetta.rosetta.protocols.canonical_sampling.PDBTrajectoryRecorder method) (pyrosetta.rosetta.protocols.canonical_sampling.ProgressBarObserver method) (pyrosetta.rosetta.protocols.canonical_sampling.SidechainMetropolisHastingsMover method) (pyrosetta.rosetta.protocols.canonical_sampling.SilentTrajectoryRecorder method) (pyrosetta.rosetta.protocols.canonical_sampling.SimulatedTempering method) (pyrosetta.rosetta.protocols.canonical_sampling.TemperatureController method) (pyrosetta.rosetta.protocols.canonical_sampling.TemperingBase method) (pyrosetta.rosetta.protocols.canonical_sampling.ThermodynamicMover method) (pyrosetta.rosetta.protocols.canonical_sampling.ThermodynamicObserver method) (pyrosetta.rosetta.protocols.canonical_sampling.TrajectoryRecorder method) (pyrosetta.rosetta.protocols.canonical_sampling.TrialCounterObserver method) (pyrosetta.rosetta.protocols.canonical_sampling.WTEBiasEnergy method) (pyrosetta.rosetta.protocols.carbohydrates.CreateGlycanSequonMover method) (pyrosetta.rosetta.protocols.carbohydrates.GlycanSampler method) (pyrosetta.rosetta.protocols.carbohydrates.GlycanTreeMinMover method) (pyrosetta.rosetta.protocols.carbohydrates.GlycanTreeModeler method) (pyrosetta.rosetta.protocols.carbohydrates.IdealizeAnomericHydrogens method) (pyrosetta.rosetta.protocols.carbohydrates.LinkageConformerMover method) (pyrosetta.rosetta.protocols.carbohydrates.RingPlaneFlipMover method) (pyrosetta.rosetta.protocols.carbohydrates.SimpleGlycosylateMover method) (pyrosetta.rosetta.protocols.carbohydrates.TautomerizeAnomerMover method) (pyrosetta.rosetta.protocols.chemically_conjugated_docking.UBQ_GTPaseMover method) (pyrosetta.rosetta.protocols.cluster.AssignToClustersMover method) (pyrosetta.rosetta.protocols.cluster.ClusterBase method) (pyrosetta.rosetta.protocols.cluster.ClusterPhilStyle method) (pyrosetta.rosetta.protocols.cluster.ClusterPhilStyle_Loop method) (pyrosetta.rosetta.protocols.cluster.ClusterPhilStyle_PoseReporter method) (pyrosetta.rosetta.protocols.cluster.EnsembleConstraints method) (pyrosetta.rosetta.protocols.cluster.EnsembleConstraints_Simple method) (pyrosetta.rosetta.protocols.cluster.GatherPosesMover method) (pyrosetta.rosetta.protocols.comparative_modeling.ExtraThreadingMover method) (pyrosetta.rosetta.protocols.comparative_modeling.LoopRelaxThreadingMover method) (pyrosetta.rosetta.protocols.comparative_modeling.MultiThreadingMover method) (pyrosetta.rosetta.protocols.comparative_modeling.PartialThreadingMover method) (pyrosetta.rosetta.protocols.comparative_modeling.RecoverSideChainsMover method) (pyrosetta.rosetta.protocols.comparative_modeling.StealLigandMover method) (pyrosetta.rosetta.protocols.comparative_modeling.StealSideChainsMover method) (pyrosetta.rosetta.protocols.comparative_modeling.ThreadingMover method) (pyrosetta.rosetta.protocols.constraint_generator.AddConstraints method) (pyrosetta.rosetta.protocols.constraint_generator.RemoveConstraints method) (pyrosetta.rosetta.protocols.constraint_movers.AddConstraintsToCurrentConformationMover method) (pyrosetta.rosetta.protocols.constraint_movers.ClearConstraintsMover method) (pyrosetta.rosetta.protocols.constraint_movers.ConstraintSetMover method) (pyrosetta.rosetta.protocols.constraint_movers.CstInfoMover method) (pyrosetta.rosetta.protocols.constraint_movers.ResidueTypeConstraintMover method) (pyrosetta.rosetta.protocols.contact_map.ContactMap method) (pyrosetta.rosetta.protocols.coupled_moves.CoupledMovesProtocol method) (pyrosetta.rosetta.protocols.cryst.CrystRMS method) (pyrosetta.rosetta.protocols.cryst.DockLatticeMover method) (pyrosetta.rosetta.protocols.cryst.FitBfactorsMover method) (pyrosetta.rosetta.protocols.cryst.LoadDensityMapMover method) (pyrosetta.rosetta.protocols.cryst.MakeLatticeMover method) (pyrosetta.rosetta.protocols.cryst.MakeLayerMover method) (pyrosetta.rosetta.protocols.cryst.RecomputeDensityMapMover method) (pyrosetta.rosetta.protocols.cryst.ReportGradientsMover method) (pyrosetta.rosetta.protocols.cryst.SetCrystWeightMover method) (pyrosetta.rosetta.protocols.cryst.SetRefinementOptionsMover method) (pyrosetta.rosetta.protocols.cryst.TagPoseWithRefinementStatsMover method) (pyrosetta.rosetta.protocols.cryst.UpdateCrystInfo method) (pyrosetta.rosetta.protocols.cryst.UpdateSolventMover method) (pyrosetta.rosetta.protocols.cutoutdomain.CutOutDomain method) (pyrosetta.rosetta.protocols.cyclic_peptide.CrankshaftFlipMover method) (pyrosetta.rosetta.protocols.cyclic_peptide.CreateAngleConstraint method) (pyrosetta.rosetta.protocols.cyclic_peptide.CreateDistanceConstraint method) (pyrosetta.rosetta.protocols.cyclic_peptide.CreateTorsionConstraint method) (pyrosetta.rosetta.protocols.cyclic_peptide.CrosslinkerMover method) (pyrosetta.rosetta.protocols.cyclic_peptide.CycpepRigidBodyPermutationMover method) (pyrosetta.rosetta.protocols.cyclic_peptide.FlipChiralityMover method) (pyrosetta.rosetta.protocols.cyclic_peptide.PeptideCyclizeMover method) (pyrosetta.rosetta.protocols.cyclic_peptide.PeptideStubMover method) (pyrosetta.rosetta.protocols.cyclic_peptide.SymmetricCycpepAlign method) (pyrosetta.rosetta.protocols.cyclic_peptide.TryDisulfPermutations method) (pyrosetta.rosetta.protocols.ddg.ddGMover method) (pyrosetta.rosetta.protocols.denovo_design.components.VLBProtected method) (pyrosetta.rosetta.protocols.denovo_design.DisulfidizeMover method) (pyrosetta.rosetta.protocols.denovo_design.movers.AddSegmentDataMover method) (pyrosetta.rosetta.protocols.denovo_design.movers.AlignResiduesMover method) (pyrosetta.rosetta.protocols.denovo_design.movers.BridgeChainsMover method) (pyrosetta.rosetta.protocols.denovo_design.movers.BuildDeNovoBackboneMover method) (pyrosetta.rosetta.protocols.denovo_design.movers.DeclareStructureDataCovalentBondMover method) (pyrosetta.rosetta.protocols.denovo_design.movers.ExtendChainMover method) (pyrosetta.rosetta.protocols.denovo_design.movers.FastDesign method) (pyrosetta.rosetta.protocols.denovo_design.movers.FoldArchitectMover method) (pyrosetta.rosetta.protocols.denovo_design.movers.FoldTreeFromFoldGraphMover method) (pyrosetta.rosetta.protocols.denovo_design.movers.MakeAsymmetricStructureDataMover method) (pyrosetta.rosetta.protocols.denovo_design.movers.RotateSegmentMover method) (pyrosetta.rosetta.protocols.denovo_design.movers.SealFoldTreeMover method) (pyrosetta.rosetta.protocols.denovo_design.movers.SetPoseSecstructFromStructureDataMover method) (pyrosetta.rosetta.protocols.denovo_design.movers.SetResidueAliasMover method) (pyrosetta.rosetta.protocols.design_opt.GreedyOptMutationMover method) (pyrosetta.rosetta.protocols.design_opt.Supercharge method) (pyrosetta.rosetta.protocols.dna.DesignProteinBackboneAroundDNA method) (pyrosetta.rosetta.protocols.dna.DnaInterfaceMinMover method) (pyrosetta.rosetta.protocols.dna.DnaInterfaceMultiStateDesign method) (pyrosetta.rosetta.protocols.dna.DnaInterfacePacker method) (pyrosetta.rosetta.protocols.dna.SeparateDnaFromNonDna method) (pyrosetta.rosetta.protocols.docking.ConformerSwitchMover method) (pyrosetta.rosetta.protocols.docking.DockingEnsemblePrepackProtocol method) (pyrosetta.rosetta.protocols.docking.DockingHighRes method) (pyrosetta.rosetta.protocols.docking.DockingHighResLegacy method) (pyrosetta.rosetta.protocols.docking.DockingInitialPerturbation method) (pyrosetta.rosetta.protocols.docking.DockingLowRes method) (pyrosetta.rosetta.protocols.docking.DockingLowResEnsemble method) (pyrosetta.rosetta.protocols.docking.DockingPrepackProtocol method) (pyrosetta.rosetta.protocols.docking.DockingProtocol method) (pyrosetta.rosetta.protocols.docking.DockingSlideIntoContact method) (pyrosetta.rosetta.protocols.docking.DockMCMCycle method) (pyrosetta.rosetta.protocols.docking.DockMCMProtocol method) (pyrosetta.rosetta.protocols.docking.DockMinMover method) (pyrosetta.rosetta.protocols.docking.DockSetupMover method) (pyrosetta.rosetta.protocols.docking.EllipsoidalRandomizationMover method) (pyrosetta.rosetta.protocols.docking.EnsureExclusivelySharedJumpMover method) (pyrosetta.rosetta.protocols.docking.FaDockingSlideIntoContact method) (pyrosetta.rosetta.protocols.docking.InterfaceSidechainMinMover method) (pyrosetta.rosetta.protocols.docking.membrane.MPDockingMover method) (pyrosetta.rosetta.protocols.docking.membrane.MPDockingSetupMover method) (pyrosetta.rosetta.protocols.docking.membrane.MPFindInterfaceMover method) (pyrosetta.rosetta.protocols.docking.membrane.QuickRelaxPartnersSeparately method) (pyrosetta.rosetta.protocols.docking.SidechainMinMover method) (pyrosetta.rosetta.protocols.docking.SlideIntoContact method) (pyrosetta.rosetta.protocols.docking.stateless.SaneDockingProtocol method) (pyrosetta.rosetta.protocols.docking.TemperedDocking method) (pyrosetta.rosetta.protocols.domain_assembly.AddAssemblyConstraints method) (pyrosetta.rosetta.protocols.domain_assembly.AssembleLinkerMover method) (pyrosetta.rosetta.protocols.domain_assembly.CombineChainsMover method) (pyrosetta.rosetta.protocols.domain_assembly.PostDockAssemblyScorer method) (pyrosetta.rosetta.protocols.drug_design.ApplyChemistryMover method) (pyrosetta.rosetta.protocols.drug_design.bcl.BCLFragmentBaseMover method) (pyrosetta.rosetta.protocols.drug_design.bcl.BCLFragmentMutateMover method) (pyrosetta.rosetta.protocols.drug_design.RDKitMetricsMover method) (pyrosetta.rosetta.protocols.electron_density.BfactorFittingMover method) (pyrosetta.rosetta.protocols.electron_density.DensityZscores method) (pyrosetta.rosetta.protocols.electron_density.DockFragmentsIntoDensityMover method) (pyrosetta.rosetta.protocols.electron_density.DockPDBIntoDensityMover method) (pyrosetta.rosetta.protocols.electron_density.ReportFSC method) (pyrosetta.rosetta.protocols.electron_density.ScaleMapIntensities method) (pyrosetta.rosetta.protocols.electron_density.SetupForDensityScoringMover method) (pyrosetta.rosetta.protocols.electron_density.VoxelSpacingRefinementMover method) (pyrosetta.rosetta.protocols.environment.ClientMover method) (pyrosetta.rosetta.protocols.environment.CoMTrackerCM method) (pyrosetta.rosetta.protocols.environment.EnvMover method) (pyrosetta.rosetta.protocols.environment.ScriptCM method) (pyrosetta.rosetta.protocols.enzdes.AddOrRemoveMatchCsts method) (pyrosetta.rosetta.protocols.enzdes.ApplyRandomStoredRBConf method) (pyrosetta.rosetta.protocols.enzdes.BackboneSampler method) (pyrosetta.rosetta.protocols.enzdes.DiversifyStoredRBConfs method) (pyrosetta.rosetta.protocols.enzdes.EnzdesBaseProtocol method) (pyrosetta.rosetta.protocols.enzdes.EnzdesFixBBProtocol method) (pyrosetta.rosetta.protocols.enzdes.EnzdesFlexBBProtocol method) (pyrosetta.rosetta.protocols.enzdes.EnzRepackMinimize method) (pyrosetta.rosetta.protocols.enzdes.GenerateStoredRBConfs method) (pyrosetta.rosetta.protocols.enzdes.MinimizeStoredRBConfs method) (pyrosetta.rosetta.protocols.enzdes.ModifyStoredRBConfs method) (pyrosetta.rosetta.protocols.enzdes.PackRotamersMoverPartGreedy method) (pyrosetta.rosetta.protocols.enzdes.PredesignPerturbMover method) (pyrosetta.rosetta.protocols.enzdes.RepackLigandSiteWithoutLigandMover method) (pyrosetta.rosetta.protocols.enzdes.SecondaryMatchProtocol method) (pyrosetta.rosetta.protocols.enzdes.UpdateEnzdesHeaderMover method) (pyrosetta.rosetta.protocols.enzymatic_movers.DNAMethyltransferaseMover method) (pyrosetta.rosetta.protocols.enzymatic_movers.EnzymaticMover method) (pyrosetta.rosetta.protocols.enzymatic_movers.GlycosyltransferaseMover method) (pyrosetta.rosetta.protocols.enzymatic_movers.KinaseMover method) (pyrosetta.rosetta.protocols.enzymatic_movers.NTerminalAcetyltransferaseMover method) (pyrosetta.rosetta.protocols.evolution.EvolutionaryDynamicsMover method) (pyrosetta.rosetta.protocols.evolution.NucleotideMutation method) (pyrosetta.rosetta.protocols.farnesyl.InstallFarnesylMover method) (pyrosetta.rosetta.protocols.farnesyl.SampleFarnesylMover method) (pyrosetta.rosetta.protocols.features.InterfaceDdGMover method) (pyrosetta.rosetta.protocols.features.ReportToDB method) (pyrosetta.rosetta.protocols.features.TrajectoryReportToDB method) (pyrosetta.rosetta.protocols.fibril.SetupForFibrilMover method) (pyrosetta.rosetta.protocols.fldsgn.BluePrintBDR method) (pyrosetta.rosetta.protocols.fldsgn.CircularPermutation method) (pyrosetta.rosetta.protocols.fldsgn.MatchResiduesMover method) (pyrosetta.rosetta.protocols.fldsgn.potentials.SetAACompositionPotential method) (pyrosetta.rosetta.protocols.fldsgn.potentials.SetSecStructEnergies method) (pyrosetta.rosetta.protocols.fldsgn.SheetRemodelConstraintGenerator method) (pyrosetta.rosetta.protocols.flexpack.FlexPacker method) (pyrosetta.rosetta.protocols.flexpack.OtherContextScoreFunction method) (pyrosetta.rosetta.protocols.flexpep_docking.FlexPepDockingAbInitio method) (pyrosetta.rosetta.protocols.flexpep_docking.FlexPepDockingLowRes method) (pyrosetta.rosetta.protocols.flexpep_docking.FlexPepDockingProtocol method) (pyrosetta.rosetta.protocols.floppy_tail.FloppyTailMover method) (pyrosetta.rosetta.protocols.flxbb.FlxbbDesign method) (pyrosetta.rosetta.protocols.flxbb.FlxbbDesignPack method) (pyrosetta.rosetta.protocols.flxbb.InterlockAroma method) (pyrosetta.rosetta.protocols.fold_from_loops.movers.AlignByResidueSelectorMover method) (pyrosetta.rosetta.protocols.fold_from_loops.movers.DisplayPoseLabelsMover method) (pyrosetta.rosetta.protocols.fold_from_loops.movers.LabelPoseFromResidueSelectorMover method) (pyrosetta.rosetta.protocols.fold_from_loops.movers.MoveMapFactoryToNamedMoveMapMover method) (pyrosetta.rosetta.protocols.fold_from_loops.movers.NubInitioLoopClosureMover method) (pyrosetta.rosetta.protocols.fold_from_loops.movers.ReleaseConstraintFromResidueMover method) (pyrosetta.rosetta.protocols.fold_from_loops.movers.ResidueLabelsToPymolSelectionMover method) (pyrosetta.rosetta.protocols.fold_from_loops.movers.SavePDBInfoMover method) (pyrosetta.rosetta.protocols.fold_from_loops.movers.SplitAndMixPoseMover method) (pyrosetta.rosetta.protocols.fold_from_loops.NubInitioMover method) (pyrosetta.rosetta.protocols.forge.components.BDR method) (pyrosetta.rosetta.protocols.forge.components.VarLengthBuild method) (pyrosetta.rosetta.protocols.forge.constraints.InverseRotamersRCG method) (pyrosetta.rosetta.protocols.forge.constraints.InvrotTreeRCG method) (pyrosetta.rosetta.protocols.forge.constraints.NtoCConstraintGenerator method) (pyrosetta.rosetta.protocols.forge.constraints.RemoveRemodelCsts method) (pyrosetta.rosetta.protocols.forge.remodel.GenericRemodelConstraintGenerator method) (pyrosetta.rosetta.protocols.forge.remodel.RemodelAccumulator method) (pyrosetta.rosetta.protocols.forge.remodel.RemodelConstraintGenerator method) (pyrosetta.rosetta.protocols.forge.remodel.RemodelDesignMover method) (pyrosetta.rosetta.protocols.forge.remodel.RemodelGlobalFrame method) (pyrosetta.rosetta.protocols.forge.remodel.RemodelLigandHandler method) (pyrosetta.rosetta.protocols.forge.remodel.RemodelLoopMover method) (pyrosetta.rosetta.protocols.forge.remodel.RemodelMover method) (pyrosetta.rosetta.protocols.forge.remodel.ResidueVicinityRCG method) (pyrosetta.rosetta.protocols.frags.TorsionFragmentMover method) (pyrosetta.rosetta.protocols.generalized_kinematic_closure.GeneralizedKIC method) (pyrosetta.rosetta.protocols.glycan_docking.GlycanDockProtocol method) (pyrosetta.rosetta.protocols.glycopeptide_docking.GlycopeptideDockingHighResRefinement method) (pyrosetta.rosetta.protocols.glycopeptide_docking.GlycopeptideDockingLowResRefinement method) (pyrosetta.rosetta.protocols.glycopeptide_docking.GlycopeptideDockingProtocol method) (pyrosetta.rosetta.protocols.grafting.AnchoredGraftMover method) (pyrosetta.rosetta.protocols.grafting.CCDEndsGraftMover method) (pyrosetta.rosetta.protocols.grafting.GraftMoverBase method) (pyrosetta.rosetta.protocols.grafting.simple_movers.DeleteRegionMover method) (pyrosetta.rosetta.protocols.grafting.simple_movers.InsertPoseIntoPoseMover method) (pyrosetta.rosetta.protocols.grafting.simple_movers.KeepRegionMover method) (pyrosetta.rosetta.protocols.grafting.simple_movers.ReplaceRegionMover method) (pyrosetta.rosetta.protocols.hbnet.HBNet method) (pyrosetta.rosetta.protocols.hbnet.HBNetStapleInterface method) (pyrosetta.rosetta.protocols.helical_bundle.BackboneGridSampler method) (pyrosetta.rosetta.protocols.helical_bundle.BundleGridSampler method) (pyrosetta.rosetta.protocols.helical_bundle.FitSimpleHelix method) (pyrosetta.rosetta.protocols.helical_bundle.MakeBundle method) (pyrosetta.rosetta.protocols.helical_bundle.MakeBundleHelix method) (pyrosetta.rosetta.protocols.helical_bundle.PerturbBundle method) (pyrosetta.rosetta.protocols.helical_bundle.PerturbBundleHelix method) (pyrosetta.rosetta.protocols.hotspot_hashing.movers.PlaceProbeMover method) (pyrosetta.rosetta.protocols.hotspot_hashing.movers.PlaceSurfaceProbe method) (pyrosetta.rosetta.protocols.hybridization.BackboneTorsionPerturbation method) (pyrosetta.rosetta.protocols.hybridization.BackboneTorsionSampler method) (pyrosetta.rosetta.protocols.hybridization.CartesianHybridize method) (pyrosetta.rosetta.protocols.hybridization.CartesianSampler method) (pyrosetta.rosetta.protocols.hybridization.ChunkTrialMover method) (pyrosetta.rosetta.protocols.hybridization.DomainAssembly method) (pyrosetta.rosetta.protocols.hybridization.FoldTreeHybridize method) (pyrosetta.rosetta.protocols.hybridization.HybridizeProtocol method) (pyrosetta.rosetta.protocols.hybridization.InsertChunkMover method) (pyrosetta.rosetta.protocols.hybridization.MRMover method) (pyrosetta.rosetta.protocols.hybridization.WeightedFragmentSmoothTrialMover method) (pyrosetta.rosetta.protocols.hybridization.WeightedFragmentTrialMover method) (pyrosetta.rosetta.protocols.hydrate.Hydrate method) (pyrosetta.rosetta.protocols.idealize.IdealizeMover method) (pyrosetta.rosetta.protocols.indel.IndelOptimizationMover method) (pyrosetta.rosetta.protocols.indexed_structure_store.movers.DirectSegmentLookupMover method) (pyrosetta.rosetta.protocols.indexed_structure_store.movers.SegmentSequenceProfileMover method) (pyrosetta.rosetta.protocols.kinematic_closure.BalancedKicMover method) (pyrosetta.rosetta.protocols.kinematic_closure.KicMover method) (pyrosetta.rosetta.protocols.legacy_sewing.LegacyAddStartnodeFragments method) (pyrosetta.rosetta.protocols.legacy_sewing.LegacyAppendAssemblyMover method) (pyrosetta.rosetta.protocols.legacy_sewing.LegacyAssemblyConstraintsMover method) (pyrosetta.rosetta.protocols.legacy_sewing.LegacyAssemblyMover method) (pyrosetta.rosetta.protocols.legacy_sewing.LegacyEnumerateAssemblyMover method) (pyrosetta.rosetta.protocols.legacy_sewing.LegacyGivenPathAssemblyMover method) (pyrosetta.rosetta.protocols.legacy_sewing.LegacyGreedyAssemblyMover method) (pyrosetta.rosetta.protocols.legacy_sewing.LegacyMonteCarloAssemblyMover method) (pyrosetta.rosetta.protocols.legacy_sewing.LegacyRepeatAssemblyMover method) (pyrosetta.rosetta.protocols.ligand_docking.AddHydrogen method) (pyrosetta.rosetta.protocols.ligand_docking.AddHydrogens method) (pyrosetta.rosetta.protocols.ligand_docking.CompoundTranslate method) (pyrosetta.rosetta.protocols.ligand_docking.ComputeLigandRDF method) (pyrosetta.rosetta.protocols.ligand_docking.FinalMinimizer method) (pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.GALigandDock method) (pyrosetta.rosetta.protocols.ligand_docking.GrowLigand method) (pyrosetta.rosetta.protocols.ligand_docking.HighResDocker method) (pyrosetta.rosetta.protocols.ligand_docking.HighResEnsemble method) (pyrosetta.rosetta.protocols.ligand_docking.InterfaceScoreCalculator method) (pyrosetta.rosetta.protocols.ligand_docking.LigandBaseProtocol method) (pyrosetta.rosetta.protocols.ligand_docking.LigandDesign method) (pyrosetta.rosetta.protocols.ligand_docking.LigandDockProtocol method) (pyrosetta.rosetta.protocols.ligand_docking.MinimizeBackbone method) (pyrosetta.rosetta.protocols.ligand_docking.MinimizeLigand method) (pyrosetta.rosetta.protocols.ligand_docking.ProtLigEnsemble method) (pyrosetta.rosetta.protocols.ligand_docking.RandomConformerMover method) (pyrosetta.rosetta.protocols.ligand_docking.RandomConformers method) (pyrosetta.rosetta.protocols.ligand_docking.RigidSearchMover method) (pyrosetta.rosetta.protocols.ligand_docking.Rotate method) (pyrosetta.rosetta.protocols.ligand_docking.Rotates method) (pyrosetta.rosetta.protocols.ligand_docking.SlideTogether method) (pyrosetta.rosetta.protocols.ligand_docking.StartFrom method) (pyrosetta.rosetta.protocols.ligand_docking.TetherLigand method) (pyrosetta.rosetta.protocols.ligand_docking.Transform method) (pyrosetta.rosetta.protocols.ligand_docking.TransformEnsemble method) (pyrosetta.rosetta.protocols.ligand_docking.Translate method) (pyrosetta.rosetta.protocols.ligand_docking.UnconstrainedTorsionsMover method) (pyrosetta.rosetta.protocols.ligand_docking.WriteLigandMolFile method) (pyrosetta.rosetta.protocols.loop_build.LoopBuildMover method) (pyrosetta.rosetta.protocols.loop_build.LoopmodelWrapper method) (pyrosetta.rosetta.protocols.loop_build.LoopMover_SlidingWindow method) (pyrosetta.rosetta.protocols.loop_grower.FragmentExtension method) (pyrosetta.rosetta.protocols.loop_grower.LoopGrower method) (pyrosetta.rosetta.protocols.loop_grower.SheetSampler method) (pyrosetta.rosetta.protocols.loop_modeler.LoopModeler method) (pyrosetta.rosetta.protocols.loop_modeling.LoopBuilder method) (pyrosetta.rosetta.protocols.loop_modeling.LoopMover method) (pyrosetta.rosetta.protocols.loop_modeling.LoopProtocol method) (pyrosetta.rosetta.protocols.loop_modeling.refiners.MinimizationRefiner method) (pyrosetta.rosetta.protocols.loop_modeling.refiners.RepackingRefiner method) (pyrosetta.rosetta.protocols.loop_modeling.refiners.RotamerTrialsRefiner method) (pyrosetta.rosetta.protocols.loop_modeling.samplers.LegacyKicSampler method) (pyrosetta.rosetta.protocols.loop_modeling.utilities.AcceptanceCheck method) (pyrosetta.rosetta.protocols.loop_modeling.utilities.LoopFilter method) (pyrosetta.rosetta.protocols.loop_modeling.utilities.LoopMoverGroup method) (pyrosetta.rosetta.protocols.loop_modeling.utilities.PrepareForCentroid method) (pyrosetta.rosetta.protocols.loop_modeling.utilities.PrepareForFullatom method) (pyrosetta.rosetta.protocols.loophash.FastGapMover method) (pyrosetta.rosetta.protocols.loophash.LoopHashDiversifier method) (pyrosetta.rosetta.protocols.loophash.LoopHashLibrary method) (pyrosetta.rosetta.protocols.loophash.LoopHashMoverWrapper method) (pyrosetta.rosetta.protocols.loophash.LoopHashRelaxProtocol method) (pyrosetta.rosetta.protocols.loophash.Mover_LoopHashRefine method) (pyrosetta.rosetta.protocols.LoopRebuild method) (pyrosetta.rosetta.protocols.LoopRefine method) (pyrosetta.rosetta.protocols.loops.FoldTreeFromLoops method) (pyrosetta.rosetta.protocols.loops.loop_closure.ccd.CCDLoopClosureMover method) (pyrosetta.rosetta.protocols.loops.loop_closure.ccd.FASelectSlidingWindowLoopClosure method) (pyrosetta.rosetta.protocols.loops.loop_closure.ccd.SlidingWindowLoopClosure method) (pyrosetta.rosetta.protocols.loops.loop_closure.ccd.WidthFirstSlidingWindowLoopClosure method) (pyrosetta.rosetta.protocols.loops.loop_closure.jacobi.JacobiLoopClosureMover method) (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.KinematicMover method) (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.KinematicWrapper method) (pyrosetta.rosetta.protocols.loops.loop_mover.IndependentLoopMover method) (pyrosetta.rosetta.protocols.loops.loop_mover.LoopCM method) (pyrosetta.rosetta.protocols.loops.loop_mover.LoopMover method) (pyrosetta.rosetta.protocols.loops.loop_mover.perturb.LoopMover_Perturb_CCD method) (pyrosetta.rosetta.protocols.loops.loop_mover.perturb.LoopMover_Perturb_KIC method) (pyrosetta.rosetta.protocols.loops.loop_mover.perturb.LoopMover_Perturb_QuickCCD method) (pyrosetta.rosetta.protocols.loops.loop_mover.perturb.LoopMover_Perturb_QuickCCD_Moves method) (pyrosetta.rosetta.protocols.loops.loop_mover.refine.LoopMover_Refine_Backrub method) (pyrosetta.rosetta.protocols.loops.loop_mover.refine.LoopMover_Refine_CCD method) (pyrosetta.rosetta.protocols.loops.loop_mover.refine.LoopMover_Refine_KIC method) (pyrosetta.rosetta.protocols.loops.loop_mover.refine.LoopRefineInnerCycle method) (pyrosetta.rosetta.protocols.loops.loop_mover.refine.LoopRefineInnerCycleContainer method) (pyrosetta.rosetta.protocols.loops.loop_mover.refine.RepackTrial method) (pyrosetta.rosetta.protocols.loops.loop_mover.refine.ShearMinCCDTrial method) (pyrosetta.rosetta.protocols.loops.loop_mover.refine.SmallMinCCDTrial method) (pyrosetta.rosetta.protocols.magnesium.MgHydrater method) (pyrosetta.rosetta.protocols.magnesium.MgMinimizer method) (pyrosetta.rosetta.protocols.magnesium.MgMonteCarlo method) (pyrosetta.rosetta.protocols.magnesium.MgOrbitalFrameFinder method) (pyrosetta.rosetta.protocols.magnesium.MgScanner method) (pyrosetta.rosetta.protocols.magnesium.MgWaterHydrogenPacker method) (pyrosetta.rosetta.protocols.make_rot_lib.MakeRotLibMover method) (pyrosetta.rosetta.protocols.match.MatcherMover method) (pyrosetta.rosetta.protocols.matdes.ExtractSubposeMover method) (pyrosetta.rosetta.protocols.matdes.MatDesGreedyOptMutationMover method) (pyrosetta.rosetta.protocols.matdes.SchemePlaceMotifsMover method) (pyrosetta.rosetta.protocols.matdes.SymDofMover method) (pyrosetta.rosetta.protocols.md.CartesianMD method) (pyrosetta.rosetta.protocols.md.MDBase method) (pyrosetta.rosetta.protocols.mean_field.GenMeanFieldMover method) (pyrosetta.rosetta.protocols.medal.MedalExchangeMover method) (pyrosetta.rosetta.protocols.medal.MedalMover method) (pyrosetta.rosetta.protocols.membrane.AddMembraneMover method) (pyrosetta.rosetta.protocols.membrane.AddMembraneSpanConstraint method) (pyrosetta.rosetta.protocols.membrane.AddMembraneSpanTermZConstraint method) (pyrosetta.rosetta.protocols.membrane.AddMPLigandMover method) (pyrosetta.rosetta.protocols.membrane.AqueousPoreFinder method) (pyrosetta.rosetta.protocols.membrane.benchmark.MakeCanonicalHelix method) (pyrosetta.rosetta.protocols.membrane.benchmark.SampleTiltAngles method) (pyrosetta.rosetta.protocols.membrane.FlipMover method) (pyrosetta.rosetta.protocols.membrane.HelixFromSequence method) (pyrosetta.rosetta.protocols.membrane.MembranePositionFromTopologyMover method) (pyrosetta.rosetta.protocols.membrane.MPLipidAccessibility method) (pyrosetta.rosetta.protocols.membrane.MPMutateRelaxMover method) (pyrosetta.rosetta.protocols.membrane.MPQuickRelaxMover method) (pyrosetta.rosetta.protocols.membrane.OptimizeMembranePositionMover method) (pyrosetta.rosetta.protocols.membrane.OptimizeProteinEmbeddingMover method) (pyrosetta.rosetta.protocols.membrane.RandomPositionRotationMover method) (pyrosetta.rosetta.protocols.membrane.RandomPositionTranslationMover method) (pyrosetta.rosetta.protocols.membrane.RotationMover method) (pyrosetta.rosetta.protocols.membrane.SetMembraneCenterMover method) (pyrosetta.rosetta.protocols.membrane.SetMembraneNormalMover method) (pyrosetta.rosetta.protocols.membrane.SetMembranePositionMover method) (pyrosetta.rosetta.protocols.membrane.SpinAroundPartnerMover method) (pyrosetta.rosetta.protocols.membrane.symmetry.SymmetricAddMembraneMover method) (pyrosetta.rosetta.protocols.membrane.TiltMover method) (pyrosetta.rosetta.protocols.membrane.TransformIntoMembraneMover method) (pyrosetta.rosetta.protocols.membrane.TranslationMover method) (pyrosetta.rosetta.protocols.membrane.TranslationRotationMover method) (pyrosetta.rosetta.protocols.membrane.visualize.VisualizeEmbeddingMover method) (pyrosetta.rosetta.protocols.membrane.visualize.VisualizeMembraneMover method) (pyrosetta.rosetta.protocols.membrane_benchmark.MembraneEnergyLandscapeSampler method) (pyrosetta.rosetta.protocols.membrane_benchmark.PeptideOrientationMover method) (pyrosetta.rosetta.protocols.metal_interface.RemoveMetalConnectionsMover method) (pyrosetta.rosetta.protocols.metal_interface.ZincHeterodimerMover method) (pyrosetta.rosetta.protocols.minimization_packing.BoltzmannRotamerMover method) (pyrosetta.rosetta.protocols.minimization_packing.DisulfideOptimizationMover method) (pyrosetta.rosetta.protocols.minimization_packing.EnergyCutRotamerTrialsMinMover method) (pyrosetta.rosetta.protocols.minimization_packing.EnergyCutRotamerTrialsMover method) (pyrosetta.rosetta.protocols.minimization_packing.GreenPacker method) (pyrosetta.rosetta.protocols.minimization_packing.MinMover method) (pyrosetta.rosetta.protocols.minimization_packing.MinPackMover method) (pyrosetta.rosetta.protocols.minimization_packing.PackRotamersMover method) (pyrosetta.rosetta.protocols.minimization_packing.PackRotamersMoverLazy method) (pyrosetta.rosetta.protocols.minimization_packing.PertMinMover method) (pyrosetta.rosetta.protocols.minimization_packing.RepackSidechainsMover method) (pyrosetta.rosetta.protocols.minimization_packing.RotamerizeMover method) (pyrosetta.rosetta.protocols.minimization_packing.RotamerTrialsMinMover method) (pyrosetta.rosetta.protocols.minimization_packing.RotamerTrialsMover method) (pyrosetta.rosetta.protocols.minimization_packing.SaneMinMover method) (pyrosetta.rosetta.protocols.minimization_packing.SetReturningPackRotamersMover method) (pyrosetta.rosetta.protocols.minimization_packing.symmetry.SymEnergyCutRotamerTrialsMover method) (pyrosetta.rosetta.protocols.minimization_packing.symmetry.SymMinMover method) (pyrosetta.rosetta.protocols.minimization_packing.symmetry.SymPackRotamersMover method) (pyrosetta.rosetta.protocols.minimization_packing.symmetry.SymRotamerTrialsMover method) (pyrosetta.rosetta.protocols.minimization_packing.symmetry.TaskAwareSymMinMover method) (pyrosetta.rosetta.protocols.minimization_packing.TaskAwareMinMover method) (pyrosetta.rosetta.protocols.monte_carlo.GenericMonteCarloMover method) (pyrosetta.rosetta.protocols.monte_carlo.GenericSimulatedAnnealer method) (pyrosetta.rosetta.protocols.monte_carlo.MonteCarloRecover method) (pyrosetta.rosetta.protocols.monte_carlo.MonteCarloReset method) (pyrosetta.rosetta.protocols.monte_carlo.MonteCarloTest method) (pyrosetta.rosetta.protocols.monte_carlo.ResetBaselineMover method) (pyrosetta.rosetta.protocols.motif_grafting.movers.MotifGraftMover method) (pyrosetta.rosetta.protocols.motifs.MotifDnaPacker method) (pyrosetta.rosetta.protocols.moves.ChangeFoldTreeMover method) (pyrosetta.rosetta.protocols.moves.CompositionMover method) (pyrosetta.rosetta.protocols.moves.CycleMover method) (pyrosetta.rosetta.protocols.moves.CyclicMover method) (pyrosetta.rosetta.protocols.moves.DsspMover method) (pyrosetta.rosetta.protocols.moves.FilterMover method) (pyrosetta.rosetta.protocols.moves.FilterReportAsPoseExtraScoresMover method) (pyrosetta.rosetta.protocols.moves.FilterReporterMover method) (pyrosetta.rosetta.protocols.moves.IfMover method) (pyrosetta.rosetta.protocols.moves.IteratedConvergenceMover method) (pyrosetta.rosetta.protocols.moves.JumpOutMover method) (pyrosetta.rosetta.protocols.moves.MCShowMover method) (pyrosetta.rosetta.protocols.moves.MonteCarloUtil method) (pyrosetta.rosetta.protocols.moves.MoveMapMover method) (pyrosetta.rosetta.protocols.moves.Mover method) (pyrosetta.rosetta.protocols.moves.MoverApplyingMover method) (pyrosetta.rosetta.protocols.moves.MoverContainer method) (pyrosetta.rosetta.protocols.moves.MoverForPoseList method) (pyrosetta.rosetta.protocols.moves.NullMover method) (pyrosetta.rosetta.protocols.moves.PDBDumpMover method) (pyrosetta.rosetta.protocols.moves.ProfilerMover method) (pyrosetta.rosetta.protocols.moves.PyMOLMover method) (pyrosetta.rosetta.protocols.moves.RampingMover method) (pyrosetta.rosetta.protocols.moves.RandomMover method) (pyrosetta.rosetta.protocols.moves.RepeatMover method) (pyrosetta.rosetta.protocols.moves.SequenceMover method) (pyrosetta.rosetta.protocols.moves.StructureRestrictor method) (pyrosetta.rosetta.protocols.moves.SwitchMover method) (pyrosetta.rosetta.protocols.moves.TrialMover method) (pyrosetta.rosetta.protocols.moves.VectorPoseMover method) (pyrosetta.rosetta.protocols.moves.WhileMover method) (pyrosetta.rosetta.protocols.mpi_refinement.StructAvrgMover method) (pyrosetta.rosetta.protocols.ncbb.NcbbDockDesignProtocol method) (pyrosetta.rosetta.protocols.ncbb.oop.OopCreatorMover method) (pyrosetta.rosetta.protocols.ncbb.oop.OopDockDesignProtocol method) (pyrosetta.rosetta.protocols.ncbb.ResidueReplacementRebuildMover method) (pyrosetta.rosetta.protocols.ncbb.SecStructFinder method) (pyrosetta.rosetta.protocols.ncbb.SecStructMinimizeMover method) (pyrosetta.rosetta.protocols.network.UIMover method) (pyrosetta.rosetta.protocols.nmr.ParaNMRScoreMover method) (pyrosetta.rosetta.protocols.nmr.pcs.PCSLigandTransformMover method) (pyrosetta.rosetta.protocols.nmr.pre.PREMover method) (pyrosetta.rosetta.protocols.noesy_assign.CrossPeak method) (pyrosetta.rosetta.protocols.noesy_assign.CrossPeak3D method) (pyrosetta.rosetta.protocols.noesy_assign.CrossPeak4D method) (pyrosetta.rosetta.protocols.noesy_assign.DistanceScoreMover method) (pyrosetta.rosetta.protocols.normalmode.NormalModeMinimizer method) (pyrosetta.rosetta.protocols.normalmode.NormalModeRelaxMover method) (pyrosetta.rosetta.protocols.pb_potential.SetupPoissonBoltzmannPotential method) (pyrosetta.rosetta.protocols.pdbinfo_manipulations.AlignPDBInfoToSequences method) (pyrosetta.rosetta.protocols.pose_creation.ExtendedPoseMover method) (pyrosetta.rosetta.protocols.pose_creation.MakeJunctionsMover method) (pyrosetta.rosetta.protocols.pose_creation.MakePolyXMover method) (pyrosetta.rosetta.protocols.pose_creation.MergePDBatOverlapMover method) (pyrosetta.rosetta.protocols.pose_creation.MergePDBMover method) (pyrosetta.rosetta.protocols.pose_creation.PoseFromSequenceMover method) (pyrosetta.rosetta.protocols.pose_creation.SliceToMiniProteinMover method) (pyrosetta.rosetta.protocols.pose_length_moves.AnalyzeLoopModeling method) (pyrosetta.rosetta.protocols.pose_length_moves.ConnectChainsMover method) (pyrosetta.rosetta.protocols.pose_length_moves.FixAllLoopsMover method) (pyrosetta.rosetta.protocols.pose_length_moves.InsertResMover method) (pyrosetta.rosetta.protocols.pose_length_moves.NearNativeLoopCloser method) (pyrosetta.rosetta.protocols.pose_sewing.movers.AddFlankingVirtualResiduesMover method) (pyrosetta.rosetta.protocols.pose_sewing.movers.BlockwiseAnalysisMover method) (pyrosetta.rosetta.protocols.pose_sewing.movers.OmnibusDisulfideAnalysisLabelerMover method) (pyrosetta.rosetta.protocols.pose_sewing.movers.PickRandomSegmentMover method) (pyrosetta.rosetta.protocols.pose_sewing.movers.SewAnythingAddMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.AddChainBreak method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.AddSidechainConstraintsToHotspots method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.BackrubDDMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.BestHotspotCstMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.BuildAlaPose method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.DesignMinimizeHbonds method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.DisulfideMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.DockAndRetrieveSidechains method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.DockWithHotspotMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.FavorNativeResiduePreCycle method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.FavorNonNativeResiduePreCycle method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.HotspotDisjointedFoldTreeMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.HotspotHasherMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.InterfaceRecapitulationMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.LoopFinder method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.LoopLengthChange method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.LoopMoverFromCommandLine method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.LoopOver method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.LoopRemodel method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.MapHotspot method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.PatchdockTransform method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.PeptideStapleDesignMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.PlacementAuctionMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.PlacementMinimizationMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.PlaceOnLoop method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.PlaceSimultaneouslyMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.PlaceStubMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.PrepackMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.ProteinInterfaceMultiStateDesignMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.RandomMutation method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.RepackMinimize method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.SaveAndRetrieveSidechains method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.SecretionOptimizationMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.SetAtomTree method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.SetTemperatureFactor method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.SetupHotspotConstraintsLoopsMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.SetupHotspotConstraintsMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.ShoveResidueMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.SpinMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.SubroutineMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.TaskAwareCsts method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.TopologyBrokerMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.TryRotamers method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.VLB method) (pyrosetta.rosetta.protocols.protein_mpnn.ProteinMPNNMover method) (pyrosetta.rosetta.protocols.qsar.qsarMover method) (pyrosetta.rosetta.protocols.qsar.RenderGridsToKinemage method) (pyrosetta.rosetta.protocols.quantum_annealing.ExternalPackerResultLoader method) (pyrosetta.rosetta.protocols.rbsegment_relax.AutoRBMover method) (pyrosetta.rosetta.protocols.rbsegment_relax.ConfChangeMover method) (pyrosetta.rosetta.protocols.rbsegment_relax.FragInsertAndAlignMover method) (pyrosetta.rosetta.protocols.rbsegment_relax.GaussianRBSegmentMover method) (pyrosetta.rosetta.protocols.rbsegment_relax.HelicalGaussianMover method) (pyrosetta.rosetta.protocols.rbsegment_relax.IdealizeHelicesMover method) (pyrosetta.rosetta.protocols.rbsegment_relax.MakeStarTopologyMover method) (pyrosetta.rosetta.protocols.rbsegment_relax.OptimizeThreadingMover method) (pyrosetta.rosetta.protocols.rbsegment_relax.RBSegmentMover method) (pyrosetta.rosetta.protocols.rbsegment_relax.RBSegmentRelax method) (pyrosetta.rosetta.protocols.rbsegment_relax.SequenceShiftMover method) (pyrosetta.rosetta.protocols.rbsegment_relax.StrandTwistingMover method) (pyrosetta.rosetta.protocols.RBSegmentRelaxImpl method) (pyrosetta.rosetta.protocols.recces.RECCES_Mover method) (pyrosetta.rosetta.protocols.recces.sampler.MC_Any method) (pyrosetta.rosetta.protocols.recces.sampler.MC_Comb method) (pyrosetta.rosetta.protocols.recces.sampler.MC_Loop method) (pyrosetta.rosetta.protocols.recces.sampler.MC_OneTorsion method) (pyrosetta.rosetta.protocols.recces.sampler.MC_Sampler method) (pyrosetta.rosetta.protocols.recces.sampler.rna.MC_RNA_KIC_Sampler method) (pyrosetta.rosetta.protocols.recces.sampler.rna.MC_RNA_MultiSuite method) (pyrosetta.rosetta.protocols.recces.sampler.rna.MC_RNA_OneJump method) (pyrosetta.rosetta.protocols.recces.sampler.rna.MC_RNA_Sugar method) (pyrosetta.rosetta.protocols.recces.sampler.rna.MC_RNA_Suite method) (pyrosetta.rosetta.protocols.recces.scratch.ThermalMinimizer method) (pyrosetta.rosetta.protocols.recces.scratch.ThermalSamplingMover method) (pyrosetta.rosetta.protocols.recon_design.FindConsensusSequence method) (pyrosetta.rosetta.protocols.recon_design.MSDMover method) (pyrosetta.rosetta.protocols.relax.AcceptToBestMover method) (pyrosetta.rosetta.protocols.relax.AtomCoordinateCstMover method) (pyrosetta.rosetta.protocols.relax.CentroidRelax method) (pyrosetta.rosetta.protocols.relax.ClassicRelax method) (pyrosetta.rosetta.protocols.relax.FastRelax method) (pyrosetta.rosetta.protocols.relax.LocalRelax method) (pyrosetta.rosetta.protocols.relax.loop.LoopRelaxMover method) (pyrosetta.rosetta.protocols.relax.membrane.MPFastRelaxMover method) (pyrosetta.rosetta.protocols.relax.membrane.MPRangeRelaxMover method) (pyrosetta.rosetta.protocols.relax.MiniRelax method) (pyrosetta.rosetta.protocols.relax.RangeRelaxMover method) (pyrosetta.rosetta.protocols.relax.RelaxProtocolBase method) (pyrosetta.rosetta.protocols.relax.RepeatProteinRelax method) (pyrosetta.rosetta.protocols.residue_selectors.StoreResidueSubsetMover method) (pyrosetta.rosetta.protocols.rigid.MembraneCenterPerturbationMover method) (pyrosetta.rosetta.protocols.rigid.MembraneNormalPerturbationMover method) (pyrosetta.rosetta.protocols.rigid.MovePoseToMembraneCenterMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyDeterministicSpinMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofPerturbMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofRandomizeMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofRandomTransMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofSeqPerturbMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofSeqRandomizeMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofSeqTransMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofTransMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyMotionMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyPerturbMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyPerturbNoCenterMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyPerturbRandomJumpMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyRandomizeMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodySpinMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyTiltMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyTransMover method) (pyrosetta.rosetta.protocols.rigid.RollMover method) (pyrosetta.rosetta.protocols.rigid.RotateJumpAxisMover method) (pyrosetta.rosetta.protocols.rigid.UniformRigidBodyCM method) (pyrosetta.rosetta.protocols.rigid.UniformRigidBodyMover method) (pyrosetta.rosetta.protocols.rigid.UniformSphereTransMover method) (pyrosetta.rosetta.protocols.rigid.WholeBodyRotationMover method) (pyrosetta.rosetta.protocols.rigid.WholeBodyTranslationMover method) (pyrosetta.rosetta.protocols.rna.denovo.coarse.CoarseRNA_LoopCloser method) (pyrosetta.rosetta.protocols.rna.denovo.coarse.MultipleDomainMover method) (pyrosetta.rosetta.protocols.rna.denovo.movers.RNA_DeNovoMasterMover method) (pyrosetta.rosetta.protocols.rna.denovo.movers.RNA_DeNovoProtocolMover method) (pyrosetta.rosetta.protocols.rna.denovo.movers.RNA_FragmentMover method) (pyrosetta.rosetta.protocols.rna.denovo.movers.RNA_HelixMover method) (pyrosetta.rosetta.protocols.rna.denovo.movers.RNA_Minimizer method) (pyrosetta.rosetta.protocols.rna.denovo.movers.RNA_Relaxer method) (pyrosetta.rosetta.protocols.rna.denovo.movers.RNP_HighResMover method) (pyrosetta.rosetta.protocols.rna.denovo.output.RNA_FragmentMonteCarloOutputter method) (pyrosetta.rosetta.protocols.rna.denovo.RNA_DeNovoProtocol method) (pyrosetta.rosetta.protocols.rna.denovo.RNA_FragmentMonteCarlo method) (pyrosetta.rosetta.protocols.rna.movers.ERRASER2Protocol method) (pyrosetta.rosetta.protocols.rna.movers.ErraserMinimizerMover method) (pyrosetta.rosetta.protocols.rna.movers.RNA_Coarsify method) (pyrosetta.rosetta.protocols.rna.movers.RNA_Decoarsify method) (pyrosetta.rosetta.protocols.rna.movers.RNA_DeNovoOptimizer method) (pyrosetta.rosetta.protocols.rna.movers.RNA_LoopCloser method) (pyrosetta.rosetta.protocols.rna.movers.RNAIdealizeMover method) (pyrosetta.rosetta.protocols.rna.movers.RNAThreadAndMinimizeMover method) (pyrosetta.rosetta.protocols.rna.setup.RNA_CSA_JobDistributor method) (pyrosetta.rosetta.protocols.rna.setup.RNA_JobDistributor method) (pyrosetta.rosetta.protocols.rna.setup.RNA_MonteCarloJobDistributor method) (pyrosetta.rosetta.protocols.rosetta_scripts.AdditionalOutputWrapper method) (pyrosetta.rosetta.protocols.rosetta_scripts.MultipleOutputWrapper method) (pyrosetta.rosetta.protocols.rosetta_scripts.MultiplePoseMover method) (pyrosetta.rosetta.protocols.rosetta_scripts.ParsedProtocol method) (pyrosetta.rosetta.protocols.rosetta_scripts.SavePoseMover method) (pyrosetta.rosetta.protocols.rotamer_recovery.RotamerRecoveryMover method) (pyrosetta.rosetta.protocols.RotamerDump.RotamerDumpMover method) (pyrosetta.rosetta.protocols.seeded_abinitio.CAcstGenerator method) (pyrosetta.rosetta.protocols.seeded_abinitio.CloseFold method) (pyrosetta.rosetta.protocols.seeded_abinitio.CoordinateCst method) (pyrosetta.rosetta.protocols.seeded_abinitio.DefineMovableLoops method) (pyrosetta.rosetta.protocols.seeded_abinitio.GrowPeptides method) (pyrosetta.rosetta.protocols.seeded_abinitio.SeedFoldTree method) (pyrosetta.rosetta.protocols.seeded_abinitio.SeedSetupMover method) (pyrosetta.rosetta.protocols.seeded_abinitio.SegmentHybridizer method) (pyrosetta.rosetta.protocols.seeded_abinitio.SwapSegment method) (pyrosetta.rosetta.protocols.sewing.hashing.AlignmentFileGeneratorMover method) (pyrosetta.rosetta.protocols.sewing.movers.AppendAssemblyMover method) (pyrosetta.rosetta.protocols.sewing.movers.AssemblyMover method) (pyrosetta.rosetta.protocols.sewing.movers.LigandBindingAssemblyMover method) (pyrosetta.rosetta.protocols.simple_ddg.ddG method) (pyrosetta.rosetta.protocols.simple_filters.EvaluatedTrialMover method) (pyrosetta.rosetta.protocols.simple_moves.a3b_hbs.A3BHbsPatcher method) (pyrosetta.rosetta.protocols.simple_moves.AddCavitiesMover method) (pyrosetta.rosetta.protocols.simple_moves.AddChainMover method) (pyrosetta.rosetta.protocols.simple_moves.AddJobPairData method) (pyrosetta.rosetta.protocols.simple_moves.AddPDBInfoMover method) (pyrosetta.rosetta.protocols.simple_moves.AddResidueCouplingConstraint method) (pyrosetta.rosetta.protocols.simple_moves.AddResidueLabelMover method) (pyrosetta.rosetta.protocols.simple_moves.AddSapConstraintMover method) (pyrosetta.rosetta.protocols.simple_moves.AddSapMathConstraintMover method) (pyrosetta.rosetta.protocols.simple_moves.AlignChainMover method) (pyrosetta.rosetta.protocols.simple_moves.asym_fold_and_dock.AsymFoldandDockMoveRbJumpMover method) (pyrosetta.rosetta.protocols.simple_moves.asym_fold_and_dock.AsymFoldandDockRbTrialMover method) (pyrosetta.rosetta.protocols.simple_moves.BackboneMover method) (pyrosetta.rosetta.protocols.simple_moves.BBConRotMover method) (pyrosetta.rosetta.protocols.simple_moves.BBDihedralSamplerMover method) (pyrosetta.rosetta.protocols.simple_moves.BBG8T3AMover method) (pyrosetta.rosetta.protocols.simple_moves.BBGaussianMover method) (pyrosetta.rosetta.protocols.simple_moves.bin_transitions.InitializeByBins method) (pyrosetta.rosetta.protocols.simple_moves.bin_transitions.PerturbByBins method) (pyrosetta.rosetta.protocols.simple_moves.ChainSplitMover method) (pyrosetta.rosetta.protocols.simple_moves.ChangeAndResetFoldTreeMover method) (pyrosetta.rosetta.protocols.simple_moves.chiral.ChiralMover method) (pyrosetta.rosetta.protocols.simple_moves.ClassicFragmentMover method) (pyrosetta.rosetta.protocols.simple_moves.CombinePoseMover method) (pyrosetta.rosetta.protocols.simple_moves.ConcatenatePosesMover method) (pyrosetta.rosetta.protocols.simple_moves.ConstrainToIdealMover method) (pyrosetta.rosetta.protocols.simple_moves.ContingentAcceptMover method) (pyrosetta.rosetta.protocols.simple_moves.ConvertRealToVirtualMover method) (pyrosetta.rosetta.protocols.simple_moves.ConvertVirtualToRealMover method) (pyrosetta.rosetta.protocols.simple_moves.CopyDofMover method) (pyrosetta.rosetta.protocols.simple_moves.CopyRotamerMover method) (pyrosetta.rosetta.protocols.simple_moves.CoupledMover method) (pyrosetta.rosetta.protocols.simple_moves.CutChainMover method) (pyrosetta.rosetta.protocols.simple_moves.CyclizationMover method) (pyrosetta.rosetta.protocols.simple_moves.DeclareBond method) (pyrosetta.rosetta.protocols.simple_moves.DEEROptimizeCoordsMover method) (pyrosetta.rosetta.protocols.simple_moves.DeleteChainMover method) (pyrosetta.rosetta.protocols.simple_moves.DeleteChainsMover method) (pyrosetta.rosetta.protocols.simple_moves.DisulfideInsertionMover method) (pyrosetta.rosetta.protocols.simple_moves.DME_FilterMover method) (pyrosetta.rosetta.protocols.simple_moves.DumpPdb method) (pyrosetta.rosetta.protocols.simple_moves.DumpSingleResidueRotamers method) (pyrosetta.rosetta.protocols.simple_moves.ExplicitWaterMover method) (pyrosetta.rosetta.protocols.simple_moves.FavorSequenceProfile method) (pyrosetta.rosetta.protocols.simple_moves.FavorSymmetricSequence method) (pyrosetta.rosetta.protocols.simple_moves.FoldTreeFromMotif method) (pyrosetta.rosetta.protocols.simple_moves.FragmentMover method) (pyrosetta.rosetta.protocols.simple_moves.hbs.HbsPatcher method) (pyrosetta.rosetta.protocols.simple_moves.LoadPDBMover method) (pyrosetta.rosetta.protocols.simple_moves.LoadUnboundRotMover method) (pyrosetta.rosetta.protocols.simple_moves.LoggedFragmentMover method) (pyrosetta.rosetta.protocols.simple_moves.MembraneTopology method) (pyrosetta.rosetta.protocols.simple_moves.MissingDensityToJumpMover method) (pyrosetta.rosetta.protocols.simple_moves.ModifyVariantTypeMover method) (pyrosetta.rosetta.protocols.simple_moves.MutateResidue method) (pyrosetta.rosetta.protocols.simple_moves.oop.OopDPuckMinusMover method) (pyrosetta.rosetta.protocols.simple_moves.oop.OopDPuckPlusMover method) (pyrosetta.rosetta.protocols.simple_moves.oop.OopMover method) (pyrosetta.rosetta.protocols.simple_moves.oop.OopPatcher method) (pyrosetta.rosetta.protocols.simple_moves.oop.OopPuckMinusMover method) (pyrosetta.rosetta.protocols.simple_moves.oop.OopPuckPlusMover method) (pyrosetta.rosetta.protocols.simple_moves.oop.OopRandomPuckMover method) (pyrosetta.rosetta.protocols.simple_moves.oop.OopRandomSmallMover method) (pyrosetta.rosetta.protocols.simple_moves.PDBReloadMover method) (pyrosetta.rosetta.protocols.simple_moves.PeptideStapleMover method) (pyrosetta.rosetta.protocols.simple_moves.PeriodicBoxMover method) (pyrosetta.rosetta.protocols.simple_moves.PoseFromPoseResourceMover method) (pyrosetta.rosetta.protocols.simple_moves.ProlineFixMover method) (pyrosetta.rosetta.protocols.simple_moves.PSSM2BfactorMover method) (pyrosetta.rosetta.protocols.simple_moves.RandomOmegaFlipMover method) (pyrosetta.rosetta.protocols.simple_moves.RandomTorsionMover method) (pyrosetta.rosetta.protocols.simple_moves.rational_mc.RationalMonteCarlo method) (pyrosetta.rosetta.protocols.simple_moves.RepeatPropagationMover method) (pyrosetta.rosetta.protocols.simple_moves.ReportEffectivePKA method) (pyrosetta.rosetta.protocols.simple_moves.ReportXYZ method) (pyrosetta.rosetta.protocols.simple_moves.RepulsiveOnlyMover method) (pyrosetta.rosetta.protocols.simple_moves.ResetFoldTree method) (pyrosetta.rosetta.protocols.simple_moves.ResetFullModelInfoMover method) (pyrosetta.rosetta.protocols.simple_moves.ResTypeFragmentMover method) (pyrosetta.rosetta.protocols.simple_moves.ReturnSidechainMover method) (pyrosetta.rosetta.protocols.simple_moves.RingConformationMover method) (pyrosetta.rosetta.protocols.simple_moves.SampleSequenceFromProbabilities method) (pyrosetta.rosetta.protocols.simple_moves.SaveProbabilitiesMetricMover method) (pyrosetta.rosetta.protocols.simple_moves.SaveSequenceToCommentsMover method) (pyrosetta.rosetta.protocols.simple_moves.ScoreMover method) (pyrosetta.rosetta.protocols.simple_moves.SequenceProfileMover method) (pyrosetta.rosetta.protocols.simple_moves.SetTorsion method) (pyrosetta.rosetta.protocols.simple_moves.SetupMetalsMover method) (pyrosetta.rosetta.protocols.simple_moves.ShakeStructureMover method) (pyrosetta.rosetta.protocols.simple_moves.ShearMover method) (pyrosetta.rosetta.protocols.simple_moves.ShortBackrubMover method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.JumpRotamerSidechainMover method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.PerturbChiSidechainMover method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.PerturbRotamerSidechainMover method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SetChiMover method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SidechainMCMover method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SidechainMover method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SidechainMoverBase method) (pyrosetta.rosetta.protocols.simple_moves.SimpleThreadingMover method) (pyrosetta.rosetta.protocols.simple_moves.SixDoFGridDockMover method) (pyrosetta.rosetta.protocols.simple_moves.SmallMover method) (pyrosetta.rosetta.protocols.simple_moves.SmoothFragmentMover method) (pyrosetta.rosetta.protocols.simple_moves.SmoothSymmetricFragmentMover method) (pyrosetta.rosetta.protocols.simple_moves.StorePoseSnapshot method) (pyrosetta.rosetta.protocols.simple_moves.StructProfileMover method) (pyrosetta.rosetta.protocols.simple_moves.SuperimposeMover method) (pyrosetta.rosetta.protocols.simple_moves.SwitchChainOrderMover method) (pyrosetta.rosetta.protocols.simple_moves.SwitchResidueTypeSetMover method) (pyrosetta.rosetta.protocols.simple_moves.SymmetricFragmentMover method) (pyrosetta.rosetta.protocols.simple_moves.TailsScoreMover method) (pyrosetta.rosetta.protocols.simple_moves.TorsionDOFMover method) (pyrosetta.rosetta.protocols.simple_moves.TorsionSetMover method) (pyrosetta.rosetta.protocols.simple_moves.triazolamer.TriazolamerMover method) (pyrosetta.rosetta.protocols.simple_moves.triazolamer.TriazolamerRandomSmallMover method) (pyrosetta.rosetta.protocols.simple_moves.Tumble method) (pyrosetta.rosetta.protocols.simple_moves.UniformRotationMover method) (pyrosetta.rosetta.protocols.simple_moves.UniformTranslationMover method) (pyrosetta.rosetta.protocols.simple_moves.VirtualRootMover method) (pyrosetta.rosetta.protocols.simple_moves.WobbleMover method) (pyrosetta.rosetta.protocols.simple_moves.WriteFiltersToPose method) (pyrosetta.rosetta.protocols.simple_moves.WriteSSEMover method) (pyrosetta.rosetta.protocols.splice.AlignEndsMover method) (pyrosetta.rosetta.protocols.splice.RBInMover method) (pyrosetta.rosetta.protocols.splice.RBOutMover method) (pyrosetta.rosetta.protocols.splice.RotLibOut method) (pyrosetta.rosetta.protocols.splice.Splice method) (pyrosetta.rosetta.protocols.splice.SpliceIn method) (pyrosetta.rosetta.protocols.splice.SpliceInAntibody method) (pyrosetta.rosetta.protocols.splice.SpliceInTail method) (pyrosetta.rosetta.protocols.splice.SpliceOut method) (pyrosetta.rosetta.protocols.splice.SpliceOutAntibody method) (pyrosetta.rosetta.protocols.splice.SpliceOutTail method) (pyrosetta.rosetta.protocols.splice.TailSegmentMover method) (pyrosetta.rosetta.protocols.star.StarAbinitio method) (pyrosetta.rosetta.protocols.stepwise.legacy.modeler.protein.StepWiseProteinMinimizer method) (pyrosetta.rosetta.protocols.stepwise.legacy.modeler.protein.StepWiseProteinPoseSetup method) (pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna.RNA_AnalyticLoopCloser method) (pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna.StepWiseRNA_PoseSetup method) (pyrosetta.rosetta.protocols.stepwise.modeler.packer.SideChainCopier method) (pyrosetta.rosetta.protocols.stepwise.modeler.packer.StepWisePacker method) (pyrosetta.rosetta.protocols.stepwise.modeler.polar_hydrogens.PolarHydrogenPacker method) (pyrosetta.rosetta.protocols.stepwise.modeler.precomputed.PrecomputedLibraryMover method) (pyrosetta.rosetta.protocols.stepwise.modeler.protein.loop_close.StepWiseProteinCCD_Closer method) (pyrosetta.rosetta.protocols.stepwise.modeler.protein.loop_close.StepWiseProteinCCD_MultiPoseCloser method) (pyrosetta.rosetta.protocols.stepwise.modeler.protein.loop_close.StepWiseProteinKIC_LoopBridger method) (pyrosetta.rosetta.protocols.stepwise.modeler.protein.StepWiseProteinBackboneSampler method) (pyrosetta.rosetta.protocols.stepwise.modeler.rna.bulge.BulgeApplyMover method) (pyrosetta.rosetta.protocols.stepwise.modeler.rna.bulge.BulgeUnApplyMover method) (pyrosetta.rosetta.protocols.stepwise.modeler.rna.checker.RNA_ChainClosureChecker method) (pyrosetta.rosetta.protocols.stepwise.modeler.rna.o2prime.O2PrimePacker method) (pyrosetta.rosetta.protocols.stepwise.modeler.rna.phosphate.MultiPhosphateSampler method) (pyrosetta.rosetta.protocols.stepwise.modeler.rna.phosphate.PhosphateMover method) (pyrosetta.rosetta.protocols.stepwise.modeler.rna.sugar.SugarInstantiateMover method) (pyrosetta.rosetta.protocols.stepwise.modeler.rna.sugar.SugarVirtualizeMover method) (pyrosetta.rosetta.protocols.stepwise.modeler.rna.sugar.VirtualSugarJustInTimeInstantiator method) (pyrosetta.rosetta.protocols.stepwise.modeler.rna.sugar.VirtualSugarSampler method) (pyrosetta.rosetta.protocols.stepwise.modeler.rna.sugar.VirtualSugarSamplerFromStringList method) (pyrosetta.rosetta.protocols.stepwise.modeler.StepWiseConnectionSampler method) (pyrosetta.rosetta.protocols.stepwise.modeler.StepWiseMinimizer method) (pyrosetta.rosetta.protocols.stepwise.modeler.StepWiseModeler method) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.mover.AddMover method) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.mover.AddOrDeleteMover method) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.mover.DeleteMover method) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.mover.FromScratchMover method) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.mover.ResampleMover method) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.mover.StepWiseMasterMover method) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.mover.VaryLoopLengthMover method) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.rna.RNA_AddDeleteMonteCarlo method) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.rna.RNA_O2PrimeMover method) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.rna.RNA_TorsionMover method) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.StepWiseMonteCarlo method) (pyrosetta.rosetta.protocols.stepwise.sampler.copy_dofs.CopyDofStepWiseSampler method) (pyrosetta.rosetta.protocols.stepwise.sampler.copy_dofs.ResidueAlternativeStepWiseSampler method) (pyrosetta.rosetta.protocols.stepwise.sampler.copy_dofs.ResidueAlternativeStepWiseSamplerComb method) (pyrosetta.rosetta.protocols.stepwise.sampler.copy_dofs.ResidueListStepWiseSampler method) (pyrosetta.rosetta.protocols.stepwise.sampler.input_streams.InputStreamStepWiseSampler method) (pyrosetta.rosetta.protocols.stepwise.sampler.jump.JumpStepWiseSampler method) (pyrosetta.rosetta.protocols.stepwise.sampler.protein.ProteinBetaAntiParallelStepWiseSampler method) (pyrosetta.rosetta.protocols.stepwise.sampler.protein.ProteinFragmentStepWiseSampler method) (pyrosetta.rosetta.protocols.stepwise.sampler.protein.ProteinMainChainStepWiseSampler method) (pyrosetta.rosetta.protocols.stepwise.sampler.rigid_body.RigidBodyStepWiseSampler method) (pyrosetta.rosetta.protocols.stepwise.sampler.rigid_body.RigidBodyStepWiseSamplerWithResidueAlternatives method) (pyrosetta.rosetta.protocols.stepwise.sampler.rigid_body.RigidBodyStepWiseSamplerWithResidueList method) (pyrosetta.rosetta.protocols.stepwise.sampler.rna.RNA_ChiStepWiseSampler method) (pyrosetta.rosetta.protocols.stepwise.sampler.rna.RNA_KIC_Sampler method) (pyrosetta.rosetta.protocols.stepwise.sampler.rna.RNA_KinematicCloser method) (pyrosetta.rosetta.protocols.stepwise.sampler.rna.RNA_NucleosideStepWiseSampler method) (pyrosetta.rosetta.protocols.stepwise.sampler.rna.RNA_SugarStepWiseSampler method) (pyrosetta.rosetta.protocols.stepwise.sampler.rna.RNA_SuiteStepWiseSampler method) (pyrosetta.rosetta.protocols.stepwise.sampler.StepWiseSampler method) (pyrosetta.rosetta.protocols.stepwise.sampler.StepWiseSamplerComb method) (pyrosetta.rosetta.protocols.stepwise.sampler.StepWiseSamplerOneDOF method) (pyrosetta.rosetta.protocols.stepwise.sampler.StepWiseSamplerOneTorsion method) (pyrosetta.rosetta.protocols.stepwise.sampler.StepWiseSamplerOneValue method) (pyrosetta.rosetta.protocols.stepwise.sampler.StepWiseSamplerOneValueComb method) (pyrosetta.rosetta.protocols.stepwise.sampler.StepWiseSamplerRingConformer method) (pyrosetta.rosetta.protocols.stepwise.sampler.StepWiseSamplerSized method) (pyrosetta.rosetta.protocols.stepwise.sampler.StepWiseSamplerSizedAny method) (pyrosetta.rosetta.protocols.stepwise.sampler.StepWiseSamplerSizedComb method) (pyrosetta.rosetta.protocols.struct_fragment.StructFragmentMover method) (pyrosetta.rosetta.protocols.surface_docking.CentroidRelaxMover method) (pyrosetta.rosetta.protocols.surface_docking.FullatomRelaxMover method) (pyrosetta.rosetta.protocols.surface_docking.SurfaceDockingProtocol method) (pyrosetta.rosetta.protocols.surface_docking.SurfaceOrientMover method) (pyrosetta.rosetta.protocols.switches.GraftSwitchMover method) (pyrosetta.rosetta.protocols.symmetric_docking.membrane.MPSymDockMover method) (pyrosetta.rosetta.protocols.symmetric_docking.SymDockBaseProtocol method) (pyrosetta.rosetta.protocols.symmetric_docking.SymDockingHiRes method) (pyrosetta.rosetta.protocols.symmetric_docking.SymDockingLowRes method) (pyrosetta.rosetta.protocols.symmetric_docking.SymDockProtocol method) (pyrosetta.rosetta.protocols.symmetric_docking.SymFoldandDockMoveRbJumpMover method) (pyrosetta.rosetta.protocols.symmetric_docking.SymFoldandDockRbTrialMover method) (pyrosetta.rosetta.protocols.symmetric_docking.SymFoldandDockSlideTrialMover method) (pyrosetta.rosetta.protocols.symmetric_docking.SymInterfaceSidechainMinMover method) (pyrosetta.rosetta.protocols.symmetric_docking.SymSidechainMinMover method) (pyrosetta.rosetta.protocols.symmetry.DetectSymmetry method) (pyrosetta.rosetta.protocols.symmetry.ExtractAsymmetricPoseMover method) (pyrosetta.rosetta.protocols.symmetry.ExtractAsymmetricUnitMover method) (pyrosetta.rosetta.protocols.symmetry.FaSymDockingSlideTogether method) (pyrosetta.rosetta.protocols.symmetry.SetupForSequenceSymmetryMover method) (pyrosetta.rosetta.protocols.symmetry.SetupForSymmetryMover method) (pyrosetta.rosetta.protocols.symmetry.SetupNCSMover method) (pyrosetta.rosetta.protocols.symmetry.SymDockingInitialPerturbation method) (pyrosetta.rosetta.protocols.symmetry.SymDockingSlideIntoContact method) (pyrosetta.rosetta.protocols.symmetry.SymmetricRMSMover method) (pyrosetta.rosetta.protocols.symmetry.SymShakeStructureMover method) (pyrosetta.rosetta.protocols.task_operations.StoreCombinedStoredTasksMover method) (pyrosetta.rosetta.protocols.task_operations.StoreCompoundTaskMover method) (pyrosetta.rosetta.protocols.task_operations.StoreTaskMover method) (pyrosetta.rosetta.protocols.testing.BenchmarkBuildRotamersMover method) (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.AlignPoseToInvrotTreeMover method) (pyrosetta.rosetta.protocols.toolbox.SamplerPlusPlus method) (pyrosetta.rosetta.protocols.topology_broker.RigidBodyRandomTMHMover method) (pyrosetta.rosetta.protocols.trRosetta_protocols.movers.trRosettaProtocolMover method) (pyrosetta.rosetta.protocols.ub_e2c.ubi_e2c_modeler method) (pyrosetta.rosetta.protocols.unfolded_state_energy_calculator.UnfoldedStateEnergyCalculatorMover method) (pyrosetta.rosetta.protocols.vardist_solaccess.LoadVarSolDistSasaCalculatorMover method) info_to_rank() (in module pyrosetta.rosetta.protocols.ligand_docking) inform_edges_of_alt_state_before_bbjump() (pyrosetta.rosetta.protocols.flexpack.interaction_graph.FlexbbNode method) (pyrosetta.rosetta.protocols.flexpack.interaction_graph.MinimalistFlexbbNode method) (pyrosetta.rosetta.protocols.flexpack.interaction_graph.OTFFlexbbNode method) inherit_cuts() (pyrosetta.rosetta.protocols.environment.Environment method) inherit_scorefxn_temperature() (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SidechainMCMover method) ini_func1() (in module pyrosetta.rosetta.numeric.random) ini_func2() (in module pyrosetta.rosetta.numeric.random) INIT (pyrosetta.rosetta.protocols.topology_broker.claims.BBClaim attribute) (pyrosetta.rosetta.protocols.topology_broker.claims.BBClaim.ClaimRight attribute) (pyrosetta.rosetta.protocols.topology_broker.claims.CutClaim attribute) (pyrosetta.rosetta.protocols.topology_broker.claims.CutClaim.ClaimRight attribute) (pyrosetta.rosetta.protocols.topology_broker.claims.DofClaim attribute) (pyrosetta.rosetta.protocols.topology_broker.claims.DofClaim.ClaimRight attribute) (pyrosetta.rosetta.protocols.topology_broker.claims.JumpClaim attribute) (pyrosetta.rosetta.protocols.topology_broker.claims.JumpClaim.ClaimRight attribute) (pyrosetta.rosetta.protocols.topology_broker.claims.LegacyRootClaim attribute) (pyrosetta.rosetta.protocols.topology_broker.claims.LegacyRootClaim.ClaimRight attribute) (pyrosetta.rosetta.protocols.topology_broker.claims.SequenceClaim attribute) (pyrosetta.rosetta.protocols.topology_broker.claims.SequenceClaim.ClaimRight attribute) (pyrosetta.rosetta.protocols.topology_broker.claims.SymmetryClaim attribute) (pyrosetta.rosetta.protocols.topology_broker.claims.SymmetryClaim.ClaimRight attribute) init() (in module pyrosetta) (in module pyrosetta.distributed) (in module pyrosetta.rosetta.basic) (in module pyrosetta.rosetta.core.init) (in module pyrosetta.rosetta.protocols.init) (pyrosetta.rosetta.basic.MemTracerImpl method) (pyrosetta.rosetta.basic.TracerImpl method) (pyrosetta.rosetta.core.pack.task.PackerTask_ method) (pyrosetta.rosetta.core.pose.xyzStripeHashPose method) (pyrosetta.rosetta.core.scoring.electron_density.ElectronDensity method) (pyrosetta.rosetta.core.scoring.fiber_diffraction.FiberDiffraction method) (pyrosetta.rosetta.core.scoring.methods.BBDepCartBondedParameters method) (pyrosetta.rosetta.core.scoring.mm.MMBondAngleResidueTypeParam method) (pyrosetta.rosetta.core.scoring.packstat.Array2D method) Init() (pyrosetta.rosetta.core.scoring.sc.ContactMolecularSurfaceCalculator method) (pyrosetta.rosetta.core.scoring.sc.ElectrostaticComplementarityCalculator method) (pyrosetta.rosetta.core.scoring.sc.ElectrostaticSimilarityCalculator method) (pyrosetta.rosetta.core.scoring.sc.MolecularSurfaceCalculator method) (pyrosetta.rosetta.core.scoring.sc.ShapeComplementarityCalculator method) (pyrosetta.rosetta.core.scoring.sc.ShapeSimilarityCalculator method) init() (pyrosetta.rosetta.numeric.fourier.SHT method) (pyrosetta.rosetta.numeric.fourier.SO3coeffs method) (pyrosetta.rosetta.numeric.geometry.hashing.MinimalClashHash method) (pyrosetta.rosetta.numeric.geometry.hashing.SixDOffsetTree method) (pyrosetta.rosetta.numeric.geometry.hashing.xyzStripeHash method) (pyrosetta.rosetta.numeric.geometry.hashing.xyzStripeHashWithMeta_double_t method) (pyrosetta.rosetta.numeric.geometry.hashing.xyzStripeHashWithMeta_float method) (pyrosetta.rosetta.numeric.geometry.hashing.xyzStripeHashWithMeta_float_t method) (pyrosetta.rosetta.protocols.abinitio.ClassicAbinitio method) (pyrosetta.rosetta.protocols.abinitio.DoubleLayerKinematicAbinitio method) (pyrosetta.rosetta.protocols.abinitio.FoldConstraints method) (pyrosetta.rosetta.protocols.abinitio.JumpingFoldConstraintsWrapper method) (pyrosetta.rosetta.protocols.abinitio.KinematicAbinitio method) (pyrosetta.rosetta.protocols.abinitio.KinematicTaskControl method) (pyrosetta.rosetta.protocols.abinitio.LoopJumpFoldCst method) (pyrosetta.rosetta.protocols.abinitio.MembraneAbinitio method) (pyrosetta.rosetta.protocols.abinitio.Protocol method) (pyrosetta.rosetta.protocols.constel.ExcludedFilter static method) (pyrosetta.rosetta.protocols.constel.FilterByProxTerm static method) (pyrosetta.rosetta.protocols.constel.FilterBySASA static method) (pyrosetta.rosetta.protocols.constel.HBondCommon static method) (pyrosetta.rosetta.protocols.constel.SingResCnlCrea static method) (pyrosetta.rosetta.protocols.cyclic_peptide.PeptideStubMover method) (pyrosetta.rosetta.protocols.docking.DockingInitialPerturbation method) (pyrosetta.rosetta.protocols.docking.DockMCMProtocol method) (pyrosetta.rosetta.protocols.electron_density.BfactorFittingMover method) (pyrosetta.rosetta.protocols.electron_density.ReportFSC method) (pyrosetta.rosetta.protocols.electron_density.ScaleMapIntensities method) (pyrosetta.rosetta.protocols.electron_density.VoxelSpacingRefinementMover method) (pyrosetta.rosetta.protocols.fldsgn.SheetRemodelConstraintGenerator method) (pyrosetta.rosetta.protocols.forge.constraints.InverseRotamersRCG method) (pyrosetta.rosetta.protocols.forge.constraints.InvrotTreeRCG method) (pyrosetta.rosetta.protocols.forge.constraints.NtoCConstraintGenerator method) (pyrosetta.rosetta.protocols.forge.remodel.GenericRemodelConstraintGenerator method) (pyrosetta.rosetta.protocols.forge.remodel.RemodelConstraintGenerator method) (pyrosetta.rosetta.protocols.forge.remodel.ResidueVicinityRCG method) (pyrosetta.rosetta.protocols.hybridization.BackboneTorsionPerturbation method) (pyrosetta.rosetta.protocols.hybridization.BackboneTorsionSampler method) (pyrosetta.rosetta.protocols.hybridization.CartesianHybridize method) (pyrosetta.rosetta.protocols.hybridization.CartesianSampler method) (pyrosetta.rosetta.protocols.hybridization.FoldTreeHybridize method) (pyrosetta.rosetta.protocols.hybridization.FragmentBiasAssigner method) (pyrosetta.rosetta.protocols.hybridization.HybridizeProtocol method) (pyrosetta.rosetta.protocols.hybridization.InsertChunkMover method) (pyrosetta.rosetta.protocols.hybridization.MRMover method) (pyrosetta.rosetta.protocols.jumping.MembraneJump method) (pyrosetta.rosetta.protocols.loop_modeling.utilities.TrajectoryLogger method) (pyrosetta.rosetta.protocols.loops.loop_mover.refine.LoopMover_Refine_KIC method) (pyrosetta.rosetta.protocols.md.CartesianMD method) (pyrosetta.rosetta.protocols.md.MDBase method) (pyrosetta.rosetta.protocols.minimization_packing.EnergyCutRotamerTrialsMinMover method) (pyrosetta.rosetta.protocols.minimization_packing.MinPackMover method) (pyrosetta.rosetta.protocols.minimization_packing.RotamerTrialsMinMover method) (pyrosetta.rosetta.protocols.moves.ReplicaExchangeMC method) (pyrosetta.rosetta.protocols.mpi_refinement.Serial_Refine method) (pyrosetta.rosetta.protocols.optimize_weights.WrapperOptEMultifunc method) (pyrosetta.rosetta.protocols.pockets.PocketConstraint method) (pyrosetta.rosetta.protocols.rbsegment_relax.ConfChangeMover method) (pyrosetta.rosetta.protocols.recces.sampler.MC_Any method) (pyrosetta.rosetta.protocols.recces.sampler.MC_Comb method) (pyrosetta.rosetta.protocols.recces.sampler.MC_Loop method) (pyrosetta.rosetta.protocols.recces.sampler.MC_OneTorsion method) (pyrosetta.rosetta.protocols.recces.sampler.MC_Sampler method) (pyrosetta.rosetta.protocols.recces.sampler.rna.MC_RNA_KIC_Sampler method) (pyrosetta.rosetta.protocols.recces.sampler.rna.MC_RNA_MultiSuite method) (pyrosetta.rosetta.protocols.recces.sampler.rna.MC_RNA_OneJump method) (pyrosetta.rosetta.protocols.recces.sampler.rna.MC_RNA_Sugar method) (pyrosetta.rosetta.protocols.recces.sampler.rna.MC_RNA_Suite method) (pyrosetta.rosetta.protocols.seeded_abinitio.SegmentHybridizer method) (pyrosetta.rosetta.protocols.sic_dock.SICFast method) (pyrosetta.rosetta.protocols.sic_dock.xyzStripeHashPoseWithMeta method) (pyrosetta.rosetta.protocols.simple_moves.BBConRotMover method) (pyrosetta.rosetta.protocols.simple_moves.BBG8T3AMover method) (pyrosetta.rosetta.protocols.simple_moves.BBGaussianMover method) (pyrosetta.rosetta.protocols.simple_moves.ExplicitWaterMover method) (pyrosetta.rosetta.protocols.simple_moves.ReportEffectivePKA method) (pyrosetta.rosetta.protocols.sparta.ANN method) (pyrosetta.rosetta.protocols.sparta.Sparta.SpartaLib method) (pyrosetta.rosetta.protocols.stepwise.modeler.protein.loop_close.StepWiseProteinCCD_Closer method) (pyrosetta.rosetta.protocols.stepwise.sampler.copy_dofs.CopyDofStepWiseSampler method) (pyrosetta.rosetta.protocols.stepwise.sampler.copy_dofs.ResidueAlternativeStepWiseSampler method) (pyrosetta.rosetta.protocols.stepwise.sampler.copy_dofs.ResidueAlternativeStepWiseSamplerComb method) (pyrosetta.rosetta.protocols.stepwise.sampler.copy_dofs.ResidueListStepWiseSampler method) (pyrosetta.rosetta.protocols.stepwise.sampler.input_streams.InputStreamStepWiseSampler method) (pyrosetta.rosetta.protocols.stepwise.sampler.jump.JumpStepWiseSampler method) (pyrosetta.rosetta.protocols.stepwise.sampler.protein.ProteinBetaAntiParallelStepWiseSampler method) (pyrosetta.rosetta.protocols.stepwise.sampler.protein.ProteinFragmentStepWiseSampler method) (pyrosetta.rosetta.protocols.stepwise.sampler.protein.ProteinMainChainStepWiseSampler method) (pyrosetta.rosetta.protocols.stepwise.sampler.rigid_body.RigidBodyStepWiseSampler method) (pyrosetta.rosetta.protocols.stepwise.sampler.rigid_body.RigidBodyStepWiseSamplerValueRange method) (pyrosetta.rosetta.protocols.stepwise.sampler.rigid_body.RigidBodyStepWiseSamplerWithResidueAlternatives method) (pyrosetta.rosetta.protocols.stepwise.sampler.rigid_body.RigidBodyStepWiseSamplerWithResidueList method) (pyrosetta.rosetta.protocols.stepwise.sampler.rna.RNA_ChiStepWiseSampler method) (pyrosetta.rosetta.protocols.stepwise.sampler.rna.RNA_KIC_Sampler method) (pyrosetta.rosetta.protocols.stepwise.sampler.rna.RNA_KinematicCloser method) (pyrosetta.rosetta.protocols.stepwise.sampler.rna.RNA_NucleosideStepWiseSampler method) (pyrosetta.rosetta.protocols.stepwise.sampler.rna.RNA_SugarStepWiseSampler method) (pyrosetta.rosetta.protocols.stepwise.sampler.rna.RNA_SuiteStepWiseSampler method) (pyrosetta.rosetta.protocols.stepwise.sampler.StepWiseSampler method) (pyrosetta.rosetta.protocols.stepwise.sampler.StepWiseSamplerComb method) (pyrosetta.rosetta.protocols.stepwise.sampler.StepWiseSamplerOneDOF method) (pyrosetta.rosetta.protocols.stepwise.sampler.StepWiseSamplerOneTorsion method) (pyrosetta.rosetta.protocols.stepwise.sampler.StepWiseSamplerOneValue method) (pyrosetta.rosetta.protocols.stepwise.sampler.StepWiseSamplerOneValueComb method) (pyrosetta.rosetta.protocols.stepwise.sampler.StepWiseSamplerRingConformer method) (pyrosetta.rosetta.protocols.stepwise.sampler.StepWiseSamplerSized method) (pyrosetta.rosetta.protocols.stepwise.sampler.StepWiseSamplerSizedAny method) (pyrosetta.rosetta.protocols.stepwise.sampler.StepWiseSamplerSizedComb method) (pyrosetta.rosetta.protocols.symmetric_docking.SymFoldandDockRbTrialMover method) (pyrosetta.rosetta.protocols.symmetry.SequentialSymmetrySlider method) (pyrosetta.rosetta.protocols.toolbox.GreedyKCenter method) (pyrosetta.rosetta.protocols.toolbox.InteratomicVarianceMatrix method) (pyrosetta.rosetta.protocols.toolbox.KCluster method) (pyrosetta.rosetta.protocols.toolbox.KMedoid method) (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.EnzConstraintParameters method) (pyrosetta.rosetta.protocols.toolbox.SamplerPlusPlus method) init_after_reading() (pyrosetta.rosetta.protocols.topology_broker.PcsEnergyController method) (pyrosetta.rosetta.protocols.topology_broker.PseudocontactShiftEnergyController method) (pyrosetta.rosetta.protocols.topology_broker.PseudocontactShiftEnergyController_Ts1 method) (pyrosetta.rosetta.protocols.topology_broker.PseudocontactShiftEnergyController_Ts2 method) (pyrosetta.rosetta.protocols.topology_broker.PseudocontactShiftEnergyController_Ts3 method) (pyrosetta.rosetta.protocols.topology_broker.PseudocontactShiftEnergyController_Ts4 method) init_angle() (pyrosetta.rosetta.protocols.matdes.GetRBDOFValues method) init_apply() (pyrosetta.rosetta.protocols.loops.loop_closure.jacobi.JacobiLoopClosureMover method) init_atype_maps() (pyrosetta.rosetta.core.scoring.packing.HolesParams method) init_bbgmover() (pyrosetta.rosetta.protocols.generalized_kinematic_closure.perturber.GeneralizedKICperturber method) init_beta_correction() (in module pyrosetta.rosetta.core.init) init_beta_july15_correction() (in module pyrosetta.rosetta.core.init) init_beta_nov16_correction() (in module pyrosetta.rosetta.core.init) init_calibrator() (pyrosetta.rosetta.protocols.noesy_assign.PeakCalibrator method) (pyrosetta.rosetta.protocols.noesy_assign.StructureDependentPeakCalibrator method) (pyrosetta.rosetta.protocols.noesy_assign.StructureIndependentPeakCalibrator method) init_centroids() (pyrosetta.rosetta.protocols.make_rot_lib.MakeRotLibMover method) init_clash_check() (pyrosetta.rosetta.protocols.scoring.ImplicitFastClashCheck method) init_common_options() (in module pyrosetta.rosetta.protocols.ncbb) init_coords() (pyrosetta.rosetta.protocols.simple_moves.DEEROptimizeCoordsMover method) init_correct_correction() (in module pyrosetta.rosetta.core.init) init_crystal_refinement_correction() (in module pyrosetta.rosetta.core.init) init_cst_score_types() (pyrosetta.rosetta.core.scoring.constraints.AmbiguousConstraint method) (pyrosetta.rosetta.core.scoring.constraints.KofNConstraint method) (pyrosetta.rosetta.core.scoring.constraints.SiteConstraint method) (pyrosetta.rosetta.core.scoring.constraints.SiteConstraintResidues method) (pyrosetta.rosetta.protocols.constraints_additional.AmbiguousMultiConstraint method) init_d77_perturbation() (pyrosetta.rosetta.protocols.ub_e2c.ubi_e2c_modeler method) init_defaults() (pyrosetta.rosetta.core.conformation.symmetry.SymmetryInfo method) init_disp() (pyrosetta.rosetta.protocols.matdes.GetRBDOFValues method) init_dna_correction() (in module pyrosetta.rosetta.core.init) init_factory() (pyrosetta.rosetta.core.scoring.epr_deer.metrics.DEERDecayData method) init_facts_correction() (in module pyrosetta.rosetta.core.init) init_fast() (pyrosetta.rosetta.protocols.stepwise.sampler.rna.RNA_SuiteStepWiseSampler method) init_fragment_sample_confs() (pyrosetta.rosetta.protocols.drug_design.bcl.BCLFragmentBaseMover method) (pyrosetta.rosetta.protocols.drug_design.bcl.BCLFragmentMutateMover method) init_from_cmd() (pyrosetta.rosetta.protocols.loophash.WorkUnit_LoopHash method) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_bbGauss method) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_CombinePose method) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_FragInsert method) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_KicCloser method) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_LoopHash method) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_MD method) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_NormalMode method) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_PartialAbinitio method) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_RamaPerturber method) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_Relax method) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_Sampler method) init_from_comand_line() (pyrosetta.rosetta.core.pack.task.operation.OptH method) init_from_current() (pyrosetta.rosetta.core.kinematics.inverse.InternalCoordGeometry method) init_from_decoy_set() (pyrosetta.rosetta.protocols.abinitio.HedgeArchive method) (pyrosetta.rosetta.protocols.abinitio.IterativeAbrelax method) (pyrosetta.rosetta.protocols.abinitio.IterativeBase method) (pyrosetta.rosetta.protocols.abinitio.IterativeCentroid method) (pyrosetta.rosetta.protocols.abinitio.IterativeFullatom method) (pyrosetta.rosetta.protocols.jd2.archive.AbstractArchiveBase method) (pyrosetta.rosetta.protocols.jd2.archive.ArchiveBase method) (pyrosetta.rosetta.protocols.jd2.archive.EvaluatedArchive method) (pyrosetta.rosetta.protocols.jd2.archive.NormalizedEvaluatedArchive method) (pyrosetta.rosetta.protocols.jd2.archive.VarianceStatisticsArchive method) init_from_file() (pyrosetta.rosetta.core.kinematics.MoveMap method) (pyrosetta.rosetta.core.pack.rotamers.SingleLigandRotamerLibrary method) (pyrosetta.rosetta.protocols.helical_bundle.BundleParametrizationCalculator method) init_from_ligand() (pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.ConstraintInfo method) init_from_ligand_pharmacophore() (pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.ConstraintInfo method) init_from_lines() (pyrosetta.rosetta.core.import_pose.PDBSilentStruct method) (pyrosetta.rosetta.core.io.silent.BinarySilentStruct method) (pyrosetta.rosetta.core.io.silent.RigidBodySilentStruct method) (pyrosetta.rosetta.core.io.silent.RNA_SilentStruct method) (pyrosetta.rosetta.core.io.silent.ScoreFileSilentStruct method) (pyrosetta.rosetta.core.io.silent.ScoreJumpFileSilentStruct method) (pyrosetta.rosetta.core.io.silent.SilentStruct method) init_from_map() (pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.ConstraintInfo method) init_from_maps() (pyrosetta.rosetta.protocols.rosetta_scripts.XmlObjects method) init_from_options() (pyrosetta.rosetta.protocols.abinitio.IterativeAbrelax method) (pyrosetta.rosetta.protocols.abinitio.IterativeBase method) (pyrosetta.rosetta.protocols.abinitio.IterativeCentroid method) (pyrosetta.rosetta.protocols.abinitio.IterativeFullatom method) (pyrosetta.rosetta.protocols.antibody.grafting.SCS_BlastFilter_by_OCD method) (pyrosetta.rosetta.protocols.antibody.grafting.SCS_BlastFilter_by_pdbid method) (pyrosetta.rosetta.protocols.antibody.grafting.SCS_BlastFilter_by_sequence_identity method) (pyrosetta.rosetta.protocols.antibody.grafting.SCS_BlastPlus method) (pyrosetta.rosetta.protocols.antibody.grafting.SCS_LoopOverSCs method) (pyrosetta.rosetta.protocols.antibody.grafting.SCS_SubstitutionMatrix method) (pyrosetta.rosetta.protocols.antibody_legacy.AntibodyModeler method) (pyrosetta.rosetta.protocols.docking.DockingInitialPerturbation method) (pyrosetta.rosetta.protocols.docking.DockTaskFactory method) (pyrosetta.rosetta.protocols.docking.EllipsoidalRandomizationMover method) (pyrosetta.rosetta.protocols.enzdes.DetectProteinLigandInterface method) (pyrosetta.rosetta.protocols.enzdes.ProteinLigandInterfaceUpweighter method) (pyrosetta.rosetta.protocols.features.strand_assembly.StrandBundleFeatures method) (pyrosetta.rosetta.protocols.jd2.archive.NormalizedEvaluatedArchive method) init_from_pose() (pyrosetta.rosetta.core.io.pose_to_sfr.PoseToStructFileRepConverter method) init_from_receptor() (pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.ConstraintInfo method) init_from_vector() (pyrosetta.rosetta.core.pack.rotamers.SingleLigandRotamerLibrary method) init_gen_potential_settings() (in module pyrosetta.rosetta.core.init) init_H5FragmentStoreProvider() (in module pyrosetta.protocols.h5_fragment_store_provider) init_H5StructureStoreProvider() (in module pyrosetta.protocols.h5_structure_store_provider) init_hbond_data() (pyrosetta.rosetta.core.energy_methods.ExactOccludedHbondSolEnergy method) init_hbond_sp2_correction() (in module pyrosetta.rosetta.core.init) init_k48r_perturbation() (pyrosetta.rosetta.protocols.ub_e2c.ubi_e2c_modeler method) init_kic_loop() (pyrosetta.rosetta.protocols.simple_moves.BBConRotMover method) (pyrosetta.rosetta.protocols.simple_moves.BBG8T3AMover method) (pyrosetta.rosetta.protocols.simple_moves.BBGaussianMover method) init_matrix() (pyrosetta.rosetta.core.sequence.NWAligner static method) init_mc() (pyrosetta.rosetta.protocols.docking.DockMCMCycle method) init_membrane_center_normal() (pyrosetta.rosetta.core.scoring.MembranePotential method) init_mini_pose() (pyrosetta.rosetta.protocols.jumping.ResiduePairJump method) init_node_info() (in module pyrosetta.rosetta.core.pack.hbonds) init_nonideal_correction() (in module pyrosetta.rosetta.core.init) init_notebook() (in module pyrosetta.distributed.dask) init_on_new_input() (pyrosetta.rosetta.protocols.analysis.InterfaceAnalyzerMover method) (pyrosetta.rosetta.protocols.antibody_legacy.AntibodyModeler method) init_option() (pyrosetta.rosetta.protocols.mean_field.DesignMeanField method) (pyrosetta.rosetta.protocols.mean_field.FlexBBDesignMeanField method) (pyrosetta.rosetta.protocols.mean_field.FlexBBMeanField method) (pyrosetta.rosetta.protocols.mean_field.GenMeanFieldMover method) (pyrosetta.rosetta.protocols.mean_field.MeanField method) init_packing_score_discrim() (in module pyrosetta.rosetta.core.scoring.packstat) init_packing_score_respred() (in module pyrosetta.rosetta.core.scoring.packstat) init_parameters() (pyrosetta.rosetta.protocols.motif_grafting.movers.MotifGraftMover method) init_params() (pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.LigandConformer method) init_paths() (in module pyrosetta.rosetta.core.init) init_pose() (pyrosetta.rosetta.protocols.abinitio.ResolutionSwitcher method) (pyrosetta.rosetta.protocols.mpi_refinement.MultiObjective method) init_posehash() (pyrosetta.rosetta.core.pose.xyzStripeHashPose method) init_pre_beta_nov15_etable() (in module pyrosetta.rosetta.core.init) init_PredErrorSurface() (pyrosetta.rosetta.protocols.sparta.Sparta.SpartaLib method) init_profiling() (in module pyrosetta.rosetta.core.init) init_random_generators() (in module pyrosetta.rosetta.basic.random) init_random_number_generators() (in module pyrosetta.rosetta.basic.random) init_res_list() (pyrosetta.rosetta.core.energy_methods.ReferenceEnergyNoncanonical method) init_resources() (in module pyrosetta.rosetta.core.init) init_restore_score12prime() (in module pyrosetta.rosetta.core.init) init_revert_to_pre_talaris_2013_mistake() (in module pyrosetta.rosetta.core.init) init_revert_to_talaris() (in module pyrosetta.rosetta.core.init) init_rotamer_recovery_with_options() (pyrosetta.rosetta.protocols.rotamer_recovery.RotamerRecovery method) init_rotamers() (pyrosetta.rosetta.protocols.make_rot_lib.MakeRotLibMover method) init_score_function_corrections() (in module pyrosetta.rosetta.core.init) init_sequence() (pyrosetta.rosetta.protocols.evolution.NucleotideMutation method) init_shapovalov_lib_fixes_enable_correction() (in module pyrosetta.rosetta.core.init) init_source_revision() (in module pyrosetta.rosetta.core.init) init_spades_score_function_correction() (in module pyrosetta.rosetta.core.init) init_standard() (pyrosetta.rosetta.protocols.stepwise.sampler.rna.RNA_SuiteStepWiseSampler method) init_static_inputs() (pyrosetta.rosetta.utility.Inline_File_Provider method) init_strength() (pyrosetta.rosetta.protocols.environment.claims.TorsionClaim method) (pyrosetta.rosetta.protocols.environment.claims.XYZClaim method) init_subsidiary_constraints() (pyrosetta.rosetta.core.scoring.constraints.BasePairConstraint method) init_task() (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.JumpRotamerSidechainMover method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.PerturbChiSidechainMover method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.PerturbRotamerSidechainMover method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SidechainMCMover method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SidechainMover method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SidechainMoverBase method) init_tracers() (in module pyrosetta.rosetta.core.init) init_vdw() (pyrosetta.rosetta.core.scoring.epr_deer.EPRSpinLabel method) init_with_options() (pyrosetta.rosetta.protocols.backrub.BackrubMover method) (pyrosetta.rosetta.protocols.rotamer_recovery.RotamerRecovery method) init_with_pose() (pyrosetta.rosetta.core.pack.guidance_scoreterms.lk_dome.LK_DomeHelper method) (pyrosetta.rosetta.core.pack.guidance_scoreterms.sap.SapConstraintHelper method) (pyrosetta.rosetta.protocols.sic_dock.xyzStripeHashPoseWithMeta method) initHBond() (pyrosetta.rosetta.protocols.sparta.PDB method) initial_cter_perturbation() (pyrosetta.rosetta.protocols.ub_e2c.ubi_e2c_modeler method) initial_perturbation() (pyrosetta.rosetta.protocols.ub_e2c.ubi_e2c_modeler method) initial_pose_for_residues() (in module pyrosetta.rosetta.protocols.indexed_structure_store) initial_repack() (pyrosetta.rosetta.protocols.ub_e2c.ubi_e2c_modeler method) initial_search() (pyrosetta.rosetta.core.scoring.epr_deer.Simulated4PDEERTraceFactory method) initial_structures_provided() (pyrosetta.rosetta.core.import_pose.options.RNA_DeNovoProtocolOptions method) (pyrosetta.rosetta.core.import_pose.options.RNA_FragmentMonteCarloOptions method) initial_value() (pyrosetta.rosetta.ObjexxFCL.FArrayTraits_bool_t static method) (pyrosetta.rosetta.ObjexxFCL.FArrayTraits_char_t static method) (pyrosetta.rosetta.ObjexxFCL.FArrayTraits_core_pack_dunbrack_BBDepNRChiSample_float_t static method) (pyrosetta.rosetta.ObjexxFCL.FArrayTraits_core_pack_dunbrack_BBDepScoreInterpData_1_t static method) (pyrosetta.rosetta.ObjexxFCL.FArrayTraits_core_pack_dunbrack_BBDepScoreInterpData_2_t static method) (pyrosetta.rosetta.ObjexxFCL.FArrayTraits_core_pack_dunbrack_BBDepScoreInterpData_3_t static method) (pyrosetta.rosetta.ObjexxFCL.FArrayTraits_core_pack_dunbrack_BBDepScoreInterpData_4_t static method) (pyrosetta.rosetta.ObjexxFCL.FArrayTraits_core_pack_dunbrack_BBDepScoreInterpData_5_t static method) (pyrosetta.rosetta.ObjexxFCL.FArrayTraits_core_pack_dunbrack_BBIndNRChiSample_float_t static method) (pyrosetta.rosetta.ObjexxFCL.FArrayTraits_core_pack_dunbrack_PackedDunbrackRotamer_1_1_float_t static method) (pyrosetta.rosetta.ObjexxFCL.FArrayTraits_core_pack_dunbrack_PackedDunbrackRotamer_1_2_float_t static method) (pyrosetta.rosetta.ObjexxFCL.FArrayTraits_core_pack_dunbrack_PackedDunbrackRotamer_1_3_float_t static method) (pyrosetta.rosetta.ObjexxFCL.FArrayTraits_core_pack_dunbrack_PackedDunbrackRotamer_1_4_float_t static method) (pyrosetta.rosetta.ObjexxFCL.FArrayTraits_core_pack_dunbrack_PackedDunbrackRotamer_1_5_float_t static method) (pyrosetta.rosetta.ObjexxFCL.FArrayTraits_core_pack_dunbrack_PackedDunbrackRotamer_2_1_float_t static method) (pyrosetta.rosetta.ObjexxFCL.FArrayTraits_core_pack_dunbrack_PackedDunbrackRotamer_2_2_float_t static method) (pyrosetta.rosetta.ObjexxFCL.FArrayTraits_core_pack_dunbrack_PackedDunbrackRotamer_2_3_float_t static method) (pyrosetta.rosetta.ObjexxFCL.FArrayTraits_core_pack_dunbrack_PackedDunbrackRotamer_2_4_float_t static method) (pyrosetta.rosetta.ObjexxFCL.FArrayTraits_core_pack_dunbrack_PackedDunbrackRotamer_2_5_float_t static method) (pyrosetta.rosetta.ObjexxFCL.FArrayTraits_core_pack_dunbrack_PackedDunbrackRotamer_3_1_float_t static method) (pyrosetta.rosetta.ObjexxFCL.FArrayTraits_core_pack_dunbrack_PackedDunbrackRotamer_3_2_float_t static method) (pyrosetta.rosetta.ObjexxFCL.FArrayTraits_core_pack_dunbrack_PackedDunbrackRotamer_3_3_float_t static method) (pyrosetta.rosetta.ObjexxFCL.FArrayTraits_core_pack_dunbrack_PackedDunbrackRotamer_3_4_float_t static method) (pyrosetta.rosetta.ObjexxFCL.FArrayTraits_core_pack_dunbrack_PackedDunbrackRotamer_3_5_float_t static method) (pyrosetta.rosetta.ObjexxFCL.FArrayTraits_core_pack_dunbrack_PackedDunbrackRotamer_4_1_float_t static method) (pyrosetta.rosetta.ObjexxFCL.FArrayTraits_core_pack_dunbrack_PackedDunbrackRotamer_4_2_float_t static method) (pyrosetta.rosetta.ObjexxFCL.FArrayTraits_core_pack_dunbrack_PackedDunbrackRotamer_4_3_float_t static method) (pyrosetta.rosetta.ObjexxFCL.FArrayTraits_core_pack_dunbrack_PackedDunbrackRotamer_4_4_float_t static method) (pyrosetta.rosetta.ObjexxFCL.FArrayTraits_core_pack_dunbrack_PackedDunbrackRotamer_4_5_float_t static method) (pyrosetta.rosetta.ObjexxFCL.FArrayTraits_core_pack_dunbrack_PackedDunbrackRotamer_5_1_float_t static method) (pyrosetta.rosetta.ObjexxFCL.FArrayTraits_core_pack_dunbrack_PackedDunbrackRotamer_5_2_float_t static method) (pyrosetta.rosetta.ObjexxFCL.FArrayTraits_core_pack_dunbrack_PackedDunbrackRotamer_5_3_float_t static method) (pyrosetta.rosetta.ObjexxFCL.FArrayTraits_core_pack_dunbrack_PackedDunbrackRotamer_5_4_float_t static method) (pyrosetta.rosetta.ObjexxFCL.FArrayTraits_core_pack_dunbrack_PackedDunbrackRotamer_5_5_float_t static method) (pyrosetta.rosetta.ObjexxFCL.FArrayTraits_double_t static method) (pyrosetta.rosetta.ObjexxFCL.FArrayTraits_float_t static method) (pyrosetta.rosetta.ObjexxFCL.FArrayTraits_int_t static method) (pyrosetta.rosetta.ObjexxFCL.FArrayTraits_std_string_t static method) (pyrosetta.rosetta.ObjexxFCL.FArrayTraits_unsigned_long_t static method) INITIALIZE (pyrosetta.rosetta.basic.ProfTag attribute) initialize() (in module pyrosetta.rosetta.basic.options) (pyrosetta.rosetta.core.chemical.AtomTypeDatabaseIO method) (pyrosetta.rosetta.core.chemical.ResidueDatabaseIO method) (pyrosetta.rosetta.core.conformation.symmetry.SymmetryInfo method) (pyrosetta.rosetta.core.energy_methods.FA_ElecEnergyAroAll method) (pyrosetta.rosetta.core.energy_methods.FA_ElecEnergyAroAro method) (pyrosetta.rosetta.core.energy_methods.FA_GrpElecEnergy method) (pyrosetta.rosetta.core.energy_methods.FAElecContextData method) (pyrosetta.rosetta.core.energy_methods.RNA_FA_ElecEnergy method) (pyrosetta.rosetta.core.io.rna.RNA_DataReader method) (pyrosetta.rosetta.core.optimization.DescentDirectionAlgorithm method) (pyrosetta.rosetta.core.pack.hbonds.HBondGraphInitializerIG method) (pyrosetta.rosetta.core.pack.interaction_graph.DensePDInteractionGraph method) (pyrosetta.rosetta.core.pack.interaction_graph.DoubleDensePDInteractionGraph method) (pyrosetta.rosetta.core.pack.interaction_graph.DoubleLazyInteractionGraph method) (pyrosetta.rosetta.core.pack.interaction_graph.FASTERInteractionGraph method) (pyrosetta.rosetta.core.pack.interaction_graph.FixedBBInteractionGraph method) (pyrosetta.rosetta.core.pack.interaction_graph.InteractionGraphBase method) (pyrosetta.rosetta.core.pack.interaction_graph.LazyInteractionGraph method) (pyrosetta.rosetta.core.pack.interaction_graph.LinearMemoryInteractionGraph method) (pyrosetta.rosetta.core.pack.interaction_graph.NPDHBSimpleInteractionGraph method) (pyrosetta.rosetta.core.pack.interaction_graph.OnTheFlyInteractionGraph method) (pyrosetta.rosetta.core.pack.interaction_graph.PDInteractionGraph method) (pyrosetta.rosetta.core.pack.interaction_graph.PrecomputedPairEnergiesInteractionGraph method) (pyrosetta.rosetta.core.pack.interaction_graph.ResidueArrayAnnealingEvaluator method) (pyrosetta.rosetta.core.pack.interaction_graph.SimpleInteractionGraph method) (pyrosetta.rosetta.core.pack.interaction_graph.SymmLinearMemoryInteractionGraph method) (pyrosetta.rosetta.core.pack.interaction_graph.SymmMinimalistInteractionGraph method) (pyrosetta.rosetta.core.pack.interaction_graph.SymmOnTheFlyInteractionGraph method) (pyrosetta.rosetta.core.scoring.CenListInfo method) (pyrosetta.rosetta.core.scoring.elec.FA_ElecEnergy method) (pyrosetta.rosetta.core.scoring.elec.GroupElec method) (pyrosetta.rosetta.core.scoring.etable.coulomb.Coulomb method) (pyrosetta.rosetta.core.scoring.facts.FACTSPoseInfo method) (pyrosetta.rosetta.core.scoring.facts.FACTSResidueInfo method) (pyrosetta.rosetta.core.scoring.facts.FACTSRotamerSetInfo method) (pyrosetta.rosetta.core.scoring.GenBornPoseInfo method) (pyrosetta.rosetta.core.scoring.GenBornResidueInfo method) (pyrosetta.rosetta.core.scoring.GenBornRotamerSetInfo method) (pyrosetta.rosetta.core.scoring.hbonds.HBondDatabase method) (pyrosetta.rosetta.core.scoring.lkball.LKB_ResidueInfo method) (pyrosetta.rosetta.core.scoring.lkball.LKD_ResidueInfo method) (pyrosetta.rosetta.core.scoring.Membrane_FAEmbed method) (pyrosetta.rosetta.core.scoring.MembraneEmbed method) (pyrosetta.rosetta.core.scoring.MembraneTopology method) (pyrosetta.rosetta.core.scoring.MultipoleElecPoseInfo method) (pyrosetta.rosetta.core.scoring.MultipoleElecResidueInfo method) (pyrosetta.rosetta.core.scoring.MultipoleElecRotamerSetInfo method) (pyrosetta.rosetta.core.scoring.ResidueNblistData method) (pyrosetta.rosetta.core.scoring.rna.data.RNA_DMS_LowResolutionPotential method) (pyrosetta.rosetta.core.scoring.rna.data.RNA_DMS_Potential method) (pyrosetta.rosetta.core.scoring.VdWTinkerPoseInfo method) (pyrosetta.rosetta.core.scoring.VdWTinkerResidueInfo method) (pyrosetta.rosetta.core.scoring.VdWTinkerRotamerSetInfo method) (pyrosetta.rosetta.core.select.util.SelectResiduesByLayer method) (pyrosetta.rosetta.core.sequence.ABEGOManager method) (pyrosetta.rosetta.ObjexxFCL.FArray1D_bool_t method) (pyrosetta.rosetta.ObjexxFCL.FArray1D_char_t method) (pyrosetta.rosetta.ObjexxFCL.FArray1D_double_t method) (pyrosetta.rosetta.ObjexxFCL.FArray1D_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray1D_int_t method) (pyrosetta.rosetta.ObjexxFCL.FArray1D_ObjexxFCL_FArray1D_int_t method) (pyrosetta.rosetta.ObjexxFCL.FArray1D_std_string_t method) (pyrosetta.rosetta.ObjexxFCL.FArray1D_unsigned_long_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_bool_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_core_pack_dunbrack_BBDepNRChiSample_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_core_pack_dunbrack_BBDepScoreInterpData_1_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_core_pack_dunbrack_BBDepScoreInterpData_2_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_core_pack_dunbrack_BBDepScoreInterpData_3_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_core_pack_dunbrack_BBDepScoreInterpData_4_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_core_pack_dunbrack_BBDepScoreInterpData_5_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_core_pack_dunbrack_BBIndNRChiSample_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_core_pack_dunbrack_PackedDunbrackRotamer_1_1_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_core_pack_dunbrack_PackedDunbrackRotamer_1_2_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_core_pack_dunbrack_PackedDunbrackRotamer_1_3_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_core_pack_dunbrack_PackedDunbrackRotamer_1_4_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_core_pack_dunbrack_PackedDunbrackRotamer_1_5_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_core_pack_dunbrack_PackedDunbrackRotamer_2_1_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_core_pack_dunbrack_PackedDunbrackRotamer_2_2_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_core_pack_dunbrack_PackedDunbrackRotamer_2_3_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_core_pack_dunbrack_PackedDunbrackRotamer_2_4_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_core_pack_dunbrack_PackedDunbrackRotamer_2_5_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_core_pack_dunbrack_PackedDunbrackRotamer_3_1_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_core_pack_dunbrack_PackedDunbrackRotamer_3_2_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_core_pack_dunbrack_PackedDunbrackRotamer_3_3_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_core_pack_dunbrack_PackedDunbrackRotamer_3_4_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_core_pack_dunbrack_PackedDunbrackRotamer_3_5_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_core_pack_dunbrack_PackedDunbrackRotamer_4_1_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_core_pack_dunbrack_PackedDunbrackRotamer_4_2_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_core_pack_dunbrack_PackedDunbrackRotamer_4_3_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_core_pack_dunbrack_PackedDunbrackRotamer_4_4_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_core_pack_dunbrack_PackedDunbrackRotamer_4_5_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_core_pack_dunbrack_PackedDunbrackRotamer_5_1_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_core_pack_dunbrack_PackedDunbrackRotamer_5_2_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_core_pack_dunbrack_PackedDunbrackRotamer_5_3_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_core_pack_dunbrack_PackedDunbrackRotamer_5_4_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_core_pack_dunbrack_PackedDunbrackRotamer_5_5_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_double_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_int_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_numeric_xyzVector_double_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_ObjexxFCL_FArray2D_float__star__t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_ObjexxFCL_ubyte_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_std_string_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_unsigned_char_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_unsigned_long_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_utility_vector1_core_pack_dunbrack_cenrot_CentroidRotamerSampleData_std_allocator_core_pack_dunbrack_cenrot_CentroidRotamerSampleData_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_utility_vector1_double_std_allocator_double_t method) (pyrosetta.rosetta.ObjexxFCL.FArray3D_core_pack_dunbrack_BBDepScoreInterpData_1_t method) (pyrosetta.rosetta.ObjexxFCL.FArray3D_core_pack_dunbrack_BBDepScoreInterpData_2_t method) (pyrosetta.rosetta.ObjexxFCL.FArray3D_core_pack_dunbrack_BBDepScoreInterpData_3_t method) (pyrosetta.rosetta.ObjexxFCL.FArray3D_core_pack_dunbrack_BBDepScoreInterpData_4_t method) (pyrosetta.rosetta.ObjexxFCL.FArray3D_core_pack_dunbrack_BBDepScoreInterpData_5_t method) (pyrosetta.rosetta.ObjexxFCL.FArray3D_double_t method) (pyrosetta.rosetta.ObjexxFCL.FArray3D_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray3D_int_t method) (pyrosetta.rosetta.ObjexxFCL.FArray3D_std_complex_double_t method) (pyrosetta.rosetta.ObjexxFCL.FArray3D_std_vector_unsigned_long_std_allocator_unsigned_long_t method) (pyrosetta.rosetta.ObjexxFCL.FArray3D_unsigned_char_t method) (pyrosetta.rosetta.ObjexxFCL.FArray3D_unsigned_long_t method) (pyrosetta.rosetta.ObjexxFCL.FArray3D_utility_vector1_double_std_allocator_double_t method) (pyrosetta.rosetta.ObjexxFCL.FArray3D_utility_vector1_numeric_xyzVector_double_std_allocator_numeric_xyzVector_double_t method) (pyrosetta.rosetta.ObjexxFCL.FArray3D_utility_vector1_unsigned_int_std_allocator_unsigned_int_t method) (pyrosetta.rosetta.ObjexxFCL.FArray4D_double_t method) (pyrosetta.rosetta.ObjexxFCL.FArray4D_int_t method) (pyrosetta.rosetta.ObjexxFCL.FArray4D_unsigned_char_t method) (pyrosetta.rosetta.ObjexxFCL.FArray5D_double_t method) (pyrosetta.rosetta.ObjexxFCL.FArray5D_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray5D_int_t method) (pyrosetta.rosetta.protocols.abinitio.abscript.AbscriptLoopCloserCM method) (pyrosetta.rosetta.protocols.abinitio.abscript.AbscriptMover method) (pyrosetta.rosetta.protocols.abinitio.abscript.ConstraintPreparer method) (pyrosetta.rosetta.protocols.abinitio.abscript.FragmentCM method) (pyrosetta.rosetta.protocols.abinitio.abscript.FragmentJumpCM method) (pyrosetta.rosetta.protocols.abinitio.abscript.RigidChunkCM method) (pyrosetta.rosetta.protocols.abinitio.abscript.StagePreparer method) (pyrosetta.rosetta.protocols.abinitio.abscript.StructPerturberCM method) (pyrosetta.rosetta.protocols.abinitio.HedgeArchive method) (pyrosetta.rosetta.protocols.abinitio.IterativeAbrelax method) (pyrosetta.rosetta.protocols.abinitio.IterativeBase method) (pyrosetta.rosetta.protocols.abinitio.IterativeCentroid method) (pyrosetta.rosetta.protocols.abinitio.IterativeFullatom method) (pyrosetta.rosetta.protocols.chemically_conjugated_docking.UBQ_GTPaseMover method) (pyrosetta.rosetta.protocols.cluster.calibur.Clustering method) (pyrosetta.rosetta.protocols.cryst.DockLatticeMover method) (pyrosetta.rosetta.protocols.dna.DnaInterfaceMinMover method) (pyrosetta.rosetta.protocols.environment.ClientMover method) (pyrosetta.rosetta.protocols.environment.CoMTrackerCM method) (pyrosetta.rosetta.protocols.environment.ScriptCM method) (pyrosetta.rosetta.protocols.evolution.EvolutionaryDynamicsMover method) (pyrosetta.rosetta.protocols.features.ProteinSilentReport method) (pyrosetta.rosetta.protocols.fldsgn.topology.HelixPairing method) (pyrosetta.rosetta.protocols.fldsgn.topology.Sheet method) (pyrosetta.rosetta.protocols.fldsgn.topology.SheetSet method) (pyrosetta.rosetta.protocols.fldsgn.topology.SS_Info2 method) (pyrosetta.rosetta.protocols.flexpack.interaction_graph.FlexbbInteractionGraph method) (pyrosetta.rosetta.protocols.flexpack.interaction_graph.MinimalistFlexbbInteractionGraph method) (pyrosetta.rosetta.protocols.flexpack.interaction_graph.OTFFlexbbInteractionGraph method) (pyrosetta.rosetta.protocols.flexpack.interaction_graph.PrecomputedFlexbbInteractionGraph method) (pyrosetta.rosetta.protocols.hybridization.HybridizeFoldtreeDynamic method) (pyrosetta.rosetta.protocols.jd2.archive.AbstractArchiveBase method) (pyrosetta.rosetta.protocols.jd2.archive.ArchiveBase method) (pyrosetta.rosetta.protocols.jd2.archive.EvaluatedArchive method) (pyrosetta.rosetta.protocols.jd2.archive.NormalizedEvaluatedArchive method) (pyrosetta.rosetta.protocols.jd2.archive.VarianceStatisticsArchive method) (pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.LigandConformer method) (pyrosetta.rosetta.protocols.loops.loop_mover.LoopCM method) (pyrosetta.rosetta.protocols.match.downstream.ActiveSiteGrid method) (pyrosetta.rosetta.protocols.match.HitHasher method) (pyrosetta.rosetta.protocols.match.HitNeighborFinder method) (pyrosetta.rosetta.protocols.match.MatchCounter method) (pyrosetta.rosetta.protocols.match.OccupiedSpaceHash method) (pyrosetta.rosetta.protocols.minimization_packing.MinMover method) (pyrosetta.rosetta.protocols.minimization_packing.symmetry.SymMinMover method) (pyrosetta.rosetta.protocols.monte_carlo.GenericMonteCarloMover method) (pyrosetta.rosetta.protocols.monte_carlo.GenericSimulatedAnnealer method) (pyrosetta.rosetta.protocols.motifs.LigandMotifSearch method) (pyrosetta.rosetta.protocols.motifs.MotifSearch method) (pyrosetta.rosetta.protocols.moves.MoveMapMover method) (pyrosetta.rosetta.protocols.moves.NullMover method) (pyrosetta.rosetta.protocols.pack_daemon.IterativeVectorExpression method) (pyrosetta.rosetta.protocols.pockets.EggshellGrid method) (pyrosetta.rosetta.protocols.pockets.ElectrostaticpotentialGrid method) (pyrosetta.rosetta.protocols.pockets.PocketGrid method) (pyrosetta.rosetta.protocols.pockets.TargetPocketGrid method) (pyrosetta.rosetta.protocols.qsar.scoring_grid.AtrGrid method) (pyrosetta.rosetta.protocols.qsar.scoring_grid.ChargeGrid method) (pyrosetta.rosetta.protocols.qsar.scoring_grid.ClassicGrid method) (pyrosetta.rosetta.protocols.qsar.scoring_grid.ConstantScoreBase method) (pyrosetta.rosetta.protocols.qsar.scoring_grid.GridBase method) (pyrosetta.rosetta.protocols.qsar.scoring_grid.HbaGrid method) (pyrosetta.rosetta.protocols.qsar.scoring_grid.HbdGrid method) (pyrosetta.rosetta.protocols.qsar.scoring_grid.LigandPropertyScore method) (pyrosetta.rosetta.protocols.qsar.scoring_grid.LipidMemGrid method) (pyrosetta.rosetta.protocols.qsar.scoring_grid.PCSMultiGrid method) (pyrosetta.rosetta.protocols.qsar.scoring_grid.PCSSingleGrid method) (pyrosetta.rosetta.protocols.qsar.scoring_grid.RepGrid method) (pyrosetta.rosetta.protocols.qsar.scoring_grid.ShapeGrid method) (pyrosetta.rosetta.protocols.qsar.scoring_grid.SingleGrid method) (pyrosetta.rosetta.protocols.qsar.scoring_grid.SiteGrid method) (pyrosetta.rosetta.protocols.qsar.scoring_grid.SolvationGrid method) (pyrosetta.rosetta.protocols.qsar.scoring_grid.SolvationMetaGrid method) (pyrosetta.rosetta.protocols.qsar.scoring_grid.VdwGrid method) (pyrosetta.rosetta.protocols.rbsegment_relax.RBSegmentRelax method) (pyrosetta.rosetta.protocols.rigid.UniformRigidBodyCM method) (pyrosetta.rosetta.protocols.rna.denovo.movers.RNP_HighResMover method) (pyrosetta.rosetta.protocols.rna.setup.RNA_CSA_JobDistributor method) (pyrosetta.rosetta.protocols.rna.setup.RNA_JobDistributor method) (pyrosetta.rosetta.protocols.rna.setup.RNA_MonteCarloJobDistributor method) (pyrosetta.rosetta.protocols.scoring.InterfaceInfo method) (pyrosetta.rosetta.protocols.simple_ddg.DdGScan method) (pyrosetta.rosetta.protocols.simple_moves.ClassicFragmentMover method) (pyrosetta.rosetta.protocols.simple_moves.FragmentMover method) (pyrosetta.rosetta.protocols.simple_moves.LoggedFragmentMover method) (pyrosetta.rosetta.protocols.simple_moves.ResTypeFragmentMover method) (pyrosetta.rosetta.protocols.simple_moves.SmoothFragmentMover method) (pyrosetta.rosetta.protocols.simple_moves.SmoothSymmetricFragmentMover method) (pyrosetta.rosetta.protocols.simple_moves.SymmetricFragmentMover method) (pyrosetta.rosetta.protocols.simple_moves.WaterRotsDB method) (pyrosetta.rosetta.protocols.simple_moves.WobbleMover method) (pyrosetta.rosetta.protocols.stepwise.modeler.align.StepWisePoseAligner method) (pyrosetta.rosetta.protocols.stepwise.modeler.packer.StepWiseMasterPacker method) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.mover.StepWiseMasterMover method) (pyrosetta.rosetta.RDKit.RingInfo method) initialize_acc_strength() (pyrosetta.rosetta.core.scoring.hbonds.HBondDatabase method) initialize_aho_numbers() (in module pyrosetta.rosetta.protocols.tcr) initialize_all_atoms() (pyrosetta.rosetta.protocols.protein_interface_design.filters.AtomicContactCountFilter method) initialize_and_check() (pyrosetta.rosetta.core.select.residue_selector.BinSelector method) initialize_and_sample_loops() (pyrosetta.rosetta.protocols.hybridization.HybridizeProtocol method) initialize_atom_numbers_sugar() (pyrosetta.rosetta.core.energy_methods.RNA_DataBackboneEnergy method) initialize_atomid_map() (in module pyrosetta.rosetta.core.pose) initialize_atomid_map_AtomID() (in module pyrosetta.rosetta.core.pose) initialize_atoms_for_which_we_need_new_dofs() (in module pyrosetta.rosetta.core.pose.rna) initialize_bcl_main() (in module pyrosetta.rosetta.core.chemical.bcl) initialize_bcl_random() (in module pyrosetta.rosetta.core.chemical.bcl) initialize_bcl_tracers() (in module pyrosetta.rosetta.core.chemical.bcl) initialize_betaresidue_minima() (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.TorsionSamplingKinematicPerturber method) initialize_by_prepack() (pyrosetta.rosetta.protocols.stepwise.modeler.rna.phosphate.MultiPhosphateSampler method) initialize_constraints_from_file() (pyrosetta.rosetta.protocols.optimize_weights.ConstraintedOptimizationWeightFunc method) initialize_core_id_globals() (in module pyrosetta.rosetta.core.id) initialize_cross_chain() (pyrosetta.rosetta.protocols.protein_interface_design.filters.AtomicContactCountFilter method) initialize_cross_jump() (pyrosetta.rosetta.protocols.protein_interface_design.filters.AtomicContactCountFilter method) initialize_data() (pyrosetta.rosetta.protocols.helical_bundle.BackboneGridSamplerHelper method) initialize_data_map() (pyrosetta.rosetta.protocols.rosetta_scripts.RosettaScriptsParser method) initialize_database() (pyrosetta.rosetta.protocols.features.ReportToDB method) (pyrosetta.rosetta.protocols.features.TrajectoryReportToDB method) initialize_default_calculator_from_default_crick_params_file() (pyrosetta.rosetta.protocols.helical_bundle.MakeBundle method) initialize_disulfide_bonds() (in module pyrosetta.rosetta.core.pose) initialize_dofs() (pyrosetta.rosetta.protocols.topology_broker.AsymFoldandDockClaimer method) (pyrosetta.rosetta.protocols.topology_broker.BasicJumpClaimer method) (pyrosetta.rosetta.protocols.topology_broker.ConstraintClaimer method) (pyrosetta.rosetta.protocols.topology_broker.CoordConstraintClaimer method) (pyrosetta.rosetta.protocols.topology_broker.CutBiasClaimer method) (pyrosetta.rosetta.protocols.topology_broker.DensityScoringClaimer method) (pyrosetta.rosetta.protocols.topology_broker.DisulfJumpClaimer method) (pyrosetta.rosetta.protocols.topology_broker.FibrilModelingClaimer method) (pyrosetta.rosetta.protocols.topology_broker.FoldandDockClaimer method) (pyrosetta.rosetta.protocols.topology_broker.FragmentClaimer method) (pyrosetta.rosetta.protocols.topology_broker.FragmentJumpClaimer method) (pyrosetta.rosetta.protocols.topology_broker.LoopFragmentClaimer method) (pyrosetta.rosetta.protocols.topology_broker.MembraneTopologyClaimer method) (pyrosetta.rosetta.protocols.topology_broker.MetalloClaimer method) (pyrosetta.rosetta.protocols.topology_broker.PcsEnergyController method) (pyrosetta.rosetta.protocols.topology_broker.PseudocontactShiftEnergyController method) (pyrosetta.rosetta.protocols.topology_broker.PseudocontactShiftEnergyController_Ts1 method) (pyrosetta.rosetta.protocols.topology_broker.PseudocontactShiftEnergyController_Ts2 method) (pyrosetta.rosetta.protocols.topology_broker.PseudocontactShiftEnergyController_Ts3 method) (pyrosetta.rosetta.protocols.topology_broker.PseudocontactShiftEnergyController_Ts4 method) (pyrosetta.rosetta.protocols.topology_broker.RigidChunkClaimer method) (pyrosetta.rosetta.protocols.topology_broker.SequenceClaimer method) (pyrosetta.rosetta.protocols.topology_broker.StartStructClaimer method) (pyrosetta.rosetta.protocols.topology_broker.SymmetryClaimer method) (pyrosetta.rosetta.protocols.topology_broker.TemplateFragmentClaimer method) (pyrosetta.rosetta.protocols.topology_broker.TemplateJumpClaimer method) (pyrosetta.rosetta.protocols.topology_broker.TMHTopologySamplerClaimer method) (pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer method) initialize_don_strength() (pyrosetta.rosetta.core.scoring.hbonds.HBondDatabase method) initialize_dun02_aa_parameters() (pyrosetta.rosetta.core.pack.dunbrack.RotamerLibrary static method) initialize_energy_method() (pyrosetta.rosetta.core.energy_methods.DEEREnergy method) initialize_espGrid() (pyrosetta.rosetta.protocols.pockets.ElectrostaticpotentialGrid method) initialize_extra_rotamer_flags_from_command_line() (pyrosetta.rosetta.core.pack.task.PackerTask method) (pyrosetta.rosetta.core.pack.task.PackerTask_ method) (pyrosetta.rosetta.core.pack.task.ResidueLevelTask method) (pyrosetta.rosetta.core.pack.task.ResidueLevelTask_ method) initialize_extra_rotamer_flags_from_options() (pyrosetta.rosetta.core.pack.task.PackerTask method) (pyrosetta.rosetta.core.pack.task.PackerTask_ method) (pyrosetta.rosetta.core.pack.task.ResidueLevelTask method) (pyrosetta.rosetta.core.pack.task.ResidueLevelTask_ method) initialize_filter() (pyrosetta.rosetta.protocols.flxbb.FlxbbDesign method) initialize_for_de_novo_generation() (pyrosetta.rosetta.core.chemical.mainchain_potential.MainchainScoreTable method) initialize_for_de_novo_protocol() (pyrosetta.rosetta.protocols.rna.denovo.RNA_DeNovoPoseInitializer method) initialize_for_farna_optimizer() (pyrosetta.rosetta.core.import_pose.options.RNA_DeNovoProtocolOptions method) (pyrosetta.rosetta.core.import_pose.options.RNA_FragmentMonteCarloOptions method) initialize_from() (pyrosetta.rosetta.core.scoring.ScoreFunctionInfo method) initialize_from_blueprint() (pyrosetta.rosetta.protocols.fldsgn.SheetConstraintGenerator method) initialize_from_command_line() (pyrosetta.rosetta.core.import_pose.options.RNA_BasicOptions method) (pyrosetta.rosetta.core.import_pose.options.RNA_DeNovoProtocolOptions method) (pyrosetta.rosetta.core.import_pose.options.RNA_FragmentMonteCarloOptions method) (pyrosetta.rosetta.core.import_pose.options.RNA_MinimizerOptions method) (pyrosetta.rosetta.core.import_pose.RNA_DeNovoSetup method) (pyrosetta.rosetta.core.pack.rotamer_set.UnboundRotamersOperation method) (pyrosetta.rosetta.core.pack.task.PackerTask method) (pyrosetta.rosetta.core.pack.task.PackerTask_ method) (pyrosetta.rosetta.core.pack.task.ResidueLevelTask method) (pyrosetta.rosetta.core.pack.task.ResidueLevelTask_ method) (pyrosetta.rosetta.protocols.match.MatcherTask method) (pyrosetta.rosetta.protocols.recces.options.RECCES_Options method) (pyrosetta.rosetta.protocols.splice.SampleRotamersFromPDB_RotamerSetOperation method) (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseModelerOptions method) (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseProteinModelerOptions method) (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseRNA_ModelerOptions method) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.mover.options.StepWiseMoveSelectorOptions method) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.options.StepWiseMonteCarloOptions method) (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.AllowedSeqposForGeomCst method) initialize_from_commandline() (pyrosetta.rosetta.basic.resource_manager.ResourceManager method) initialize_from_correspondence_file() (pyrosetta.rosetta.protocols.pack_daemon.EntityCorrespondence method) initialize_from_enzcst_io() (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.InvrotTreeNode method) initialize_from_enzcst_io_and_invrots() (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.InvrotTreeNode method) initialize_from_file() (pyrosetta.rosetta.core.scoring.aa_composition_energy.AACompositionConstraint method) (pyrosetta.rosetta.core.scoring.aa_composition_energy.AACompositionEnergySetup method) (pyrosetta.rosetta.core.scoring.DockingScoreFunction method) (pyrosetta.rosetta.core.scoring.mhc_epitope_energy.MHCEpitopeConstraint method) (pyrosetta.rosetta.core.scoring.mhc_epitope_energy.MHCEpitopeEnergySetup method) (pyrosetta.rosetta.core.scoring.MinScoreScoreFunction method) (pyrosetta.rosetta.core.scoring.netcharge_energy.NetChargeConstraint method) (pyrosetta.rosetta.core.scoring.netcharge_energy.NetChargeEnergySetup method) (pyrosetta.rosetta.core.scoring.ScoreFunction method) (pyrosetta.rosetta.core.scoring.symmetry.SymmetricScoreFunction method) (pyrosetta.rosetta.protocols.chromophore.ChromophoreDataReader method) (pyrosetta.rosetta.protocols.flexpack.OtherContextScoreFunction method) (pyrosetta.rosetta.protocols.match.Matcher method) initialize_from_file_contents() (pyrosetta.rosetta.core.pack.palette.CustomBaseTypePackerPalette method) (pyrosetta.rosetta.core.scoring.aa_composition_energy.AACompositionConstraint method) (pyrosetta.rosetta.core.scoring.aa_composition_energy.AACompositionEnergySetup method) (pyrosetta.rosetta.core.scoring.mhc_epitope_energy.MHCEpitopeConstraint method) (pyrosetta.rosetta.core.scoring.mhc_epitope_energy.MHCEpitopeEnergySetup method) (pyrosetta.rosetta.core.scoring.netcharge_energy.NetChargeConstraint method) (pyrosetta.rosetta.core.scoring.netcharge_energy.NetChargeEnergySetup method) (pyrosetta.rosetta.protocols.helical_bundle_predict.HBPHelixAssignments method) initialize_from_global_options() (pyrosetta.rosetta.protocols.energy_based_clustering.EnergyBasedClusteringOptions method) initialize_from_gridlig_file() (pyrosetta.rosetta.protocols.match.downstream.ActiveSiteGrid method) initialize_from_input_file() (pyrosetta.rosetta.protocols.pack_daemon.DynamicAggregateFunctionDriver method) (pyrosetta.rosetta.protocols.pack_daemon.EntityFunc method) initialize_from_matcher_task() (pyrosetta.rosetta.protocols.match.output.CloudPDBWriter method) (pyrosetta.rosetta.protocols.match.output.OutputWriter method) (pyrosetta.rosetta.protocols.match.output.PDBWriter method) (pyrosetta.rosetta.protocols.match.output.PoseMatchOutputWriter method) (pyrosetta.rosetta.protocols.match.output.WriteKinemageOutputter method) initialize_from_options() (pyrosetta.rosetta.basic.random.RandomGeneratorSettings method) (pyrosetta.rosetta.core.import_pose.options.RNA_BasicOptions method) (pyrosetta.rosetta.core.import_pose.options.RNA_DeNovoProtocolOptions method) (pyrosetta.rosetta.core.import_pose.options.RNA_FragmentMonteCarloOptions method) (pyrosetta.rosetta.core.import_pose.options.RNA_MinimizerOptions method) (pyrosetta.rosetta.core.import_pose.RNA_DeNovoSetup method) (pyrosetta.rosetta.core.pack.task.PackerTask method) (pyrosetta.rosetta.core.pack.task.PackerTask_ method) (pyrosetta.rosetta.core.pack.task.ResidueLevelTask method) (pyrosetta.rosetta.core.pack.task.ResidueLevelTask_ method) (pyrosetta.rosetta.core.scoring.etable.EtableOptions method) (pyrosetta.rosetta.core.scoring.hbonds.HBondOptions method) (pyrosetta.rosetta.core.scoring.methods.EnergyMethodOptions method) (pyrosetta.rosetta.core.scoring.methods.FreeDOF_Options method) (pyrosetta.rosetta.core.scoring.methods.NMerRefEnergy method) (pyrosetta.rosetta.core.scoring.rna.RNA_EnergyMethodOptions method) (pyrosetta.rosetta.protocols.cyclic_peptide_predict.SimpleCycpepPredictApplication method) (pyrosetta.rosetta.protocols.helical_bundle_predict.HelicalBundlePredictApplicationOptions method) (pyrosetta.rosetta.protocols.rna.movers.ErraserMinimizerMover method) (pyrosetta.rosetta.protocols.sewing.hashing.BasisMapGenerator method) (pyrosetta.rosetta.protocols.sewing.hashing.EdgeMapGenerator method) (pyrosetta.rosetta.protocols.sewing.hashing.Hasher method) initialize_from_options_collection() (pyrosetta.rosetta.protocols.stepwise.monte_carlo.mover.options.StepWiseMoveSelectorOptions method) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.options.StepWiseMonteCarloOptions method) initialize_from_params() (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.EnzCstTemplateRes method) initialize_from_psipred_file_contents() (pyrosetta.rosetta.protocols.helical_bundle_predict.HBPHelixAssignments method) initialize_from_residue() (pyrosetta.rosetta.protocols.match.downstream.LigandConformerBuilder method) (pyrosetta.rosetta.protocols.match.downstream.RigidLigandBuilder method) (pyrosetta.rosetta.protocols.match.upstream.OriginalBackboneBuildPoint method) (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.LigandConformer method) initialize_from_residue_type() (pyrosetta.rosetta.protocols.match.upstream.UpstreamResTypeGeometry method) initialize_from_residues() (pyrosetta.rosetta.core.scoring.ResiduePairNeighborList method) initialize_from_rotation_matrix() (pyrosetta.rosetta.protocols.stepwise.sampler.rigid_body.EulerAngles method) initialize_from_string() (pyrosetta.rosetta.basic.citation_manager.Citation method) initialize_from_tag() (pyrosetta.rosetta.core.import_pose.options.RNA_BasicOptions method) (pyrosetta.rosetta.core.import_pose.options.RNA_DeNovoProtocolOptions method) (pyrosetta.rosetta.core.import_pose.options.RNA_FragmentMonteCarloOptions method) (pyrosetta.rosetta.core.import_pose.options.RNA_MinimizerOptions method) (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.MatchConstraintFileInfo method) initialize_from_task() (pyrosetta.rosetta.core.pack.annealer.SmartFixbbSimAnnealer method) (pyrosetta.rosetta.protocols.match.Matcher method) initialize_from_tokens() (pyrosetta.rosetta.core.pack.task.ALLAA method) (pyrosetta.rosetta.core.pack.task.ALLAAwc method) (pyrosetta.rosetta.core.pack.task.ALLAAxc method) (pyrosetta.rosetta.core.pack.task.APOLA method) (pyrosetta.rosetta.core.pack.task.APOLAR method) (pyrosetta.rosetta.core.pack.task.AROMATIC method) (pyrosetta.rosetta.core.pack.task.AUTO method) (pyrosetta.rosetta.core.pack.task.CHARGED method) (pyrosetta.rosetta.core.pack.task.EX method) (pyrosetta.rosetta.core.pack.task.EX_CUTOFF method) (pyrosetta.rosetta.core.pack.task.FIX_HIS_TAUTOMER method) (pyrosetta.rosetta.core.pack.task.NATAA method) (pyrosetta.rosetta.core.pack.task.NATRO method) (pyrosetta.rosetta.core.pack.task.NO_ADDUCTS method) (pyrosetta.rosetta.core.pack.task.NOTAA method) (pyrosetta.rosetta.core.pack.task.PIKAA method) (pyrosetta.rosetta.core.pack.task.PIKNA method) (pyrosetta.rosetta.core.pack.task.POLAR method) (pyrosetta.rosetta.core.pack.task.PROPERTY method) (pyrosetta.rosetta.core.pack.task.ResfileCommand method) (pyrosetta.rosetta.core.pack.task.SCAN method) (pyrosetta.rosetta.core.pack.task.TARGET method) (pyrosetta.rosetta.core.pack.task.USE_INPUT_SC method) initialize_full_model_parameters() (pyrosetta.rosetta.core.import_pose.FullModelPoseBuilder method) initialize_further_from_options() (pyrosetta.rosetta.core.import_pose.FullModelPoseBuilder method) initialize_ga_randomizer_from_entity_task() (in module pyrosetta.rosetta.protocols.pack_daemon) initialize_graph_for_packing() (pyrosetta.rosetta.core.pack.guidance_scoreterms.buried_unsat_penalty.graph.BuriedUnsatPenaltyGraph method) initialize_graph_for_scoring() (pyrosetta.rosetta.core.pack.guidance_scoreterms.buried_unsat_penalty.graph.BuriedUnsatPenaltyGraph method) initialize_hashmap() (pyrosetta.rosetta.protocols.sewing.hashing.Hasher method) initialize_HBEval() (pyrosetta.rosetta.core.scoring.hbonds.HBondDatabase method) initialize_HBEval_lookup() (in module pyrosetta.rosetta.core.scoring.hbonds) initialize_HBFadeInterval() (pyrosetta.rosetta.core.scoring.hbonds.HBondDatabase method) initialize_HBPoly1D() (pyrosetta.rosetta.core.scoring.hbonds.HBondDatabase method) initialize_hbs() (in module pyrosetta.rosetta.core.pose.ncbb) INITIALIZE_HIERARCHY (pyrosetta.rosetta.basic.ProfTag attribute) initialize_implicit_lipid_parameters() (pyrosetta.rosetta.core.conformation.membrane.ImplicitLipidInfo method) initialize_input_poses_from_options() (pyrosetta.rosetta.core.import_pose.FullModelPoseBuilder method) initialize_input_streams() (in module pyrosetta.rosetta.protocols.stepwise.modeler.protein) initialize_input_streams_with_residue_info() (in module pyrosetta.rosetta.protocols.stepwise.modeler.protein) initialize_inputs_from_options() (pyrosetta.rosetta.core.import_pose.RNA_DeNovoSetup method) initialize_jump_sampler() (in module pyrosetta.rosetta.protocols.recces.sampler) initialize_kernel() (pyrosetta.rosetta.core.scoring.epr_deer.Simulated4PDEERTraceFactory method) initialize_modeler_scorefxn() (pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna.StepWiseRNA_PoseSelection method) initialize_movers() (pyrosetta.rosetta.protocols.docking.DockingLowResEnsemble method) initialize_native_and_align_pose() (in module pyrosetta.rosetta.core.import_pose) initialize_ncbbs() (in module pyrosetta.rosetta.core.pose.ncbb) initialize_node() (pyrosetta.rosetta.core.pack.guidance_scoreterms.buried_unsat_penalty.graph.BuriedUnsatPenaltyNode method) initialize_o2prime_pack_scorefxn() (in module pyrosetta.rosetta.protocols.stepwise.modeler) initialize_oops() (in module pyrosetta.rosetta.core.pose.ncbb) initialize_pack_scorefxn() (in module pyrosetta.rosetta.protocols.stepwise.modeler) initialize_packer() (pyrosetta.rosetta.protocols.recon_design.FindConsensusSequence method) initialize_parameters() (in module pyrosetta.rosetta.core.pose.full_model_info) (pyrosetta.rosetta.core.sequence.ProfSimScoringScheme method) initialize_pose() (pyrosetta.rosetta.protocols.features.ReportToDB method) (pyrosetta.rosetta.protocols.features.TrajectoryReportToDB method) initialize_pose_and_other_poses_from_command_line() (in module pyrosetta.rosetta.core.import_pose) initialize_pose_and_other_poses_from_options() (in module pyrosetta.rosetta.core.import_pose) initialize_pose_and_other_poses_from_options_and_input_poses() (in module pyrosetta.rosetta.core.import_pose) initialize_pose_for_rotset_creation() (pyrosetta.rosetta.core.pack.rotamer_set.RotamerSet method) (pyrosetta.rosetta.core.pack.rotamer_set.RotamerSet_ method) (pyrosetta.rosetta.core.pack.rotamer_set.RotamerSubset method) (pyrosetta.rosetta.core.pack.rotamer_set.symmetry.SymmetricRotamerSet_ method) (pyrosetta.rosetta.protocols.flexpack.rotamer_set.FlexbbRotamerSet method) initialize_pose_for_rotsets_creation() (pyrosetta.rosetta.core.pack.rotamer_set.FixbbRotamerSets method) (pyrosetta.rosetta.core.pack.rotamer_set.RotamerSets method) (pyrosetta.rosetta.core.pack.rotamer_set.RotamerSubsets method) (pyrosetta.rosetta.core.pack.rotamer_set.symmetry.SymmetricRotamerSets method) (pyrosetta.rosetta.core.pack_basic.RotamerSetsBase method) (pyrosetta.rosetta.protocols.flexpack.rotamer_set.FlexbbRotamerSets method) initialize_pose_if_empty() (pyrosetta.rosetta.protocols.stepwise.monte_carlo.mover.StepWiseMasterMover method) initialize_random_chunks() (pyrosetta.rosetta.core.import_pose.libraries.RNA_ChunkLibrary method) initialize_rdkit_random() (in module pyrosetta.rosetta.core.chemical.rdkit) initialize_rdkit_tracers() (in module pyrosetta.rosetta.core.chemical.rdkit) initialize_relevant_residues() (pyrosetta.rosetta.protocols.features.ReportToDB method) (pyrosetta.rosetta.protocols.features.TrajectoryReportToDB method) initialize_reporters() (pyrosetta.rosetta.protocols.features.ReportToDB method) (pyrosetta.rosetta.protocols.features.TrajectoryReportToDB method) initialize_residue_level_task() (pyrosetta.rosetta.core.pack.palette.CustomBaseTypePackerPalette method) (pyrosetta.rosetta.core.pack.palette.DefaultPackerPalette method) (pyrosetta.rosetta.core.pack.palette.NCAADefaultPackerPalette method) (pyrosetta.rosetta.core.pack.palette.NoDesignPackerPalette method) (pyrosetta.rosetta.core.pack.palette.PackerPalette method) initialize_residue_map_from_pose() (pyrosetta.rosetta.core.pose.reference_pose.ReferencePose method) initialize_residue_type() (pyrosetta.rosetta.core.scoring.lkball.LKBallDatabase method) initialize_resources_for_preliminary_job_nodes() (pyrosetta.rosetta.protocols.rosetta_scripts.RosettaScriptsJobQueen method) initialize_rna_chunk_library() (pyrosetta.rosetta.core.import_pose.libraries.RNA_ChunkLibrary method) initialize_rnp_aa_rna_backbone() (pyrosetta.rosetta.core.scoring.rna.RNP_LowResPotential method) initialize_rnp_base_pair() (pyrosetta.rosetta.core.scoring.rna.RNP_LowResPotential method) initialize_rnp_pair() (pyrosetta.rosetta.core.scoring.rna.RNP_LowResPotential method) initialize_rnp_pair_dist() (pyrosetta.rosetta.core.scoring.rna.RNP_LowResPairDistPotential method) initialize_rnp_stack_xy() (pyrosetta.rosetta.core.scoring.rna.RNP_LowResStackData method) initialize_rnp_vdw_parameters() (pyrosetta.rosetta.core.scoring.rna.RNA_AtomVDW method) initialize_sample_scorefxn() (in module pyrosetta.rosetta.protocols.stepwise.modeler) initialize_sampler() (in module pyrosetta.rosetta.protocols.recces.sampler) initialize_samples() (pyrosetta.rosetta.protocols.helical_bundle.BundleGridSamplerHelper method) initialize_simulation() (pyrosetta.rosetta.protocols.backrub.BackrubMover method) (pyrosetta.rosetta.protocols.backrub.BackrubSidechainMover method) (pyrosetta.rosetta.protocols.canonical_sampling.AsyncMPITemperingBase method) (pyrosetta.rosetta.protocols.canonical_sampling.BiasEnergy method) (pyrosetta.rosetta.protocols.canonical_sampling.DbTrajectoryRecorder method) (pyrosetta.rosetta.protocols.canonical_sampling.FixedTemperatureController method) (pyrosetta.rosetta.protocols.canonical_sampling.HamiltonianExchange method) (pyrosetta.rosetta.protocols.canonical_sampling.MetricRecorder method) (pyrosetta.rosetta.protocols.canonical_sampling.ParallelTempering method) (pyrosetta.rosetta.protocols.canonical_sampling.PDBTrajectoryRecorder method) (pyrosetta.rosetta.protocols.canonical_sampling.ProgressBarObserver method) (pyrosetta.rosetta.protocols.canonical_sampling.SilentTrajectoryRecorder method) (pyrosetta.rosetta.protocols.canonical_sampling.SimulatedTempering method) (pyrosetta.rosetta.protocols.canonical_sampling.TemperatureController method) (pyrosetta.rosetta.protocols.canonical_sampling.TemperingBase method) (pyrosetta.rosetta.protocols.canonical_sampling.ThermodynamicMover method) (pyrosetta.rosetta.protocols.canonical_sampling.ThermodynamicObserver method) (pyrosetta.rosetta.protocols.canonical_sampling.TrajectoryRecorder method) (pyrosetta.rosetta.protocols.canonical_sampling.TrialCounterObserver method) (pyrosetta.rosetta.protocols.canonical_sampling.WTEBiasEnergy method) (pyrosetta.rosetta.protocols.enzdes.PredesignPerturbMover method) (pyrosetta.rosetta.protocols.kinematic_closure.BalancedKicMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyDeterministicSpinMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofPerturbMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofRandomizeMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofRandomTransMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofSeqPerturbMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofSeqRandomizeMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofSeqTransMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofTransMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyPerturbMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyPerturbNoCenterMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyPerturbRandomJumpMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyRandomizeMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodySpinMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyTiltMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyTransMover method) (pyrosetta.rosetta.protocols.rigid.UniformRigidBodyMover method) (pyrosetta.rosetta.protocols.rigid.UniformSphereTransMover method) (pyrosetta.rosetta.protocols.simple_moves.BackboneMover method) (pyrosetta.rosetta.protocols.simple_moves.BBConRotMover method) (pyrosetta.rosetta.protocols.simple_moves.BBG8T3AMover method) (pyrosetta.rosetta.protocols.simple_moves.BBGaussianMover method) (pyrosetta.rosetta.protocols.simple_moves.ShearMover method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.JumpRotamerSidechainMover method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.PerturbChiSidechainMover method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.PerturbRotamerSidechainMover method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SidechainMCMover method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SidechainMover method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SidechainMoverBase method) (pyrosetta.rosetta.protocols.simple_moves.SmallMover method) (pyrosetta.rosetta.protocols.topology_broker.RigidBodyRandomTMHMover method) (pyrosetta.rosetta.utility.SimulateMPI static method) initialize_ss() (in module pyrosetta.rosetta.protocols.comparative_modeling) initialize_starting_rama_scores() (pyrosetta.rosetta.protocols.loops.loop_closure.ccd.RamaCheck1B method) (pyrosetta.rosetta.protocols.loops.loop_closure.ccd.RamaCheck2B method) (pyrosetta.rosetta.protocols.loops.loop_closure.ccd.RamaCheckBase method) initialize_stub() (in module pyrosetta.rosetta.protocols.toolbox.rigid_body) initialize_sturm() (in module pyrosetta.rosetta.numeric.kinematic_closure) initialize_tag_is_done() (in module pyrosetta.rosetta.core.io.silent) initialize_task_factory() (pyrosetta.rosetta.protocols.features.RotamerRecoveryFeatures method) initialize_task_factory_with_operations() (pyrosetta.rosetta.protocols.dna.DesignProteinBackboneAroundDNA method) (pyrosetta.rosetta.protocols.dna.DnaInterfaceMultiStateDesign method) (pyrosetta.rosetta.protocols.dna.DnaInterfacePacker method) (pyrosetta.rosetta.protocols.flxbb.FlxbbDesignPack method) (pyrosetta.rosetta.protocols.minimization_packing.PackRotamersMover method) (pyrosetta.rosetta.protocols.minimization_packing.PackRotamersMoverLazy method) (pyrosetta.rosetta.protocols.minimization_packing.SetReturningPackRotamersMover method) (pyrosetta.rosetta.protocols.minimization_packing.symmetry.SymPackRotamersMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.PrepackMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.ProteinInterfaceMultiStateDesignMover method) (pyrosetta.rosetta.protocols.testing.BenchmarkBuildRotamersMover method) initialize_task_from_entity_resfile_and_secondary_resfile() (in module pyrosetta.rosetta.protocols.pack_daemon) initialize_template_db_files() (in module pyrosetta.rosetta.protocols.tcr) initialize_template_ignore_list() (in module pyrosetta.rosetta.protocols.tcr) initialize_thermal_sampler() (in module pyrosetta.rosetta.protocols.recces.sampler) initialize_tracker() (pyrosetta.rosetta.protocols.jd3.standard.PreliminaryLarvalJobTracker method) initialize_tree_nodes_from_enzcst_io() (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.InvrotTarget method) (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.SingleResidueInvrotTarget method) initialize_typGrid() (pyrosetta.rosetta.protocols.pockets.ElectrostaticpotentialGrid method) initialize_upstream_residue() (pyrosetta.rosetta.protocols.match.downstream.LigandConformerBuilder method) (pyrosetta.rosetta.protocols.match.downstream.RigidLigandBuilder method) initialize_weights() (pyrosetta.rosetta.protocols.moves.TrialMover method) (pyrosetta.rosetta.protocols.simple_filters.EvaluatedTrialMover method) initialize_with_mcfi_list() (pyrosetta.rosetta.protocols.forge.remodel.RemodelEnzdesCstModule method) (pyrosetta.rosetta.protocols.match.MatcherTask method) (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.EnzConstraintIO method) initialize_xyz_parameters() (in module pyrosetta.rosetta.protocols.stepwise.modeler.rna.rigid_body) InitializeByBins (class in pyrosetta.rosetta.protocols.simple_moves.bin_transitions) InitializeByBinsCreator (class in pyrosetta.rosetta.protocols.simple_moves.bin_transitions) initialized() (pyrosetta.rosetta.core.chemical.mainchain_potential.MainchainScoreTable method) (pyrosetta.rosetta.core.scoring.hbonds.HBondDatabase method) (pyrosetta.rosetta.core.scoring.MembraneTopology method) (pyrosetta.rosetta.numeric.random.RandomGenerator method) (pyrosetta.rosetta.ObjexxFCL.Dimension method) (pyrosetta.rosetta.ObjexxFCL.DimensionExpression method) (pyrosetta.rosetta.ObjexxFCL.DimensionExpressionCon method) (pyrosetta.rosetta.ObjexxFCL.DimensionExpressionCube method) (pyrosetta.rosetta.ObjexxFCL.DimensionExpressionDiv method) (pyrosetta.rosetta.ObjexxFCL.DimensionExpressionMax method) (pyrosetta.rosetta.ObjexxFCL.DimensionExpressionMin method) (pyrosetta.rosetta.ObjexxFCL.DimensionExpressionMul method) (pyrosetta.rosetta.ObjexxFCL.DimensionExpressionPow method) (pyrosetta.rosetta.ObjexxFCL.DimensionExpressionRef method) (pyrosetta.rosetta.ObjexxFCL.DimensionExpressionSquare method) (pyrosetta.rosetta.ObjexxFCL.DimensionExpressionSub method) (pyrosetta.rosetta.ObjexxFCL.DimensionExpressionSum method) (pyrosetta.rosetta.ObjexxFCL.DynamicIndexRange method) (pyrosetta.rosetta.ObjexxFCL.IndexRange method) (pyrosetta.rosetta.ObjexxFCL.StaticIndexRange method) (pyrosetta.rosetta.protocols.branch_angle.BranchAngleOptimizer method) (pyrosetta.rosetta.protocols.dna.DnaInterfaceFinder method) (pyrosetta.rosetta.protocols.dna.DnaInterfacePacker method) (pyrosetta.rosetta.protocols.rbsegment_relax.RBSegment method) (pyrosetta.rosetta.protocols.rotamer_recovery.PerNativeRRReporterHuman method) InitializeExtraRotsFromCommandline (class in pyrosetta.rosetta.core.pack.task.operation) InitializeExtraRotsFromCommandlineCreator (class in pyrosetta.rosetta.core.pack.task.operation) InitializeFromCommandline (class in pyrosetta.rosetta.core.pack.task.operation) InitializeFromCommandlineCreator (class in pyrosetta.rosetta.core.pack.task.operation) InitializeFromOptionCollection (class in pyrosetta.rosetta.core.pack.task.operation) InitializeFromOptionCollectionCreator (class in pyrosetta.rosetta.core.pack.task.operation) initializer() (pyrosetta.rosetta.ObjexxFCL.FArray1D_bool_t method) (pyrosetta.rosetta.ObjexxFCL.FArray1D_char_t method) (pyrosetta.rosetta.ObjexxFCL.FArray1D_double_t method) (pyrosetta.rosetta.ObjexxFCL.FArray1D_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray1D_int_t method) (pyrosetta.rosetta.ObjexxFCL.FArray1D_ObjexxFCL_FArray1D_int_t method) (pyrosetta.rosetta.ObjexxFCL.FArray1D_std_string_t method) (pyrosetta.rosetta.ObjexxFCL.FArray1D_unsigned_long_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_bool_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_core_pack_dunbrack_BBDepNRChiSample_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_core_pack_dunbrack_BBDepScoreInterpData_1_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_core_pack_dunbrack_BBDepScoreInterpData_2_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_core_pack_dunbrack_BBDepScoreInterpData_3_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_core_pack_dunbrack_BBDepScoreInterpData_4_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_core_pack_dunbrack_BBDepScoreInterpData_5_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_core_pack_dunbrack_BBIndNRChiSample_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_core_pack_dunbrack_PackedDunbrackRotamer_1_1_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_core_pack_dunbrack_PackedDunbrackRotamer_1_2_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_core_pack_dunbrack_PackedDunbrackRotamer_1_3_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_core_pack_dunbrack_PackedDunbrackRotamer_1_4_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_core_pack_dunbrack_PackedDunbrackRotamer_1_5_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_core_pack_dunbrack_PackedDunbrackRotamer_2_1_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_core_pack_dunbrack_PackedDunbrackRotamer_2_2_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_core_pack_dunbrack_PackedDunbrackRotamer_2_3_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_core_pack_dunbrack_PackedDunbrackRotamer_2_4_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_core_pack_dunbrack_PackedDunbrackRotamer_2_5_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_core_pack_dunbrack_PackedDunbrackRotamer_3_1_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_core_pack_dunbrack_PackedDunbrackRotamer_3_2_float_t method) 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(pyrosetta.rosetta.ObjexxFCL.FArray_core_pack_dunbrack_BBDepScoreInterpData_3_t method) (pyrosetta.rosetta.ObjexxFCL.FArray_core_pack_dunbrack_BBDepScoreInterpData_4_t method) (pyrosetta.rosetta.ObjexxFCL.FArray_core_pack_dunbrack_BBDepScoreInterpData_5_t method) (pyrosetta.rosetta.ObjexxFCL.FArray_core_pack_dunbrack_BBIndNRChiSample_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray_core_pack_dunbrack_PackedDunbrackRotamer_1_1_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray_core_pack_dunbrack_PackedDunbrackRotamer_1_2_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray_core_pack_dunbrack_PackedDunbrackRotamer_1_3_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray_core_pack_dunbrack_PackedDunbrackRotamer_1_4_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray_core_pack_dunbrack_PackedDunbrackRotamer_1_5_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray_core_pack_dunbrack_PackedDunbrackRotamer_2_1_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray_core_pack_dunbrack_PackedDunbrackRotamer_2_2_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray_core_pack_dunbrack_PackedDunbrackRotamer_2_3_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray_core_pack_dunbrack_PackedDunbrackRotamer_2_4_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray_core_pack_dunbrack_PackedDunbrackRotamer_2_5_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray_core_pack_dunbrack_PackedDunbrackRotamer_3_1_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray_core_pack_dunbrack_PackedDunbrackRotamer_3_2_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray_core_pack_dunbrack_PackedDunbrackRotamer_3_3_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray_core_pack_dunbrack_PackedDunbrackRotamer_3_4_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray_core_pack_dunbrack_PackedDunbrackRotamer_3_5_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray_core_pack_dunbrack_PackedDunbrackRotamer_4_1_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray_core_pack_dunbrack_PackedDunbrackRotamer_4_2_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray_core_pack_dunbrack_PackedDunbrackRotamer_4_3_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray_core_pack_dunbrack_PackedDunbrackRotamer_4_4_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray_core_pack_dunbrack_PackedDunbrackRotamer_4_5_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray_core_pack_dunbrack_PackedDunbrackRotamer_5_1_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray_core_pack_dunbrack_PackedDunbrackRotamer_5_2_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray_core_pack_dunbrack_PackedDunbrackRotamer_5_3_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray_core_pack_dunbrack_PackedDunbrackRotamer_5_4_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray_core_pack_dunbrack_PackedDunbrackRotamer_5_5_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray_double_t method) (pyrosetta.rosetta.ObjexxFCL.FArray_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray_int_t method) (pyrosetta.rosetta.ObjexxFCL.FArray_numeric_xyzVector_double_t method) (pyrosetta.rosetta.ObjexxFCL.FArray_ObjexxFCL_FArray1D_int_t method) (pyrosetta.rosetta.ObjexxFCL.FArray_ObjexxFCL_FArray2D_float__star__t method) (pyrosetta.rosetta.ObjexxFCL.FArray_ObjexxFCL_ubyte_t method) (pyrosetta.rosetta.ObjexxFCL.FArray_std_complex_double_t method) (pyrosetta.rosetta.ObjexxFCL.FArray_std_string_t method) (pyrosetta.rosetta.ObjexxFCL.FArray_std_vector_unsigned_long_std_allocator_unsigned_long_t method) (pyrosetta.rosetta.ObjexxFCL.FArray_unsigned_char_t method) (pyrosetta.rosetta.ObjexxFCL.FArray_unsigned_long_t method) (pyrosetta.rosetta.ObjexxFCL.FArray_utility_vector1_core_pack_dunbrack_cenrot_CentroidRotamerSampleData_std_allocator_core_pack_dunbrack_cenrot_CentroidRotamerSampleData_t method) (pyrosetta.rosetta.ObjexxFCL.FArray_utility_vector1_double_std_allocator_double_t method) (pyrosetta.rosetta.ObjexxFCL.FArray_utility_vector1_numeric_xyzVector_double_std_allocator_numeric_xyzVector_double_t method) (pyrosetta.rosetta.ObjexxFCL.FArray_utility_vector1_unsigned_int_std_allocator_unsigned_int_t method) initializer_clear() (pyrosetta.rosetta.ObjexxFCL.FArray1D_bool_t method) (pyrosetta.rosetta.ObjexxFCL.FArray1D_char_t method) (pyrosetta.rosetta.ObjexxFCL.FArray1D_double_t method) (pyrosetta.rosetta.ObjexxFCL.FArray1D_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray1D_int_t method) (pyrosetta.rosetta.ObjexxFCL.FArray1D_ObjexxFCL_FArray1D_int_t method) (pyrosetta.rosetta.ObjexxFCL.FArray1D_std_string_t method) (pyrosetta.rosetta.ObjexxFCL.FArray1D_unsigned_long_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_bool_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_core_pack_dunbrack_BBDepNRChiSample_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_core_pack_dunbrack_BBDepScoreInterpData_1_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_core_pack_dunbrack_BBDepScoreInterpData_2_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_core_pack_dunbrack_BBDepScoreInterpData_3_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_core_pack_dunbrack_BBDepScoreInterpData_4_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_core_pack_dunbrack_BBDepScoreInterpData_5_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_core_pack_dunbrack_BBIndNRChiSample_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_core_pack_dunbrack_PackedDunbrackRotamer_1_1_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_core_pack_dunbrack_PackedDunbrackRotamer_1_2_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_core_pack_dunbrack_PackedDunbrackRotamer_1_3_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_core_pack_dunbrack_PackedDunbrackRotamer_1_4_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_core_pack_dunbrack_PackedDunbrackRotamer_1_5_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_core_pack_dunbrack_PackedDunbrackRotamer_2_1_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_core_pack_dunbrack_PackedDunbrackRotamer_2_2_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_core_pack_dunbrack_PackedDunbrackRotamer_2_3_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_core_pack_dunbrack_PackedDunbrackRotamer_2_4_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_core_pack_dunbrack_PackedDunbrackRotamer_2_5_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_core_pack_dunbrack_PackedDunbrackRotamer_3_1_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_core_pack_dunbrack_PackedDunbrackRotamer_3_2_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_core_pack_dunbrack_PackedDunbrackRotamer_3_3_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_core_pack_dunbrack_PackedDunbrackRotamer_3_4_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_core_pack_dunbrack_PackedDunbrackRotamer_3_5_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_core_pack_dunbrack_PackedDunbrackRotamer_4_1_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_core_pack_dunbrack_PackedDunbrackRotamer_4_2_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_core_pack_dunbrack_PackedDunbrackRotamer_4_3_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_core_pack_dunbrack_PackedDunbrackRotamer_4_4_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_core_pack_dunbrack_PackedDunbrackRotamer_4_5_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_core_pack_dunbrack_PackedDunbrackRotamer_5_1_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_core_pack_dunbrack_PackedDunbrackRotamer_5_2_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_core_pack_dunbrack_PackedDunbrackRotamer_5_3_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_core_pack_dunbrack_PackedDunbrackRotamer_5_4_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_core_pack_dunbrack_PackedDunbrackRotamer_5_5_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_double_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_int_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_numeric_xyzVector_double_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_ObjexxFCL_FArray2D_float__star__t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_ObjexxFCL_ubyte_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_std_string_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_unsigned_char_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_unsigned_long_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_utility_vector1_core_pack_dunbrack_cenrot_CentroidRotamerSampleData_std_allocator_core_pack_dunbrack_cenrot_CentroidRotamerSampleData_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_utility_vector1_double_std_allocator_double_t method) (pyrosetta.rosetta.ObjexxFCL.FArray3D_core_pack_dunbrack_BBDepScoreInterpData_1_t method) (pyrosetta.rosetta.ObjexxFCL.FArray3D_core_pack_dunbrack_BBDepScoreInterpData_2_t method) (pyrosetta.rosetta.ObjexxFCL.FArray3D_core_pack_dunbrack_BBDepScoreInterpData_3_t method) (pyrosetta.rosetta.ObjexxFCL.FArray3D_core_pack_dunbrack_BBDepScoreInterpData_4_t method) (pyrosetta.rosetta.ObjexxFCL.FArray3D_core_pack_dunbrack_BBDepScoreInterpData_5_t method) (pyrosetta.rosetta.ObjexxFCL.FArray3D_double_t method) (pyrosetta.rosetta.ObjexxFCL.FArray3D_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray3D_int_t method) (pyrosetta.rosetta.ObjexxFCL.FArray3D_std_complex_double_t method) (pyrosetta.rosetta.ObjexxFCL.FArray3D_std_vector_unsigned_long_std_allocator_unsigned_long_t method) (pyrosetta.rosetta.ObjexxFCL.FArray3D_unsigned_char_t method) (pyrosetta.rosetta.ObjexxFCL.FArray3D_unsigned_long_t method) (pyrosetta.rosetta.ObjexxFCL.FArray3D_utility_vector1_double_std_allocator_double_t method) (pyrosetta.rosetta.ObjexxFCL.FArray3D_utility_vector1_numeric_xyzVector_double_std_allocator_numeric_xyzVector_double_t method) (pyrosetta.rosetta.ObjexxFCL.FArray3D_utility_vector1_unsigned_int_std_allocator_unsigned_int_t method) (pyrosetta.rosetta.ObjexxFCL.FArray4D_double_t method) (pyrosetta.rosetta.ObjexxFCL.FArray4D_int_t method) (pyrosetta.rosetta.ObjexxFCL.FArray4D_unsigned_char_t method) (pyrosetta.rosetta.ObjexxFCL.FArray5D_double_t method) (pyrosetta.rosetta.ObjexxFCL.FArray5D_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray5D_int_t method) InitializerSentinel (class in pyrosetta.rosetta.ObjexxFCL.internal) initials() (pyrosetta.rosetta.basic.citation_manager.AuthorNames method) initiate_voxel() (pyrosetta.rosetta.protocols.scoring.methods.TargetClashEnergy method) initOrbitalShift() (pyrosetta.rosetta.protocols.sparta.PDB method) initRef() (pyrosetta.rosetta.protocols.cluster.calibur.Clustering method) Inline_File_Provider (class in pyrosetta.rosetta.utility) Inline_File_Provider_Hook (class in pyrosetta.rosetta.utility) inName (pyrosetta.rosetta.protocols.sparta.Sparta.SpartaLib property) inNames (pyrosetta.rosetta.protocols.sparta.Sparta.SpartaLib property) inner_cycles() (pyrosetta.rosetta.protocols.loops.loop_mover.refine.LoopMover_Refine_CCD method) inner_job (pyrosetta.rosetta.protocols.jd3.chunk_library.ChunkLibraryPreliminaryLarvalJob property) (pyrosetta.rosetta.protocols.jd3.full_model.FullModelPreliminaryLarvalJob property) (pyrosetta.rosetta.protocols.jd3.standard.PreliminaryLarvalJob property) inner_job() (pyrosetta.rosetta.protocols.jd2.Job method) (pyrosetta.rosetta.protocols.jd2.MultiThreadingJob method) (pyrosetta.rosetta.protocols.jd3.LarvalJob method) (pyrosetta.rosetta.protocols.make_rot_lib.MakeRotLibJob method) inner_job_nonconst() (pyrosetta.rosetta.protocols.jd2.Job method) (pyrosetta.rosetta.protocols.jd2.MultiThreadingJob method) (pyrosetta.rosetta.protocols.make_rot_lib.MakeRotLibJob method) inner_product() (pyrosetta.rosetta.core.scoring.sc.Atom method) (pyrosetta.rosetta.numeric.xyzTriple_unsigned_long_t method) (pyrosetta.rosetta.numeric.xyzVector_double_t method) (pyrosetta.rosetta.numeric.xyzVector_float_t method) (pyrosetta.rosetta.numeric.xyzVector_int_t method) (pyrosetta.rosetta.numeric.xyzVector_unsigned_long_t method) InnerJob (class in pyrosetta.rosetta.protocols.jd2) InnerLarvalJob (class in pyrosetta.rosetta.protocols.jd3) InnerMultiThreadingJob (class in pyrosetta.rosetta.protocols.jd2) inout (pyrosetta.rosetta.core.scoring.atomic_depth.volumepixel property) inPDB (pyrosetta.rosetta.protocols.sparta.Sparta.SpartaLib property) inplace_product() (in module pyrosetta.rosetta.numeric) inplace_transpose_product() (in module pyrosetta.rosetta.numeric) inprogress() (pyrosetta.rosetta.protocols.jobdist.AtomTreeDiffJobDistributor method) (pyrosetta.rosetta.protocols.jobdist.BaseJobDistributor method) (pyrosetta.rosetta.protocols.jobdist.PlainPdbJobDistributor method) (pyrosetta.rosetta.protocols.jobdist.PlainRawJobDistributor method) (pyrosetta.rosetta.protocols.jobdist.PlainSilentFileJobDistributor method) input_code (pyrosetta.rosetta.protocols.sparta.ANN property) input_conformation() (pyrosetta.rosetta.protocols.match.upstream.OriginalBackboneBuildPoint method) INPUT_DOMAIN (pyrosetta.rosetta.core.pose.full_model_info.FullModelParameterType attribute) input_domain_map() (pyrosetta.rosetta.core.pose.full_model_info.FullModelInfo method) input_etable() (pyrosetta.rosetta.core.scoring.etable.Etable method) (pyrosetta.rosetta.core.scoring.etable.MembEtable method) INPUT_FILE_TYPE (class in pyrosetta.rosetta.protocols.cluster.calibur) input_filename() (pyrosetta.rosetta.core.io.silent.SilentFileData method) input_job_result_indices() (pyrosetta.rosetta.protocols.jd3.chunk_library.ChunkLibraryInnerLarvalJob method) (pyrosetta.rosetta.protocols.jd3.full_model.FullModelInnerLarvalJob method) (pyrosetta.rosetta.protocols.jd3.InnerLarvalJob method) (pyrosetta.rosetta.protocols.jd3.LarvalJob method) (pyrosetta.rosetta.protocols.jd3.standard.StandardInnerLarvalJob method) input_legrand_sasa_dats() (in module pyrosetta.rosetta.core.scoring.sasa) input_pdb_files_from_command_line() (in module pyrosetta.rosetta.protocols.jd2) input_pose_deallocation_msg (pyrosetta.rosetta.protocols.jd3.deallocation.deallocation_msg_type attribute) input_pose_id (pyrosetta.rosetta.protocols.multistage_rosetta_scripts.ParsedTagCache property) input_pose_no_longer_needed() (pyrosetta.rosetta.protocols.jd3.standard.PreliminaryLarvalJobTracker method) input_res() (pyrosetta.rosetta.core.import_pose.options.RNA_DeNovoProtocolOptions method) (pyrosetta.rosetta.core.import_pose.options.RNA_FragmentMonteCarloOptions method) (pyrosetta.rosetta.protocols.stepwise.modeler.protein.InputStreamWithResidueInfo method) input_res_initialize() (pyrosetta.rosetta.core.import_pose.options.RNA_DeNovoProtocolOptions method) (pyrosetta.rosetta.core.import_pose.options.RNA_FragmentMonteCarloOptions method) input_res_vectors() (pyrosetta.rosetta.protocols.stepwise.modeler.working_parameters.StepWiseWorkingParameters method) input_sasa_dats() (in module pyrosetta.rosetta.core.scoring) (in module pyrosetta.rosetta.core.scoring.packstat.old) input_scan_res() (pyrosetta.rosetta.protocols.magnesium.MgScanner method) (pyrosetta.rosetta.protocols.magnesium.SampleGrid method) input_set() (pyrosetta.rosetta.core.select.residue_selector.BondedResidueSelector method) input_set_defined() (pyrosetta.rosetta.core.select.residue_selector.BondedResidueSelector method) input_set_selector() (pyrosetta.rosetta.core.select.residue_selector.BondedResidueSelector method) input_set_selector_defined() (pyrosetta.rosetta.core.select.residue_selector.BondedResidueSelector method) input_set_string() (pyrosetta.rosetta.core.select.residue_selector.BondedResidueSelector method) input_source() (pyrosetta.rosetta.protocols.comparative_modeling.GenericJobInputter method) (pyrosetta.rosetta.protocols.comparative_modeling.ThreadingJobInputter method) (pyrosetta.rosetta.protocols.enzdes.EnzdesJobInputter method) (pyrosetta.rosetta.protocols.features.DatabaseJobInputter method) (pyrosetta.rosetta.protocols.jd2.AtomTreeDiffJobInputter method) (pyrosetta.rosetta.protocols.jd2.BatchJobInputter method) (pyrosetta.rosetta.protocols.jd2.EmptyPoseJobInputter method) (pyrosetta.rosetta.protocols.jd2.EnsembleJobInputter method) (pyrosetta.rosetta.protocols.jd2.JobInputter method) (pyrosetta.rosetta.protocols.jd2.LargeNstructJobInputter method) (pyrosetta.rosetta.protocols.jd2.LazySilentFileJobInputter method) (pyrosetta.rosetta.protocols.jd2.PDBJobInputter method) (pyrosetta.rosetta.protocols.jd2.PoseInputStreamJobInputter method) (pyrosetta.rosetta.protocols.jd2.ScreeningJobInputter method) (pyrosetta.rosetta.protocols.jd2.SerializedPoseJobInputter method) (pyrosetta.rosetta.protocols.jd2.SilentFileJobInputter method) (pyrosetta.rosetta.protocols.jd3.chunk_library.ChunkLibraryInnerLarvalJob method) (pyrosetta.rosetta.protocols.jd3.full_model.FullModelInnerLarvalJob method) (pyrosetta.rosetta.protocols.jd3.InnerLarvalJob method) (pyrosetta.rosetta.protocols.jd3.standard.StandardInnerLarvalJob method) (pyrosetta.rosetta.protocols.make_rot_lib.MakeRotLibJobInputter method) (pyrosetta.rosetta.protocols.protein_interface_design.ParserJobInputter method) input_source_cop() (pyrosetta.rosetta.protocols.jd3.chunk_library.ChunkLibraryInnerLarvalJob method) (pyrosetta.rosetta.protocols.jd3.full_model.FullModelInnerLarvalJob method) (pyrosetta.rosetta.protocols.jd3.InnerLarvalJob method) (pyrosetta.rosetta.protocols.jd3.standard.StandardInnerLarvalJob method) input_source_for_job() (pyrosetta.rosetta.protocols.jd3.JobGenealogist method) input_source_id() (pyrosetta.rosetta.protocols.jd3.JGJobNode method) INPUT_STREAM (pyrosetta.rosetta.protocols.toolbox.SamplerPlusPlusType attribute) input_string (pyrosetta.rosetta.core.pose.rna.VDW_RepScreenInfo property) input_stub_atom0() (pyrosetta.rosetta.core.kinematics.tree.Atom method) (pyrosetta.rosetta.core.kinematics.tree.Atom_ method) (pyrosetta.rosetta.core.kinematics.tree.BondedAtom method) (pyrosetta.rosetta.core.kinematics.tree.JumpAtom method) input_stub_atom0_id() (pyrosetta.rosetta.core.kinematics.tree.Atom method) (pyrosetta.rosetta.core.kinematics.tree.Atom_ method) (pyrosetta.rosetta.core.kinematics.tree.BondedAtom method) (pyrosetta.rosetta.core.kinematics.tree.JumpAtom method) input_stub_atom1() (pyrosetta.rosetta.core.kinematics.tree.Atom method) (pyrosetta.rosetta.core.kinematics.tree.Atom_ method) (pyrosetta.rosetta.core.kinematics.tree.BondedAtom method) (pyrosetta.rosetta.core.kinematics.tree.JumpAtom method) input_stub_atom1_id() (pyrosetta.rosetta.core.kinematics.tree.Atom method) (pyrosetta.rosetta.core.kinematics.tree.Atom_ method) (pyrosetta.rosetta.core.kinematics.tree.BondedAtom method) (pyrosetta.rosetta.core.kinematics.tree.JumpAtom method) input_stub_atom2() (pyrosetta.rosetta.core.kinematics.tree.Atom method) (pyrosetta.rosetta.core.kinematics.tree.Atom_ method) (pyrosetta.rosetta.core.kinematics.tree.BondedAtom method) (pyrosetta.rosetta.core.kinematics.tree.JumpAtom method) input_stub_atom2_id() (pyrosetta.rosetta.core.kinematics.tree.Atom method) (pyrosetta.rosetta.core.kinematics.tree.Atom_ method) (pyrosetta.rosetta.core.kinematics.tree.BondedAtom method) (pyrosetta.rosetta.core.kinematics.tree.JumpAtom method) input_stub_atom3() (pyrosetta.rosetta.core.kinematics.tree.Atom method) (pyrosetta.rosetta.core.kinematics.tree.Atom_ method) (pyrosetta.rosetta.core.kinematics.tree.BondedAtom method) (pyrosetta.rosetta.core.kinematics.tree.JumpAtom method) input_stub_atom3_id() (pyrosetta.rosetta.core.kinematics.tree.Atom method) (pyrosetta.rosetta.core.kinematics.tree.Atom_ method) (pyrosetta.rosetta.core.kinematics.tree.BondedAtom method) (pyrosetta.rosetta.core.kinematics.tree.JumpAtom method) input_tag() (pyrosetta.rosetta.protocols.comparative_modeling.ThreadingJob method) (pyrosetta.rosetta.protocols.jd2.InnerJob method) (pyrosetta.rosetta.protocols.jd2.InnerMultiThreadingJob method) (pyrosetta.rosetta.protocols.jd2.Job method) (pyrosetta.rosetta.protocols.jd2.MultiThreadingJob method) (pyrosetta.rosetta.protocols.jd3.chunk_library.ChunkLibraryInnerLarvalJob method) (pyrosetta.rosetta.protocols.jd3.chunk_library_inputters.ChunkLibraryInputSource method) (pyrosetta.rosetta.protocols.jd3.full_model.FullModelInnerLarvalJob method) (pyrosetta.rosetta.protocols.jd3.full_model_inputters.FullModelInputSource method) (pyrosetta.rosetta.protocols.jd3.InnerLarvalJob method) (pyrosetta.rosetta.protocols.jd3.InputSource method) (pyrosetta.rosetta.protocols.jd3.LarvalJob method) (pyrosetta.rosetta.protocols.jd3.pose_inputters.PoseInputSource method) (pyrosetta.rosetta.protocols.jd3.standard.StandardInnerLarvalJob method) (pyrosetta.rosetta.protocols.jobdist.BasicJob method) (pyrosetta.rosetta.protocols.make_rot_lib.MakeRotLibJob method) InputPoseDeallocationMessage (class in pyrosetta.rosetta.protocols.jd3.deallocation) InputSource (class in pyrosetta.rosetta.protocols.jd3) InputStreamStepWiseSampler (class in pyrosetta.rosetta.protocols.stepwise.sampler.input_streams) InputStreamWithResidueInfo (class in pyrosetta.rosetta.protocols.stepwise.modeler.protein) insCodes_ (pyrosetta.rosetta.protocols.pdbinfo_manipulations.SequenceSpecification property) insert() (pyrosetta.rosetta.basic.datacache.WriteableCacheableMap method) (pyrosetta.rosetta.core.io.Remarks method) (pyrosetta.rosetta.core.pose.PDBPoseMap method) (pyrosetta.rosetta.core.scoring.constraints.ResidueConstraints method) (pyrosetta.rosetta.core.scoring.motif.Xfrag method) (pyrosetta.rosetta.core.scoring.saxs.DistanceHistogram method) (pyrosetta.rosetta.numeric.DiscreteIntervalEncodingTree_unsigned_long_t method) (pyrosetta.rosetta.numeric.kdtree.KDPointList method) (pyrosetta.rosetta.protocols.comparative_modeling.AlignmentSet method) (pyrosetta.rosetta.protocols.denovo_design.components.SegmentPairSet method) (pyrosetta.rosetta.protocols.frag_picker.BoundedCollector_CompareTotalScore method) (pyrosetta.rosetta.protocols.frag_picker.BoundedCollector_protocols_frag_picker_CompareTotalScore_t method) (pyrosetta.rosetta.protocols.frag_picker.CandidatesCollector method) (pyrosetta.rosetta.protocols.frag_picker.GrabAllCollector method) (pyrosetta.rosetta.protocols.frag_picker.quota.ABEGO_SS_Pool method) (pyrosetta.rosetta.protocols.frag_picker.quota.QuotaCollector method) (pyrosetta.rosetta.protocols.frag_picker.quota.QuotaPool method) (pyrosetta.rosetta.protocols.frag_picker.quota.SecondaryStructurePool method) (pyrosetta.rosetta.protocols.frag_picker.scores.AdaptiveScoreHistogram method) (pyrosetta.rosetta.protocols.frags.TorsionFragment method) (pyrosetta.rosetta.protocols.jd3.dag_node_managers.NodeManagerStorageMatrix method) (pyrosetta.rosetta.protocols.legacy_sewing.Hasher method) (pyrosetta.rosetta.protocols.match.upstream.OriginalBackboneBuildPoint method) (pyrosetta.rosetta.protocols.match.upstream.ProteinBackboneBuildPoint method) (pyrosetta.rosetta.protocols.match.upstream.ScaffoldBuildPoint method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.PlacementAuctionMover method) (pyrosetta.rosetta.std.set_core_chemical_gasteiger_GasteigerAtomTypeData_AtomicOrbitalTypes_t method) (pyrosetta.rosetta.std.set_core_id_DOF_ID_t method) (pyrosetta.rosetta.std.set_core_id_PartialAtomID_t method) (pyrosetta.rosetta.std.set_double_t method) (pyrosetta.rosetta.std.set_int_t method) (pyrosetta.rosetta.std.set_std_pair_std_string_std_string_t method) (pyrosetta.rosetta.std.set_std_pair_unsigned_long_unsigned_long_t method) (pyrosetta.rosetta.std.set_std_set_unsigned_long_t method) (pyrosetta.rosetta.std.set_std_shared_ptr_protocols_environment_ClientMover_t method) (pyrosetta.rosetta.std.set_std_string_t method) (pyrosetta.rosetta.std.set_unsigned_long_t method) (pyrosetta.rosetta.std.unordered_map_basic_datacache_ResRotPair_float_basic_datacache_ResRotPairHasher_std_equal_to_basic_datacache_ResRotPair_std_allocator_std_pair_const_basic_datacache_ResRotPair_float_t method) (pyrosetta.rosetta.std.unordered_map_std_pair_char_char_int_core_sequence_CharPairHash_std_equal_to_std_pair_char_char_std_allocator_std_pair_const_std_pair_char_char_int_t method) (pyrosetta.rosetta.std.unordered_map_unsigned_long_numeric_MathMatrix_float_t method) (pyrosetta.rosetta.std.vector_core_io_AtomInformation method) (pyrosetta.rosetta.std.vector_core_io_RemarkInfo method) (pyrosetta.rosetta.std.vector_core_pose_Pose method) (pyrosetta.rosetta.std.vector_core_scoring_hbonds_graph_HBondInfo method) (pyrosetta.rosetta.std.vector_core_scoring_sc__DOT method) (pyrosetta.rosetta.std.vector_core_scoring_sc_Atom method) (pyrosetta.rosetta.std.vector_double method) (pyrosetta.rosetta.std.vector_float method) (pyrosetta.rosetta.std.vector_int method) (pyrosetta.rosetta.std.vector_numeric_xyzMatrix_double_t method) (pyrosetta.rosetta.std.vector_numeric_xyzVector_double_t method) (pyrosetta.rosetta.std.vector_protocols_cluster_Cluster method) (pyrosetta.rosetta.std.vector_protocols_motif_grafting_movers_MotifMatch method) (pyrosetta.rosetta.std.vector_RDGeom_Point3D method) (pyrosetta.rosetta.std.vector_RDKit_Dict_Pair method) (pyrosetta.rosetta.std.vector_std_list_std_shared_ptr_const_core_conformation_Residue_t method) (pyrosetta.rosetta.std.vector_std_map_std_string_core_io_pdb_Field_std_less_std_string_std_allocator_std_pair_const_std_string_core_io_pdb_Field_t method) (pyrosetta.rosetta.std.vector_std_map_unsigned_long_unsigned_long_std_less_unsigned_long_std_allocator_std_pair_const_unsigned_long_unsigned_long_t method) (pyrosetta.rosetta.std.vector_std_pair_std_shared_ptr_protocols_filters_Filter_protocols_filters_boolean_operations_t method) (pyrosetta.rosetta.std.vector_std_pair_unsigned_long_unsigned_long_t method) (pyrosetta.rosetta.std.vector_std_set_unsigned_long_t method) (pyrosetta.rosetta.std.vector_std_shared_ptr_const_core_conformation_Residue_t method) (pyrosetta.rosetta.std.vector_std_shared_ptr_core_chemical_Orbital_t method) (pyrosetta.rosetta.std.vector_std_shared_ptr_core_fragment_FragSet_t method) (pyrosetta.rosetta.std.vector_std_shared_ptr_core_io_silent_SilentStruct_t method) (pyrosetta.rosetta.std.vector_std_shared_ptr_core_pose_Pose_t method) (pyrosetta.rosetta.std.vector_std_shared_ptr_protocols_cluster_calibur_Stru_t method) (pyrosetta.rosetta.std.vector_std_shared_ptr_protocols_hbnet_HBondNetStruct_t method) (pyrosetta.rosetta.std.vector_std_shared_ptr_std_list_std_shared_ptr_const_utility_tag_Tag_t method) (pyrosetta.rosetta.std.vector_std_string method) (pyrosetta.rosetta.std.vector_std_vector_double_t method) (pyrosetta.rosetta.std.vector_std_vector_int_t method) (pyrosetta.rosetta.std.vector_std_vector_std_string_t method) (pyrosetta.rosetta.std.vector_std_vector_std_vector_double_t method) (pyrosetta.rosetta.std.vector_std_vector_unsigned_long_t method) (pyrosetta.rosetta.std.vector_unsigned_int method) (pyrosetta.rosetta.std.vector_unsigned_long method) (pyrosetta.rosetta.std.vector_utility_file_FileName method) (pyrosetta.rosetta.std.vector_utility_json_spirit_Pair_impl_utility_json_spirit_Config_vector_std_string_t method) (pyrosetta.rosetta.std.vector_utility_json_spirit_Value_impl_utility_json_spirit_Config_map_std_string_t method) (pyrosetta.rosetta.std.vector_utility_json_spirit_Value_impl_utility_json_spirit_Config_vector_std_string_t method) (pyrosetta.rosetta.std.vector_utility_signals_Link method) (pyrosetta.rosetta.std.vector_utility_vector1_double_std_allocator_double_t method) (pyrosetta.rosetta.std.vector_utility_vector1_protocols_mean_field_AAProb_std_allocator_protocols_mean_field_AAProb_t method) (pyrosetta.rosetta.std.vector_utility_vector1_protocols_mean_field_RotProb_std_allocator_protocols_mean_field_RotProb_t method) (pyrosetta.rosetta.std.vector_utility_vector1_std_shared_ptr_const_protocols_denovo_design_components_Segment_std_allocator_std_shared_ptr_const_protocols_denovo_design_components_Segment_t method) (pyrosetta.rosetta.utility.graph.DirectedEdgeList method) (pyrosetta.rosetta.utility.graph.EdgeList method) insert_after() (pyrosetta.rosetta.utility.graph.NegSpaceElement_double_t method) insert_aligned_residue() (pyrosetta.rosetta.core.id.SequenceMapping method) (pyrosetta.rosetta.core.sequence.DerivedSequenceMapping method) insert_aligned_residue_safe() (pyrosetta.rosetta.core.id.SequenceMapping method) (pyrosetta.rosetta.core.sequence.DerivedSequenceMapping method) insert_atom() (pyrosetta.rosetta.core.kinematics.tree.Atom method) (pyrosetta.rosetta.core.kinematics.tree.Atom_ method) (pyrosetta.rosetta.core.kinematics.tree.BondedAtom method) (pyrosetta.rosetta.core.kinematics.tree.JumpAtom method) insert_atoms_defining_dof() (pyrosetta.rosetta.core.pack.dunbrack.MainchainTorsionReporter method) (pyrosetta.rosetta.core.pack.dunbrack.PeptideTorsionReporter method) (pyrosetta.rosetta.core.pack.dunbrack.PeptoidGeneralDOFReporter method) (pyrosetta.rosetta.core.pack.dunbrack.PeptoidOmegaReporter method) (pyrosetta.rosetta.core.pack.dunbrack.ResidueDOFReporter method) insert_cdr_into_antibody() (in module pyrosetta.rosetta.protocols.antibody.design) insert_chain_ending() (pyrosetta.rosetta.core.conformation.Conformation method) (pyrosetta.rosetta.core.conformation.symmetry.MirrorSymmetricConformation method) (pyrosetta.rosetta.core.conformation.symmetry.SymmetricConformation method) (pyrosetta.rosetta.protocols.environment.ProtectedConformation method) insert_char() (pyrosetta.rosetta.core.sequence.ChemicalShiftSequence method) (pyrosetta.rosetta.core.sequence.CompositeSequence method) (pyrosetta.rosetta.core.sequence.Sequence method) (pyrosetta.rosetta.core.sequence.SequenceCoupling method) (pyrosetta.rosetta.core.sequence.SequenceProfile method) insert_chunk_into_pose() (pyrosetta.rosetta.core.import_pose.libraries.ChunkSet method) (pyrosetta.rosetta.core.import_pose.libraries.RNA_ChunkLibrary method) insert_conformation_by_jump() (pyrosetta.rosetta.core.conformation.Conformation method) (pyrosetta.rosetta.core.conformation.symmetry.MirrorSymmetricConformation method) (pyrosetta.rosetta.core.conformation.symmetry.SymmetricConformation method) (pyrosetta.rosetta.protocols.environment.ProtectedConformation method) insert_connected_segment() (pyrosetta.rosetta.protocols.legacy_sewing.SegmentGraph method) insert_connection_scheme() (pyrosetta.rosetta.protocols.forge.build.SegmentInsert method) insert_cut() (pyrosetta.rosetta.core.environment.FoldTreeSketch method) insert_data() (pyrosetta.rosetta.numeric.histograms.TwoDHistogram_unsigned_long_long_t method) insert_dssp_ss_into_pose() (pyrosetta.rosetta.core.scoring.dssp.Dssp method) insert_edge_ss_into_pose() (pyrosetta.rosetta.core.scoring.dssp.Dssp method) insert_fold_tree_by_jump() (pyrosetta.rosetta.core.kinematics.FoldTree method) insert_fragment() (in module pyrosetta.rosetta.protocols.frags) (pyrosetta.rosetta.core.fragment.rna.FullAtomRNA_Fragments method) (pyrosetta.rosetta.core.fragment.rna.RNA_Fragments method) (pyrosetta.rosetta.protocols.frags.SingleResidueTorsionFragmentLibrary method) (pyrosetta.rosetta.protocols.rna.denovo.coarse.CoarseRNA_Fragments method) INSERT_FRAGS (pyrosetta.rosetta.basic.ProfTag attribute) insert_gap() (pyrosetta.rosetta.core.sequence.ChemicalShiftSequence method) (pyrosetta.rosetta.core.sequence.CompositeSequence method) (pyrosetta.rosetta.core.sequence.Sequence method) (pyrosetta.rosetta.core.sequence.SequenceCoupling method) (pyrosetta.rosetta.core.sequence.SequenceProfile method) insert_hbond_dehydron_row() (pyrosetta.rosetta.protocols.features.HBondFeatures method) insert_hbond_geom_coords() (pyrosetta.rosetta.protocols.features.HBondFeatures method) insert_hbond_lennard_jones_row() (pyrosetta.rosetta.protocols.features.HBondFeatures method) insert_hit() (pyrosetta.rosetta.protocols.match.HitHasher method) insert_hit_geometry() (pyrosetta.rosetta.protocols.match.OccupiedSpaceHash method) insert_ideal_bonds_at_polymer_junction() (in module pyrosetta.rosetta.core.conformation) insert_ideal_geometry_at_polymer_bond() (pyrosetta.rosetta.core.conformation.Conformation method) (pyrosetta.rosetta.core.conformation.symmetry.MirrorSymmetricConformation method) (pyrosetta.rosetta.core.conformation.symmetry.SymmetricConformation method) (pyrosetta.rosetta.protocols.environment.ProtectedConformation method) insert_ideal_geometry_at_residue_connection() (pyrosetta.rosetta.core.conformation.Conformation method) (pyrosetta.rosetta.core.conformation.symmetry.MirrorSymmetricConformation method) (pyrosetta.rosetta.core.conformation.symmetry.SymmetricConformation method) (pyrosetta.rosetta.protocols.environment.ProtectedConformation method) insert_ideal_mainchain_bonds() (in module pyrosetta.rosetta.core.conformation) insert_jump() (pyrosetta.rosetta.core.environment.FoldTreeSketch method) insert_loop_at_index() (pyrosetta.rosetta.protocols.loops.LoopsFileData method) insert_map() (pyrosetta.rosetta.protocols.simple_moves.ClassicFragmentMover method) (pyrosetta.rosetta.protocols.simple_moves.FragmentMover method) (pyrosetta.rosetta.protocols.simple_moves.LoggedFragmentMover method) (pyrosetta.rosetta.protocols.simple_moves.ResTypeFragmentMover method) (pyrosetta.rosetta.protocols.simple_moves.SmoothFragmentMover method) (pyrosetta.rosetta.protocols.simple_moves.SmoothSymmetricFragmentMover method) (pyrosetta.rosetta.protocols.simple_moves.SymmetricFragmentMover method) (pyrosetta.rosetta.protocols.simple_moves.WobbleMover method) insert_match_into_pose() (pyrosetta.rosetta.protocols.match.output.PoseMatchOutputWriter method) insert_observer() (pyrosetta.rosetta.ObjexxFCL.Dimension method) (pyrosetta.rosetta.ObjexxFCL.DimensionExpression method) (pyrosetta.rosetta.ObjexxFCL.DimensionExpressionCon method) (pyrosetta.rosetta.ObjexxFCL.DimensionExpressionCube method) (pyrosetta.rosetta.ObjexxFCL.DimensionExpressionDiv method) (pyrosetta.rosetta.ObjexxFCL.DimensionExpressionMax method) (pyrosetta.rosetta.ObjexxFCL.DimensionExpressionMin method) (pyrosetta.rosetta.ObjexxFCL.DimensionExpressionMul method) (pyrosetta.rosetta.ObjexxFCL.DimensionExpressionPow method) (pyrosetta.rosetta.ObjexxFCL.DimensionExpressionRef method) (pyrosetta.rosetta.ObjexxFCL.DimensionExpressionSquare method) (pyrosetta.rosetta.ObjexxFCL.DimensionExpressionSub method) (pyrosetta.rosetta.ObjexxFCL.DimensionExpressionSum method) (pyrosetta.rosetta.ObjexxFCL.DynamicIndexRange method) (pyrosetta.rosetta.ObjexxFCL.FArray1D_bool_t method) (pyrosetta.rosetta.ObjexxFCL.FArray1D_char_t method) (pyrosetta.rosetta.ObjexxFCL.FArray1D_double_t method) (pyrosetta.rosetta.ObjexxFCL.FArray1D_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray1D_int_t method) (pyrosetta.rosetta.ObjexxFCL.FArray1D_ObjexxFCL_FArray1D_int_t method) (pyrosetta.rosetta.ObjexxFCL.FArray1D_std_string_t method) (pyrosetta.rosetta.ObjexxFCL.FArray1D_unsigned_long_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_bool_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_core_pack_dunbrack_BBDepNRChiSample_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_core_pack_dunbrack_BBDepScoreInterpData_1_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_core_pack_dunbrack_BBDepScoreInterpData_2_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_core_pack_dunbrack_BBDepScoreInterpData_3_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_core_pack_dunbrack_BBDepScoreInterpData_4_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_core_pack_dunbrack_BBDepScoreInterpData_5_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_core_pack_dunbrack_BBIndNRChiSample_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_core_pack_dunbrack_PackedDunbrackRotamer_1_1_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_core_pack_dunbrack_PackedDunbrackRotamer_1_2_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_core_pack_dunbrack_PackedDunbrackRotamer_1_3_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_core_pack_dunbrack_PackedDunbrackRotamer_1_4_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_core_pack_dunbrack_PackedDunbrackRotamer_1_5_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_core_pack_dunbrack_PackedDunbrackRotamer_2_1_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_core_pack_dunbrack_PackedDunbrackRotamer_2_2_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_core_pack_dunbrack_PackedDunbrackRotamer_2_3_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_core_pack_dunbrack_PackedDunbrackRotamer_2_4_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_core_pack_dunbrack_PackedDunbrackRotamer_2_5_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_core_pack_dunbrack_PackedDunbrackRotamer_3_1_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_core_pack_dunbrack_PackedDunbrackRotamer_3_2_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_core_pack_dunbrack_PackedDunbrackRotamer_3_3_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_core_pack_dunbrack_PackedDunbrackRotamer_3_4_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_core_pack_dunbrack_PackedDunbrackRotamer_3_5_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_core_pack_dunbrack_PackedDunbrackRotamer_4_1_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_core_pack_dunbrack_PackedDunbrackRotamer_4_2_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_core_pack_dunbrack_PackedDunbrackRotamer_4_3_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_core_pack_dunbrack_PackedDunbrackRotamer_4_4_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_core_pack_dunbrack_PackedDunbrackRotamer_4_5_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_core_pack_dunbrack_PackedDunbrackRotamer_5_1_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_core_pack_dunbrack_PackedDunbrackRotamer_5_2_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_core_pack_dunbrack_PackedDunbrackRotamer_5_3_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_core_pack_dunbrack_PackedDunbrackRotamer_5_4_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_core_pack_dunbrack_PackedDunbrackRotamer_5_5_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_double_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_int_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_numeric_xyzVector_double_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_ObjexxFCL_FArray2D_float__star__t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_ObjexxFCL_ubyte_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_std_string_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_unsigned_char_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_unsigned_long_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_utility_vector1_core_pack_dunbrack_cenrot_CentroidRotamerSampleData_std_allocator_core_pack_dunbrack_cenrot_CentroidRotamerSampleData_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_utility_vector1_double_std_allocator_double_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2P_double_t method) (pyrosetta.rosetta.ObjexxFCL.FArray3D_core_pack_dunbrack_BBDepScoreInterpData_1_t method) (pyrosetta.rosetta.ObjexxFCL.FArray3D_core_pack_dunbrack_BBDepScoreInterpData_2_t method) (pyrosetta.rosetta.ObjexxFCL.FArray3D_core_pack_dunbrack_BBDepScoreInterpData_3_t method) (pyrosetta.rosetta.ObjexxFCL.FArray3D_core_pack_dunbrack_BBDepScoreInterpData_4_t method) (pyrosetta.rosetta.ObjexxFCL.FArray3D_core_pack_dunbrack_BBDepScoreInterpData_5_t method) (pyrosetta.rosetta.ObjexxFCL.FArray3D_double_t method) (pyrosetta.rosetta.ObjexxFCL.FArray3D_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray3D_int_t method) (pyrosetta.rosetta.ObjexxFCL.FArray3D_std_complex_double_t method) (pyrosetta.rosetta.ObjexxFCL.FArray3D_std_vector_unsigned_long_std_allocator_unsigned_long_t method) (pyrosetta.rosetta.ObjexxFCL.FArray3D_unsigned_char_t method) (pyrosetta.rosetta.ObjexxFCL.FArray3D_unsigned_long_t method) (pyrosetta.rosetta.ObjexxFCL.FArray3D_utility_vector1_double_std_allocator_double_t method) (pyrosetta.rosetta.ObjexxFCL.FArray3D_utility_vector1_numeric_xyzVector_double_std_allocator_numeric_xyzVector_double_t method) (pyrosetta.rosetta.ObjexxFCL.FArray3D_utility_vector1_unsigned_int_std_allocator_unsigned_int_t method) (pyrosetta.rosetta.ObjexxFCL.FArray3P_double_t method) (pyrosetta.rosetta.ObjexxFCL.FArray4D_double_t method) (pyrosetta.rosetta.ObjexxFCL.FArray4D_int_t method) (pyrosetta.rosetta.ObjexxFCL.FArray4D_unsigned_char_t method) (pyrosetta.rosetta.ObjexxFCL.FArray5D_double_t method) (pyrosetta.rosetta.ObjexxFCL.FArray5D_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray5D_int_t method) (pyrosetta.rosetta.ObjexxFCL.Observer method) (pyrosetta.rosetta.ObjexxFCL.ObserverMulti method) (pyrosetta.rosetta.ObjexxFCL.ObserverSingle method) insert_or_ignore() (in module pyrosetta.rosetta.basic.database) insert_pair() (pyrosetta.rosetta.protocols.task_operations.RestrictInterGroupVectorOperation method) insert_partial_atom_ids_for_mainchain_torsion() (in module pyrosetta.rosetta.core.conformation) insert_peptide_edges() (in module pyrosetta.rosetta.protocols.denovo_design) insert_point() (pyrosetta.rosetta.numeric.RocCurve method) insert_polymer_residue() (pyrosetta.rosetta.core.kinematics.FoldTree method) insert_pose() (pyrosetta.rosetta.protocols.forge.build.SegmentInsert method) insert_pose_into_pose() (in module pyrosetta.rosetta.protocols.grafting) insert_pose_torsion_override_movemap() (pyrosetta.rosetta.protocols.forge.build.SegmentInsert method) insert_position() (pyrosetta.rosetta.core.fragment.picking_old.vall.eval.EnergyEval method) insert_protein_chunk_into_pose() (pyrosetta.rosetta.core.import_pose.libraries.ChunkSet method) insert_random_fragments_in_flexible_protein_regions() (in module pyrosetta.rosetta.protocols.frags) insert_random_protein_chunks() (pyrosetta.rosetta.core.import_pose.libraries.RNA_ChunkLibrary method) insert_residue_by_atoms() (pyrosetta.rosetta.core.pose.Pose method) insert_residue_by_bond() (pyrosetta.rosetta.core.conformation.Conformation method) (pyrosetta.rosetta.core.conformation.symmetry.MirrorSymmetricConformation method) (pyrosetta.rosetta.core.conformation.symmetry.SymmetricConformation method) (pyrosetta.rosetta.core.pose.Pose method) (pyrosetta.rosetta.protocols.environment.ProtectedConformation method) insert_residue_by_chemical_bond() (pyrosetta.rosetta.core.kinematics.FoldTree method) insert_residue_by_jump() (pyrosetta.rosetta.core.conformation.Conformation method) (pyrosetta.rosetta.core.conformation.symmetry.MirrorSymmetricConformation method) (pyrosetta.rosetta.core.conformation.symmetry.SymmetricConformation method) (pyrosetta.rosetta.core.kinematics.FoldTree method) (pyrosetta.rosetta.core.pose.Pose method) (pyrosetta.rosetta.protocols.environment.ProtectedConformation method) insert_residue_into_atom_tree() (in module pyrosetta.rosetta.core.conformation) insert_residue_rows() (pyrosetta.rosetta.protocols.features.ResidueFeatures method) insert_rms() (pyrosetta.rosetta.protocols.simple_moves.ScoreMover method) (pyrosetta.rosetta.protocols.simple_moves.TailsScoreMover method) insert_sampled_torsion_string_into_taboo_map() (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.KinematicMover method) insert_score_function_method_options_rows() (pyrosetta.rosetta.core.scoring.methods.EnergyMethodOptions method) insert_score_function_weights_rows() (pyrosetta.rosetta.protocols.features.ScoreFunctionFeatures method) insert_site_atoms_row() (pyrosetta.rosetta.protocols.features.HBondFeatures method) insert_site_pdb_row() (pyrosetta.rosetta.protocols.features.HBondFeatures method) insert_site_row() (pyrosetta.rosetta.protocols.features.HBondFeatures method) insert_size() (pyrosetta.rosetta.protocols.simple_moves.ClassicFragmentMover method) (pyrosetta.rosetta.protocols.simple_moves.FragmentMover method) (pyrosetta.rosetta.protocols.simple_moves.LoggedFragmentMover method) (pyrosetta.rosetta.protocols.simple_moves.ResTypeFragmentMover method) (pyrosetta.rosetta.protocols.simple_moves.SmoothFragmentMover method) (pyrosetta.rosetta.protocols.simple_moves.SmoothSymmetricFragmentMover method) (pyrosetta.rosetta.protocols.simple_moves.SymmetricFragmentMover method) (pyrosetta.rosetta.protocols.simple_moves.WobbleMover method) insert_source_residue() (pyrosetta.rosetta.core.id.SequenceMapping method) (pyrosetta.rosetta.core.sequence.DerivedSequenceMapping method) insert_ss_into_pose() (pyrosetta.rosetta.core.scoring.dssp.Dssp method) (pyrosetta.rosetta.protocols.parser.BluePrint method) insert_ss_into_pose_no_IG_helix() (pyrosetta.rosetta.core.scoring.dssp.Dssp method) insert_structure_score_rows() (pyrosetta.rosetta.protocols.features.StructureScoresFeatures method) insert_target_residue() (pyrosetta.rosetta.core.id.SequenceMapping method) (pyrosetta.rosetta.core.sequence.DerivedSequenceMapping method) insert_task_operation_residue_effects_row() (pyrosetta.rosetta.protocols.features.TaskOperationFeatures method) insert_task_operations_row() (pyrosetta.rosetta.protocols.features.TaskOperationFeatures method) InsertChunkMover (class in pyrosetta.rosetta.protocols.hybridization) InsertGenerator (class in pyrosetta.rosetta.basic.database.insert_statement_generator) insertion() (pyrosetta.rosetta.protocols.parser.BluePrint method) insertion_char() (pyrosetta.rosetta.protocols.forge.build.SegmentInsert static method) insertion_code() (pyrosetta.rosetta.core.pose.ResidueIndexDescriptionPDB method) (pyrosetta.rosetta.protocols.antibody.PDBLandmark method) insertion_end_residue() (pyrosetta.rosetta.protocols.forge.build.SegmentInsert method) insertion_length() (pyrosetta.rosetta.protocols.grafting.AnchoredGraftMover method) (pyrosetta.rosetta.protocols.grafting.CCDEndsGraftMover method) (pyrosetta.rosetta.protocols.grafting.GraftMoverBase method) insertion_point_absolute_index() (pyrosetta.rosetta.protocols.forge.build.SegmentInsert method) insertion_start_residue() (pyrosetta.rosetta.protocols.forge.build.SegmentInsert method) insertionEndIndex (pyrosetta.rosetta.protocols.forge.remodel.RemodelWorkingSet property) insertionSize (pyrosetta.rosetta.protocols.forge.remodel.RemodelData property) insertionSS (pyrosetta.rosetta.protocols.forge.remodel.RemodelData property) insertionStartIndex (pyrosetta.rosetta.protocols.forge.remodel.RemodelWorkingSet property) insertMol() (pyrosetta.rosetta.RDKit.RWMol method) insertPose (pyrosetta.rosetta.protocols.forge.remodel.RemodelData property) InsertPoseIntoPoseMover (class in pyrosetta.rosetta.protocols.grafting.simple_movers) InsertPoseIntoPoseMoverCreator (class in pyrosetta.rosetta.protocols.grafting.simple_movers) InsertResMover (class in pyrosetta.rosetta.protocols.pose_length_moves) InsertResMoverCreator (class in pyrosetta.rosetta.protocols.pose_length_moves) InSetExpression (class in pyrosetta.rosetta.protocols.pack_daemon) inside_boundaries() (in module pyrosetta.rosetta.core.membrane) inside_polygon() (in module pyrosetta.rosetta.core.membrane) install_crash_handler() (in module pyrosetta.rosetta.utility) InstallFarnesylMover (class in pyrosetta.rosetta.protocols.farnesyl) InstallFarnesylMoverCreator (class in pyrosetta.rosetta.protocols.farnesyl) instance (pyrosetta.protocols.h5_fragment_store_provider.H5PyFragmentStoreProvider attribute) (pyrosetta.protocols.h5_structure_store_provider.H5StructureStoreProvider attribute) Instance() (pyrosetta.rosetta.core.pose.metrics.CalculatorFactory static method) instance() (pyrosetta.rosetta.protocols.checkpoint.Timer static method) instantiate_any_virtual_sugars() (in module pyrosetta.rosetta.protocols.stepwise.modeler.rna.sugar) instantiate_filter() (pyrosetta.rosetta.protocols.rosetta_scripts.RosettaScriptsParser method) instantiate_mover() (pyrosetta.rosetta.protocols.rosetta_scripts.RosettaScriptsParser method) instantiate_packer_palette() (pyrosetta.rosetta.protocols.rosetta_scripts.RosettaScriptsParser method) instantiate_sugars_at_cutpoint_closed() (pyrosetta.rosetta.protocols.stepwise.modeler.rna.sugar.VirtualSugarJustInTimeInstantiator method) instantiate_taskoperation() (pyrosetta.rosetta.protocols.rosetta_scripts.RosettaScriptsParser method) instantiate_water_at_octahedral_vertex() (in module pyrosetta.rosetta.protocols.magnesium) instantiated_phosphate() (pyrosetta.rosetta.protocols.stepwise.modeler.rna.phosphate.PhosphateMover method) instantiated_some_phosphate() (pyrosetta.rosetta.protocols.stepwise.modeler.rna.phosphate.MultiPhosphateSampler method) instruction_size() (pyrosetta.rosetta.protocols.fldsgn.BluePrintBDR method) int2afteroption() (in module pyrosetta.rosetta.basic.options) int64_groups (pyrosetta.rosetta.protocols.indexed_structure_store.FragmentStore property) int_of() (in module pyrosetta.rosetta.ObjexxFCL) (pyrosetta.rosetta.ObjexxFCL.Fstring method) (pyrosetta.rosetta.ObjexxFCL.Fsubstring method) int_to_orientation() (pyrosetta.rosetta.protocols.denovo_design.architects.StrandArchitect static method) int_type (pyrosetta.rosetta.utility.json_spirit.Value_type attribute) int_value_ (pyrosetta.rosetta.utility.py.Base property) inTab (pyrosetta.rosetta.protocols.sparta.Sparta.SpartaLib property) intafteroption() (in module pyrosetta.rosetta.basic.options) integer() (pyrosetta.rosetta.ObjexxFCL.DimensionExpression method) (pyrosetta.rosetta.ObjexxFCL.DimensionExpressionCon method) (pyrosetta.rosetta.ObjexxFCL.DimensionExpressionCube method) (pyrosetta.rosetta.ObjexxFCL.DimensionExpressionDiv method) (pyrosetta.rosetta.ObjexxFCL.DimensionExpressionMax method) (pyrosetta.rosetta.ObjexxFCL.DimensionExpressionMin method) (pyrosetta.rosetta.ObjexxFCL.DimensionExpressionMul method) (pyrosetta.rosetta.ObjexxFCL.DimensionExpressionPow method) (pyrosetta.rosetta.ObjexxFCL.DimensionExpressionRef method) (pyrosetta.rosetta.ObjexxFCL.DimensionExpressionSquare method) (pyrosetta.rosetta.ObjexxFCL.DimensionExpressionSub method) (pyrosetta.rosetta.ObjexxFCL.DimensionExpressionSum method) integer_msg() (pyrosetta.rosetta.utility.SimulateMPIMessage method) INTEGER_OPTION (pyrosetta.rosetta.utility.options.OptionTypes attribute) integer_range_restriction() (in module pyrosetta.rosetta.utility.tag) INTEGER_VECTOR_OPTION (pyrosetta.rosetta.utility.options.OptionTypes attribute) IntegerOption (class in pyrosetta.rosetta.utility.options) IntegerOptionKey (class in pyrosetta.rosetta.utility.options) integers_msg() (pyrosetta.rosetta.utility.SimulateMPIMessage method) IntegerVectorOption (class in pyrosetta.rosetta.utility.options) IntegerVectorOptionKey (class in pyrosetta.rosetta.utility.options) integral() (pyrosetta.rosetta.core.scoring.epr_deer.metrics.DEERChiSqMethod method) (pyrosetta.rosetta.core.scoring.epr_deer.metrics.DEERDistanceDistribution method) (pyrosetta.rosetta.core.scoring.epr_deer.metrics.DEERJaccardMethod method) (pyrosetta.rosetta.core.scoring.epr_deer.metrics.DEERJSMethod method) (pyrosetta.rosetta.core.scoring.epr_deer.metrics.DEERMiscMethod method) (pyrosetta.rosetta.core.scoring.epr_deer.metrics.DEEROverlapMethod method) integral_constant_bool_false_t (class in pyrosetta.rosetta.std) integral_constant_bool_true_t (class in pyrosetta.rosetta.std) INTEGRATION_TEST (pyrosetta.rosetta.protocols.stepwise.screener.StepWiseScreenerType attribute) integration_test() (pyrosetta.rosetta.protocols.magnesium.MgScanner method) integration_test_mode() (pyrosetta.rosetta.core.import_pose.ImportPoseOptions method) (pyrosetta.rosetta.core.io.StructFileReaderOptions method) (pyrosetta.rosetta.core.io.StructFileRepOptions method) (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseModelerOptions method) (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseRNA_ModelerOptions method) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.options.StepWiseMonteCarloOptions method) IntegrationTestBreaker (class in pyrosetta.rosetta.protocols.stepwise.screener) intensity() (pyrosetta.rosetta.protocols.noesy_assign.FloatingResonance method) (pyrosetta.rosetta.protocols.noesy_assign.LabelResonance method) (pyrosetta.rosetta.protocols.noesy_assign.ProtonResonance method) (pyrosetta.rosetta.protocols.noesy_assign.Resonance method) inter() (pyrosetta.rosetta.core.scoring.power_diagram.SAnode method) (pyrosetta.rosetta.core.scoring.SAnode method) inter_chain() (pyrosetta.rosetta.protocols.constraint_movers.AddConstraintsToCurrentConformationMover method) inter_clash1() (pyrosetta.rosetta.core.scoring.motif.ResPairMotifQuery method) inter_clash1_xform() (pyrosetta.rosetta.core.scoring.motif.ResPairMotifQuery method) inter_clash2() (pyrosetta.rosetta.core.scoring.motif.ResPairMotifQuery method) inter_clash2_xform() (pyrosetta.rosetta.core.scoring.motif.ResPairMotifQuery method) inter_residue_connection_partner() (pyrosetta.rosetta.core.conformation.Conformation method) (pyrosetta.rosetta.core.conformation.Residue method) (pyrosetta.rosetta.core.conformation.symmetry.MirrorSymmetricConformation method) (pyrosetta.rosetta.core.conformation.symmetry.SymmetricConformation method) (pyrosetta.rosetta.protocols.environment.ProtectedConformation method) InteractingRotamerExplosion (class in pyrosetta.rosetta.protocols.task_operations) InteractingRotamerExplosionCreator (class in pyrosetta.rosetta.protocols.task_operations) interaction_cutoff() (pyrosetta.rosetta.core.energy_methods.CustomAtomPairEnergy method) (pyrosetta.rosetta.core.energy_methods.GaussianOverlapEnergy method) (pyrosetta.rosetta.core.energy_methods.PairEnergy method) (pyrosetta.rosetta.core.energy_methods.SuckerEnergy method) interaction_graph_threads() (pyrosetta.rosetta.protocols.minimization_packing.DisulfideOptimizationMover method) InteractionEnergyMetric (class in pyrosetta.rosetta.core.simple_metrics.metrics) InteractionEnergyMetricCreator (class in pyrosetta.rosetta.core.simple_metrics.metrics) InteractionGraphBase (class in pyrosetta.rosetta.core.pack.interaction_graph) InteractionGraphFactory (class in pyrosetta.rosetta.core.pack.interaction_graph) InteractionGraphSummaryMetric (class in pyrosetta.rosetta.protocols.quantum_annealing) InteractionGraphSummaryMetricCreator (class in pyrosetta.rosetta.protocols.quantum_annealing) InteratomicVarianceMatrix (class in pyrosetta.rosetta.protocols.toolbox) InterbondAngleScore (class in pyrosetta.rosetta.protocols.frag_picker.scores) INTERCALATED_T_LOOP (pyrosetta.rosetta.core.scoring.rna.RNA_MotifType attribute) intercept (pyrosetta.rosetta.core.sequence.Line property) (pyrosetta.rosetta.numeric.interpolation.spline.LinearFunction property)

intercept() (pyrosetta.rosetta.core.scoring.packing.HolesParams method) interchain_contact (pyrosetta.rosetta.core.scoring.ScoreType attribute) interchain_env (pyrosetta.rosetta.core.scoring.ScoreType attribute) interchain_pair (pyrosetta.rosetta.core.scoring.ScoreType attribute) interchain_vdw (pyrosetta.rosetta.core.scoring.ScoreType attribute) InterchainEnvEnergy (class in pyrosetta.rosetta.protocols.scoring.methods) InterchainEnvEnergyCreator (class in pyrosetta.rosetta.protocols.scoring.methods) InterchainJumpSelector (class in pyrosetta.rosetta.core.select.jump_selector) InterchainJumpSelectorCreator (class in pyrosetta.rosetta.core.select.jump_selector) InterchainPairEnergy (class in pyrosetta.rosetta.protocols.scoring.methods) InterchainPairEnergyCreator (class in pyrosetta.rosetta.protocols.scoring.methods) InterchainPotential (class in pyrosetta.rosetta.protocols.scoring) interchangeability_group() (pyrosetta.rosetta.core.chemical.MutableResidueType method) (pyrosetta.rosetta.core.chemical.ResidueType method) (pyrosetta.rosetta.core.chemical.ResidueTypeBase method) (pyrosetta.rosetta.core.chemical.ResidueTypeFinder method) interchangeability_group_generated_by_base_residue_name() (pyrosetta.rosetta.core.chemical.ResidueTypeSetCache method) interE (pyrosetta.rosetta.protocols.simple_moves.ThermodynamicData property) Interface (class in pyrosetta.rosetta.protocols.ligand_docking.ligand_options) (class in pyrosetta.rosetta.protocols.scoring) interface() (pyrosetta.rosetta.protocols.dna.RestrictDesignToProteinDNAInterface method) (pyrosetta.rosetta.protocols.scoring.InterfaceInfo method) interface_builder_ct_namer() (pyrosetta.rosetta.protocols.ligand_docking.InterfaceBuilderLoader static method) interface_calc() (pyrosetta.rosetta.protocols.anchored_design.AnchorMoversData method) interface_dd_pair (pyrosetta.rosetta.core.scoring.ScoreType attribute) INTERFACE_DDG_MUTATION (pyrosetta.rosetta.core.pose.datacache.CacheableDataType attribute) (pyrosetta.rosetta.core.pose.datacache.CacheableDataType.Enum attribute) interface_detection_dis() (pyrosetta.rosetta.protocols.antibody.design.GeneralAntibodyModeler method) interface_distance_cutoff() (pyrosetta.rosetta.protocols.task_operations.ProteinInterfaceDesignOperation method) interface_from_pose() (pyrosetta.rosetta.protocols.scoring.InterchainPotential method) interface_hbonds (pyrosetta.rosetta.protocols.analysis.InterfaceData property) INTERFACE_INFO (pyrosetta.rosetta.core.pose.datacache.CacheableDataType attribute) (pyrosetta.rosetta.core.pose.datacache.CacheableDataType.Enum attribute) interface_interaction_energy() (pyrosetta.rosetta.protocols.calc_taskop_filters.RotamerBoltzmannWeight method) interface_motif_score() (pyrosetta.rosetta.protocols.legacy_sewing.scoring.LegacyPartnerMotifScorer method) (pyrosetta.rosetta.protocols.sewing.scoring.PartnerMotifScorer method) (pyrosetta.rosetta.protocols.sewing.scoring.SubsetPartnerMotifScorer method) interface_nres (pyrosetta.rosetta.protocols.analysis.InterfaceData property) interface_nres() (pyrosetta.rosetta.protocols.scoring.Interface method) (pyrosetta.rosetta.protocols.scoring.InterfaceInfo method) interface_number() (pyrosetta.rosetta.core.conformation.symmetry.SymmetryInfo method) interface_only() (pyrosetta.rosetta.core.scoring.motif.ResPairMotifQuery method) interface_radius() (pyrosetta.rosetta.protocols.protein_interface_design.movers.HotspotDisjointedFoldTreeMover method) interface_residues (pyrosetta.rosetta.protocols.analysis.InterfaceData property) (pyrosetta.rosetta.protocols.analysis.PerResidueInterfaceData property) interface_separate_and_score() (in module pyrosetta.rosetta.protocols.ddg.CartesianddG) interface_to_surface_fraction (pyrosetta.rosetta.protocols.analysis.InterfaceData property) interface_trim_radius() (pyrosetta.rosetta.core.scoring.sc.ElectrostaticComplementarityCalculator method) (pyrosetta.rosetta.core.simple_metrics.composite_metrics.ElectrostaticComplementarityMetric method) InterfaceAnalyzerMover (class in pyrosetta.rosetta.protocols.analysis) InterfaceAnalyzerMoverCreator (class in pyrosetta.rosetta.protocols.analysis) InterfaceBindingEnergyDensityFilter (class in pyrosetta.rosetta.protocols.simple_ddg) InterfaceBindingEnergyDensityFilterCreator (class in pyrosetta.rosetta.protocols.simple_ddg) InterfaceBuilder (class in pyrosetta.rosetta.protocols.ligand_docking) InterfaceBuilderLoader (class in pyrosetta.rosetta.protocols.ligand_docking) InterfaceBuilderLoaderCreator (class in pyrosetta.rosetta.protocols.ligand_docking) InterfaceData (class in pyrosetta.rosetta.protocols.analysis) InterfaceDdGMover (class in pyrosetta.rosetta.protocols.features) InterfaceDdGMoverCreator (class in pyrosetta.rosetta.protocols.features) InterfaceDefinitionCalculator (class in pyrosetta.rosetta.core.pose.metrics.simple_calculators) InterfaceDeltaEnergeticsCalculator (class in pyrosetta.rosetta.core.pose.metrics.simple_calculators) InterfaceFeatures (class in pyrosetta.rosetta.protocols.features) InterfaceFeaturesCreator (class in pyrosetta.rosetta.protocols.features) InterfaceHbondsFilter (class in pyrosetta.rosetta.protocols.simple_filters) InterfaceHbondsFilterCreator (class in pyrosetta.rosetta.protocols.simple_filters) InterfaceHolesFilter (class in pyrosetta.rosetta.protocols.protein_interface_design.filters) InterfaceHolesFilterCreator (class in pyrosetta.rosetta.protocols.protein_interface_design.filters) InterfaceHydrophobicResidueContactsFilter (class in pyrosetta.rosetta.protocols.simple_filters) InterfaceHydrophobicResidueContactsFilterCreator (class in pyrosetta.rosetta.protocols.simple_filters) InterfaceInfo (class in pyrosetta.rosetta.protocols.ligand_docking.ligand_options) (class in pyrosetta.rosetta.protocols.scoring) InterfaceInfo.Type (class in pyrosetta.rosetta.protocols.ligand_docking.ligand_options) InterfaceNeighborDefinitionCalculator (class in pyrosetta.rosetta.core.pose.metrics.simple_calculators) InterfacePackingFilter (class in pyrosetta.rosetta.protocols.matdes) InterfacePackingFilterCreator (class in pyrosetta.rosetta.protocols.matdes) InterfaceRecapitulationMover (class in pyrosetta.rosetta.protocols.protein_interface_design.movers) InterfaceRecapitulationMoverCreator (class in pyrosetta.rosetta.protocols.protein_interface_design.movers) InterfaceRegion (class in pyrosetta.rosetta.protocols.analysis) InterfaceSasaDefinitionCalculator (class in pyrosetta.rosetta.core.pose.metrics.simple_calculators) InterfaceSasaFilter (class in pyrosetta.rosetta.protocols.simple_filters) InterfaceSasaFilterCreator (class in pyrosetta.rosetta.protocols.simple_filters) InterfaceScoreCalculator (class in pyrosetta.rosetta.protocols.ligand_docking) InterfaceScoreCalculatorCreator (class in pyrosetta.rosetta.protocols.ligand_docking) InterfaceSidechainMinMover (class in pyrosetta.rosetta.protocols.docking) InterfaceTaskOperation (class in pyrosetta.rosetta.protocols.simple_task_operations) InterGroupInterfaceByVectorSelector (class in pyrosetta.rosetta.core.select.residue_selector) InterGroupInterfaceByVectorSelectorCreator (class in pyrosetta.rosetta.core.select.residue_selector) InterGroupNeighborsCalculator (class in pyrosetta.rosetta.protocols.pose_metric_calculators) interhelical_contact() (pyrosetta.rosetta.protocols.hbnet.HBNetStapleInterface method) InterlockAroma (class in pyrosetta.rosetta.protocols.flxbb) InterlockAromaCreator (class in pyrosetta.rosetta.protocols.flxbb) InterlockingAromaFilter (class in pyrosetta.rosetta.protocols.fldsgn.filters) InterlockingAromaFilterCreator (class in pyrosetta.rosetta.protocols.fldsgn.filters) intermediate_structs() (pyrosetta.rosetta.protocols.jd2.archive.Batch method) intermedrelax() (pyrosetta.rosetta.protocols.indel.IndelOptimizationMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.LoopMoverFromCommandLine method) (pyrosetta.rosetta.protocols.relax.loop.LoopRelaxMover method) InterModelMotifScorer (class in pyrosetta.rosetta.protocols.sewing.scoring) InterModelMotifScorerCreator (class in pyrosetta.rosetta.protocols.sewing.scoring) intermol (pyrosetta.rosetta.core.scoring.ScoreType attribute) IntermolEnergy (class in pyrosetta.rosetta.core.energy_methods) IntermolEnergyCreator (class in pyrosetta.rosetta.core.energy_methods) INTERNAL (pyrosetta.rosetta.core.chemical.ICoordAtomIDType attribute) internal_add_edge() (pyrosetta.rosetta.core.scoring.hbonds.graph.HBondNode method) (pyrosetta.rosetta.utility.graph.LowMemNode method) internal_allowed_ (pyrosetta.rosetta.core.scoring.packstat.Slice property) internal_delete_self() (pyrosetta.rosetta.core.scoring.hbonds.graph.HBondEdge method) (pyrosetta.rosetta.utility.graph.LowMemEdge method) internal_drop_edge() (pyrosetta.rosetta.core.scoring.hbonds.graph.HBondNode method) (pyrosetta.rosetta.utility.graph.LowMemNode method) internal_edge_list_size() (pyrosetta.rosetta.core.scoring.hbonds.graph.HBondGraph method) (pyrosetta.rosetta.utility.graph.LowMemGraph_core_scoring_hbonds_graph_HBondNode_core_scoring_hbonds_graph_HBondEdge_t method) (pyrosetta.rosetta.utility.graph.LowMemGraphBase method) internal_get_edge_list() (pyrosetta.rosetta.core.scoring.hbonds.graph.HBondNode method) (pyrosetta.rosetta.utility.graph.LowMemNode method) InternalCoordAtoms (class in pyrosetta.rosetta.core.kinematics.inverse) InternalCoordGeometry (class in pyrosetta.rosetta.core.kinematics.inverse) InternalWorkingResidueParameter (class in pyrosetta.rosetta.protocols.stepwise.modeler.rna) interp (pyrosetta.rosetta.numeric.interpolation.spline.interp_range property) interp_dspline() (in module pyrosetta.rosetta.core.scoring.electron_density) interp_range (class in pyrosetta.rosetta.numeric.interpolation.spline) interp_spline() (in module pyrosetta.rosetta.core.scoring.electron_density) interpolate() (pyrosetta.rosetta.numeric.interpolation.spline.CompoundInterpolator method) (pyrosetta.rosetta.numeric.interpolation.spline.Interpolator method) (pyrosetta.rosetta.numeric.interpolation.spline.SimpleInterpolator method) interpolate_2d_func_of_angles() (in module pyrosetta.rosetta.basic) interpolate_bilinear() (in module pyrosetta.rosetta.basic) interpolate_bilinear_by_value() (in module pyrosetta.rosetta.basic) interpolate_get_angle_bins() (in module pyrosetta.rosetta.basic) interpolate_nrchi_values() (pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_1_1_t method) (pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_1_2_t method) (pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_1_3_t method) (pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_1_4_t method) (pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_1_5_t method) (pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_2_1_t method) (pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_2_2_t method) (pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_2_3_t method) (pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_2_4_t method) (pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_2_5_t method) interpolate_on_statistics() (pyrosetta.rosetta.protocols.noesy_assign.PeakCalibrator method) (pyrosetta.rosetta.protocols.noesy_assign.StructureDependentPeakCalibrator method) (pyrosetta.rosetta.protocols.noesy_assign.StructureIndependentPeakCalibrator method) interpolate_polylinear_by_value() (in module pyrosetta.rosetta.core.pack.dunbrack) interpolate_polylinear_by_value_angles_degrees() (in module pyrosetta.rosetta.core.pack.dunbrack) interpolate_polylinear_by_value_noangles() (in module pyrosetta.rosetta.core.pack.dunbrack) interpolate_rotamers() (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_1_1_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_1_2_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_1_3_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_1_4_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_1_5_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_2_1_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_2_2_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_2_3_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_2_4_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_2_5_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_3_1_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_3_2_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_3_3_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_3_4_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_3_5_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_4_1_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_4_2_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_4_3_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_4_4_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_4_5_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_5_1_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_5_2_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_5_3_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_5_4_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_5_5_t method) (pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_1_1_t method) (pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_1_2_t method) (pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_1_3_t method) (pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_1_4_t method) (pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_1_5_t method) (pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_2_1_t method) (pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_2_2_t method) (pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_2_3_t method) (pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_2_4_t method) (pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_2_5_t method) interpolate_too_big() (pyrosetta.rosetta.protocols.noesy_assign.PeakCalibrator method) (pyrosetta.rosetta.protocols.noesy_assign.StructureDependentPeakCalibrator method) (pyrosetta.rosetta.protocols.noesy_assign.StructureIndependentPeakCalibrator method) interpolate_too_small() (pyrosetta.rosetta.protocols.noesy_assign.PeakCalibrator method) (pyrosetta.rosetta.protocols.noesy_assign.StructureDependentPeakCalibrator method) (pyrosetta.rosetta.protocols.noesy_assign.StructureIndependentPeakCalibrator method) interpolate_trilinear() (in module pyrosetta.rosetta.basic) interpolate_trilinear_by_value() (in module pyrosetta.rosetta.basic) interpolate_value_and_deriv() (in module pyrosetta.rosetta.core.scoring) interpolated_analytic_etable_evaluation() (pyrosetta.rosetta.core.scoring.etable.Etable method) (pyrosetta.rosetta.core.scoring.etable.MembEtable method) interpolation_type_enum_to_string() (in module pyrosetta.rosetta.protocols.canonical_sampling) interpolation_type_string_to_enum() (in module pyrosetta.rosetta.protocols.canonical_sampling) InterpolationType (class in pyrosetta.rosetta.protocols.canonical_sampling) Interpolator (class in pyrosetta.rosetta.numeric.interpolation.spline) InterRepeatContactFilter (class in pyrosetta.rosetta.protocols.simple_filters) InterRepeatContactFilterCreator (class in pyrosetta.rosetta.protocols.simple_filters) interres_evaluator() (pyrosetta.rosetta.core.scoring.etable.AnalyticEtableEnergy method) (pyrosetta.rosetta.core.scoring.etable.TableLookupEtableEnergy method) intersect() (in module pyrosetta.rosetta.core.membrane) (pyrosetta.rosetta.ObjexxFCL.DynamicIndexRange method) (pyrosetta.rosetta.ObjexxFCL.IndexRange method) (pyrosetta.rosetta.ObjexxFCL.StaticIndexRange method) intersect_nic() (pyrosetta.rosetta.ObjexxFCL.DynamicIndexRange method) intersect_residues() (pyrosetta.rosetta.protocols.vardist_solaccess.VarSolDRotamerDots method) intersects() (pyrosetta.rosetta.numeric.geometry.BoundingBox_numeric_xyzVector_double_t method) (pyrosetta.rosetta.ObjexxFCL.DynamicIndexRange method) (pyrosetta.rosetta.ObjexxFCL.IndexRange method) (pyrosetta.rosetta.ObjexxFCL.StaticIndexRange method) (pyrosetta.rosetta.protocols.forge.build.Interval method) Interval (class in pyrosetta.rosetta.protocols.forge.build) (class in pyrosetta.rosetta.protocols.jumping) interval() (pyrosetta.rosetta.protocols.forge.build.Bridge method) (pyrosetta.rosetta.protocols.forge.build.BuildInstruction method) (pyrosetta.rosetta.protocols.forge.build.ConnectRight method) (pyrosetta.rosetta.protocols.forge.build.GrowLeft method) (pyrosetta.rosetta.protocols.forge.build.GrowRight method) (pyrosetta.rosetta.protocols.forge.build.RelativeConnectRight method) (pyrosetta.rosetta.protocols.forge.build.SegmentInsert method) (pyrosetta.rosetta.protocols.forge.build.SegmentRebuild method) (pyrosetta.rosetta.protocols.forge.build.SegmentSwap method) interval_to_loop() (in module pyrosetta.rosetta.protocols.forge.methods) IntervalSet_Double (class in pyrosetta.rosetta.numeric) IntervalSet_double_t (class in pyrosetta.rosetta.numeric) intra_elec_scale() (pyrosetta.rosetta.core.scoring.facts.FACTSRsdTypeInfo method) intra_residue_energy() (pyrosetta.rosetta.core.scoring.constraints.Constraints method) intra_solv_scale() (pyrosetta.rosetta.core.scoring.facts.FACTSRsdTypeInfo method) intracomponent_contact() (in module pyrosetta.rosetta.core.pose.symmetry) IntraDesignTerminusMotifScorer (class in pyrosetta.rosetta.protocols.sewing.scoring) IntraDesignTerminusMotifScorerCreator (class in pyrosetta.rosetta.protocols.sewing.scoring) intraE (pyrosetta.rosetta.protocols.simple_moves.ThermodynamicData property) IntraRepeatContactFilter (class in pyrosetta.rosetta.protocols.simple_filters) IntraRepeatContactFilterCreator (class in pyrosetta.rosetta.protocols.simple_filters) intrares_evaluator() (pyrosetta.rosetta.core.scoring.etable.AnalyticEtableEnergy method) (pyrosetta.rosetta.core.scoring.etable.TableLookupEtableEnergy method) intrares_side_chain_score() (pyrosetta.rosetta.core.scoring.rna.RNA_TorsionPotential method) ints_of() (in module pyrosetta.rosetta.ObjexxFCL) inv_all (pyrosetta.rosetta.core.kinematics.jacobian.ModuleType1.jacobian_struct property) inv_cons (pyrosetta.rosetta.core.kinematics.jacobian.ModuleType1.jacobian_struct property) inv_dist6() (pyrosetta.rosetta.core.scoring.constraints.AmbiguousNMRDistanceConstraint method) inv_dofs (pyrosetta.rosetta.core.kinematics.jacobian.ModuleType1.jacobian_struct property) inv_virtual_type_for_conf() (in module pyrosetta.rosetta.core.conformation) inv_xform() (pyrosetta.rosetta.numeric.Py_xyzTransform_double method) (pyrosetta.rosetta.numeric.xyzTransform_double_t method) (pyrosetta.rosetta.numeric.xyzTransform_float_t method) INVALID (pyrosetta.rosetta.basic.thread_manager.RosettaThreadRequestOriginatingLevel attribute) (pyrosetta.rosetta.protocols.comparative_modeling.features.TorsionBin attribute) invalid() (pyrosetta.rosetta.core.chemical.RefConvert_std_string_t static method) (pyrosetta.rosetta.core.chemical.RefConvert_unsigned_long_t static method) (pyrosetta.rosetta.core.chemical.RefConvert_void__star__t static method) INVALID_BEHAVIOUR (pyrosetta.rosetta.core.pack.palette.SpecialPackerPaletteBehaviour attribute) INVALID_DOF (pyrosetta.rosetta.core.id.DOF_Type attribute) invalid_entry() (pyrosetta.rosetta.core.chemical.AtomRefMapping_unsigned_long_void__star__t method) (pyrosetta.rosetta.core.chemical.AtomRefMapping_void__star__unsigned_long_t method) (pyrosetta.rosetta.core.chemical.AtomRefMapping_void__star__void__star__t method) invalid_key() (pyrosetta.rosetta.core.chemical.AtomRefMapping_unsigned_long_void__star__t method) (pyrosetta.rosetta.core.chemical.AtomRefMapping_void__star__unsigned_long_t method) (pyrosetta.rosetta.core.chemical.AtomRefMapping_void__star__void__star__t method) INVALID_MODE (pyrosetta.rosetta.core.scoring.sasa.SasaMethodHPMode attribute) (pyrosetta.rosetta.core.simple_metrics.metrics.SequenceMetricMode attribute) (pyrosetta.rosetta.protocols.ptm_prediction.PTMPredictionMetric.PTMPredictionMetricModes attribute) INVALID_SS (pyrosetta.rosetta.protocols.comparative_modeling.features.SSType attribute) INVALID_t (pyrosetta.rosetta.core.chemical.TypeSetMode attribute) INVALID_TOKEN_TYPE (pyrosetta.rosetta.numeric.expression_parser.TokenType attribute) INVALIDATE (pyrosetta.rosetta.core.conformation.signals.IdentityEvent attribute) (pyrosetta.rosetta.core.conformation.signals.IdentityEvent.Tag attribute) (pyrosetta.rosetta.core.conformation.signals.LengthEvent attribute) (pyrosetta.rosetta.core.conformation.signals.LengthEvent.Tag attribute) invalidate() (pyrosetta.rosetta.core.chemical.AtomRefMapping_unsigned_long_void__star__t method) (pyrosetta.rosetta.core.chemical.AtomRefMapping_void__star__unsigned_long_t method) (pyrosetta.rosetta.core.chemical.AtomRefMapping_void__star__void__star__t method) (pyrosetta.rosetta.utility.signals.Link method) invalidate_residues_spanning_cuts() (in module pyrosetta.rosetta.protocols.medal) invDcnst() (pyrosetta.rosetta.core.scoring.RDC_Rohl method) inverse() (in module pyrosetta.rosetta.numeric) (pyrosetta.rosetta.core.kinematics.RT method) (pyrosetta.rosetta.numeric.fourier.kiss_dct_state method) (pyrosetta.rosetta.numeric.fourier.kiss_fft_state method) (pyrosetta.rosetta.numeric.fourier.kiss_fftnd_state method) (pyrosetta.rosetta.numeric.fourier.kiss_fftndr_state method) (pyrosetta.rosetta.numeric.fourier.kiss_fftr_state method) (pyrosetta.rosetta.numeric.fourier.kiss_fftsplit_state method) (pyrosetta.rosetta.numeric.HomogeneousTransform_Double method) (pyrosetta.rosetta.numeric.HomogeneousTransform_double_t method) (pyrosetta.rosetta.numeric.MathMatrix_double_t method) (pyrosetta.rosetta.numeric.MathMatrix_float_t method) (pyrosetta.rosetta.numeric.Py_xyzTransform_double method) (pyrosetta.rosetta.numeric.Quaternion_double_t method) (pyrosetta.rosetta.numeric.xyzMatrix_double_t method) (pyrosetta.rosetta.numeric.xyzMatrix_float_t method) (pyrosetta.rosetta.numeric.xyzTransform_double_t method) (pyrosetta.rosetta.numeric.xyzTransform_float_t method) inverse_diagonal_matrix() (pyrosetta.rosetta.numeric.MathMatrix_double_t method) (pyrosetta.rosetta.numeric.MathMatrix_float_t method) inverse_dimensions() (pyrosetta.rosetta.numeric.MathMatrix_double_t method) (pyrosetta.rosetta.numeric.MathMatrix_float_t method) inverse_rectangular_matrix() (pyrosetta.rosetta.numeric.MathMatrix_double_t method) (pyrosetta.rosetta.numeric.MathMatrix_float_t method) inverse_rotamers_against_residue() (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.MatchConstraintFileInfo method) (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.MatchConstraintFileInfoList method) inverse_rt6() (in module pyrosetta.rosetta.core.scoring.motif) inverse_square_matrix() (pyrosetta.rosetta.numeric.MathMatrix_double_t method) (pyrosetta.rosetta.numeric.MathMatrix_float_t method) inverse_tridiagonal_matrix() (pyrosetta.rosetta.numeric.MathMatrix_double_t method) (pyrosetta.rosetta.numeric.MathMatrix_float_t method) InverseRotamersCstGeneratorCreator (class in pyrosetta.rosetta.protocols.forge.constraints) InverseRotamersRCG (class in pyrosetta.rosetta.protocols.forge.constraints) inversion_random() (pyrosetta.rosetta.protocols.cyclic_peptide.CycpepRigidBodyPermutationMover method) inversion_setting() (pyrosetta.rosetta.protocols.cyclic_peptide.CycpepRigidBodyPermutationMover method) invert() (pyrosetta.rosetta.core.pack.task.residue_selector.ClashBasedShellSelector method) (pyrosetta.rosetta.numeric.Quaternion_double_t method) (pyrosetta.rosetta.protocols.cyclic_peptide.SymmetricCycpepAlign method) (pyrosetta.rosetta.protocols.filters.CompoundFilter method) (pyrosetta.rosetta.protocols.loops.Loops method) (pyrosetta.rosetta.protocols.membrane.geometry.Embedding method) (pyrosetta.rosetta.protocols.membrane.geometry.EmbeddingDef method) (pyrosetta.rosetta.protocols.task_operations.StoreCompoundTaskMover method) invert_direction() (pyrosetta.rosetta.protocols.normalmode.NormalModeRelaxMover method) invert_exclude_residues() (in module pyrosetta.rosetta.core.scoring) invert_include_residues() (in module pyrosetta.rosetta.protocols.evaluation) invert_to_boolmasks() (pyrosetta.rosetta.core.pack.interaction_graph.RotamerDots method) invertChirality() (pyrosetta.rosetta.RDKit.Atom method) INVERTED_VIRTUAL_RESIDUE (pyrosetta.rosetta.core.chemical.ResidueProperty attribute) InvGeometricFunc (class in pyrosetta.rosetta.protocols.moves) InvLegendre() (pyrosetta.rosetta.numeric.fourier.SO3coeffs method) invoke() (pyrosetta.rosetta.core.scoring.etable.count_pair.Invoker method) Invoker (class in pyrosetta.rosetta.core.scoring.etable.count_pair) involved_in_phosphate_torsion() (in module pyrosetta.rosetta.core.import_pose) (in module pyrosetta.rosetta.protocols.rna.denovo) involves_current_pose() (pyrosetta.rosetta.core.scoring.loop_graph.evaluator.GaussianChainFuncPotentialEvaluator method) (pyrosetta.rosetta.core.scoring.loop_graph.evaluator.LoopClosePotentialEvaluator method) (pyrosetta.rosetta.core.scoring.loop_graph.evaluator.SixDTransRotPotentialEvaluator method) involves_prolines() (in module pyrosetta.rosetta.protocols.ddg.CartesianddG) InvRotamerDots (class in pyrosetta.rosetta.core.pack.interaction_graph) InvrotCollector (class in pyrosetta.rosetta.protocols.toolbox.match_enzdes_util) invrots() (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.InvrotCollector method) InvrotTarget (class in pyrosetta.rosetta.protocols.toolbox.match_enzdes_util) InvrotTree (class in pyrosetta.rosetta.protocols.toolbox.match_enzdes_util) InvrotTreeCstGeneratorCreator (class in pyrosetta.rosetta.protocols.forge.constraints) InvrotTreeNode (class in pyrosetta.rosetta.protocols.toolbox.match_enzdes_util) InvrotTreeNodeBase (class in pyrosetta.rosetta.protocols.toolbox.match_enzdes_util) InvrotTreeRCG (class in pyrosetta.rosetta.protocols.forge.constraints) invstub() (in module pyrosetta.rosetta.protocols.sic_dock) inward_normal_to_plane() (pyrosetta.rosetta.protocols.docking.EllipsoidalRandomizationMover method) IOError (class in pyrosetta.rosetta.utility.excn) IonizableResidue (class in pyrosetta.rosetta.protocols.simple_moves) ionized_restypes() (pyrosetta.rosetta.protocols.simple_moves.IonizableResidue method) ios_base (class in pyrosetta.rosetta.std) ios_base.event (class in pyrosetta.rosetta.std) ios_base.failure (class in pyrosetta.rosetta.std) ios_base.Init (class in pyrosetta.rosetta.std) iostream (class in pyrosetta.rosetta.std) iostream.sentry (class in pyrosetta.rosetta.std) IOTA_ATOM (pyrosetta.rosetta.core.chemical.GreekDistance attribute) IOTraits_double_t (class in pyrosetta.rosetta.numeric) IOTraits_float_t (class in pyrosetta.rosetta.numeric) IOTraits_int_t (class in pyrosetta.rosetta.numeric) IOTraits_long_double_t (class in pyrosetta.rosetta.numeric) IOTraits_long_t (class in pyrosetta.rosetta.numeric) IOTraits_short_t (class in pyrosetta.rosetta.numeric) IOTraits_unsigned_int_t (class in pyrosetta.rosetta.numeric) IOTraits_unsigned_long_t (class in pyrosetta.rosetta.numeric) IOTraits_unsigned_short_t (class in pyrosetta.rosetta.numeric) iparam19 (pyrosetta.rosetta.core.scoring.APBSConfig.I_PARAM property) ipdb (pyrosetta.rosetta.protocols.simple_filters.ResidueDepthData property) ipdb() (pyrosetta.rosetta.protocols.simple_filters.ResidueDepthFrag method) Ir (pyrosetta.rosetta.core.chemical.element.Elements attribute) IRCollection (class in pyrosetta.rosetta.protocols.motifs) ires (pyrosetta.rosetta.protocols.simple_filters.ResidueDepthData property) ires() (pyrosetta.rosetta.protocols.simple_filters.ResidueDepthFrag method) IRmsdFilter (class in pyrosetta.rosetta.protocols.protein_interface_design.filters) IRmsdFilterCreator (class in pyrosetta.rosetta.protocols.protein_interface_design.filters) irstream (class in pyrosetta.rosetta.utility.io) irun (pyrosetta.rosetta.protocols.mpi_refinement.MethodParams property) is3D() (pyrosetta.rosetta.RDKit.Conformer method) is4D() (pyrosetta.rosetta.protocols.noesy_assign.CrossPeak method) (pyrosetta.rosetta.protocols.noesy_assign.CrossPeak3D method) (pyrosetta.rosetta.protocols.noesy_assign.CrossPeak4D method) is_a_neighbor_ (pyrosetta.rosetta.protocols.canonical_sampling.mc_convergence_checks.DataBuffer property) is_a_submotif() (pyrosetta.rosetta.core.pose.full_model_info.FullModelInfo method) is_a_submotif_seed() (pyrosetta.rosetta.core.pose.full_model_info.FullModelInfo method) is_aa_name_unknown() (in module pyrosetta.rosetta.core.chemical) is_acc_chem_type() (pyrosetta.rosetta.core.scoring.hbonds.HBondTypeManager static method) is_acceptor() (pyrosetta.rosetta.core.chemical.AtomType method) (pyrosetta.rosetta.core.pack.guidance_scoreterms.buried_unsat_penalty.graph.BuriedUnsatPenaltyGraphHbondDonorAcceptorGroup method) (pyrosetta.rosetta.core.scoring.hbonds.graph.AtomInfo method) (pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.Pharmacophore method) is_acetylated() (pyrosetta.rosetta.core.chemical.carbohydrates.CarbohydrateInfo method) is_acetylated_nterminus() (pyrosetta.rosetta.core.chemical.ResidueType method) is_achiral_backbone() (pyrosetta.rosetta.core.chemical.MutableResidueType method) (pyrosetta.rosetta.core.chemical.ResidueType method) (pyrosetta.rosetta.core.chemical.ResidueTypeBase method) is_achiral_sidechain() (pyrosetta.rosetta.core.chemical.MutableResidueType method) (pyrosetta.rosetta.core.chemical.ResidueType method) (pyrosetta.rosetta.core.chemical.ResidueTypeBase method) is_actcoord() (pyrosetta.rosetta.core.chemical.Atom method) is_active() (pyrosetta.rosetta.ObjexxFCL.FArrayInitializer_bool_ObjexxFCL_FArray1D_t method) (pyrosetta.rosetta.ObjexxFCL.FArrayInitializer_bool_ObjexxFCL_FArray2D_t method) (pyrosetta.rosetta.ObjexxFCL.FArrayInitializer_char_ObjexxFCL_FArray1D_t method) (pyrosetta.rosetta.ObjexxFCL.FArrayInitializer_core_pack_dunbrack_BBDepNRChiSample_float_ObjexxFCL_FArray2D_t method) (pyrosetta.rosetta.ObjexxFCL.FArrayInitializer_core_pack_dunbrack_BBDepScoreInterpData_1_ObjexxFCL_FArray2D_t method) (pyrosetta.rosetta.ObjexxFCL.FArrayInitializer_core_pack_dunbrack_BBDepScoreInterpData_1_ObjexxFCL_FArray3D_t method) (pyrosetta.rosetta.ObjexxFCL.FArrayInitializer_core_pack_dunbrack_BBDepScoreInterpData_2_ObjexxFCL_FArray2D_t method) (pyrosetta.rosetta.ObjexxFCL.FArrayInitializer_core_pack_dunbrack_BBDepScoreInterpData_2_ObjexxFCL_FArray3D_t method) (pyrosetta.rosetta.ObjexxFCL.FArrayInitializer_core_pack_dunbrack_BBDepScoreInterpData_3_ObjexxFCL_FArray2D_t method) (pyrosetta.rosetta.ObjexxFCL.FArrayInitializer_core_pack_dunbrack_BBDepScoreInterpData_3_ObjexxFCL_FArray3D_t method) (pyrosetta.rosetta.ObjexxFCL.FArrayInitializer_core_pack_dunbrack_BBDepScoreInterpData_4_ObjexxFCL_FArray2D_t method) (pyrosetta.rosetta.ObjexxFCL.FArrayInitializer_core_pack_dunbrack_BBDepScoreInterpData_4_ObjexxFCL_FArray3D_t method) (pyrosetta.rosetta.ObjexxFCL.FArrayInitializer_core_pack_dunbrack_BBDepScoreInterpData_5_ObjexxFCL_FArray2D_t method) (pyrosetta.rosetta.ObjexxFCL.FArrayInitializer_core_pack_dunbrack_BBDepScoreInterpData_5_ObjexxFCL_FArray3D_t method) (pyrosetta.rosetta.ObjexxFCL.FArrayInitializer_core_pack_dunbrack_BBIndNRChiSample_float_ObjexxFCL_FArray2D_t method) (pyrosetta.rosetta.ObjexxFCL.FArrayInitializer_core_pack_dunbrack_PackedDunbrackRotamer_1_1_float_ObjexxFCL_FArray2D_t method) (pyrosetta.rosetta.ObjexxFCL.FArrayInitializer_core_pack_dunbrack_PackedDunbrackRotamer_1_2_float_ObjexxFCL_FArray2D_t method) (pyrosetta.rosetta.ObjexxFCL.FArrayInitializer_core_pack_dunbrack_PackedDunbrackRotamer_1_3_float_ObjexxFCL_FArray2D_t method) (pyrosetta.rosetta.ObjexxFCL.FArrayInitializer_core_pack_dunbrack_PackedDunbrackRotamer_1_4_float_ObjexxFCL_FArray2D_t method) (pyrosetta.rosetta.ObjexxFCL.FArrayInitializer_core_pack_dunbrack_PackedDunbrackRotamer_1_5_float_ObjexxFCL_FArray2D_t method) (pyrosetta.rosetta.ObjexxFCL.FArrayInitializer_core_pack_dunbrack_PackedDunbrackRotamer_2_1_float_ObjexxFCL_FArray2D_t method) (pyrosetta.rosetta.ObjexxFCL.FArrayInitializer_core_pack_dunbrack_PackedDunbrackRotamer_2_2_float_ObjexxFCL_FArray2D_t method) (pyrosetta.rosetta.ObjexxFCL.FArrayInitializer_core_pack_dunbrack_PackedDunbrackRotamer_2_3_float_ObjexxFCL_FArray2D_t method) (pyrosetta.rosetta.ObjexxFCL.FArrayInitializer_core_pack_dunbrack_PackedDunbrackRotamer_2_4_float_ObjexxFCL_FArray2D_t method) (pyrosetta.rosetta.ObjexxFCL.FArrayInitializer_core_pack_dunbrack_PackedDunbrackRotamer_2_5_float_ObjexxFCL_FArray2D_t method) (pyrosetta.rosetta.ObjexxFCL.FArrayInitializer_core_pack_dunbrack_PackedDunbrackRotamer_3_1_float_ObjexxFCL_FArray2D_t method) (pyrosetta.rosetta.ObjexxFCL.FArrayInitializer_core_pack_dunbrack_PackedDunbrackRotamer_3_2_float_ObjexxFCL_FArray2D_t method) (pyrosetta.rosetta.ObjexxFCL.FArrayInitializer_core_pack_dunbrack_PackedDunbrackRotamer_3_3_float_ObjexxFCL_FArray2D_t method) (pyrosetta.rosetta.ObjexxFCL.FArrayInitializer_core_pack_dunbrack_PackedDunbrackRotamer_3_4_float_ObjexxFCL_FArray2D_t method) (pyrosetta.rosetta.ObjexxFCL.FArrayInitializer_core_pack_dunbrack_PackedDunbrackRotamer_3_5_float_ObjexxFCL_FArray2D_t method) (pyrosetta.rosetta.ObjexxFCL.FArrayInitializer_core_pack_dunbrack_PackedDunbrackRotamer_4_1_float_ObjexxFCL_FArray2D_t method) (pyrosetta.rosetta.ObjexxFCL.FArrayInitializer_core_pack_dunbrack_PackedDunbrackRotamer_4_2_float_ObjexxFCL_FArray2D_t method) (pyrosetta.rosetta.ObjexxFCL.FArrayInitializer_core_pack_dunbrack_PackedDunbrackRotamer_4_3_float_ObjexxFCL_FArray2D_t method) (pyrosetta.rosetta.ObjexxFCL.FArrayInitializer_core_pack_dunbrack_PackedDunbrackRotamer_4_4_float_ObjexxFCL_FArray2D_t method) (pyrosetta.rosetta.ObjexxFCL.FArrayInitializer_core_pack_dunbrack_PackedDunbrackRotamer_4_5_float_ObjexxFCL_FArray2D_t method) (pyrosetta.rosetta.ObjexxFCL.FArrayInitializer_core_pack_dunbrack_PackedDunbrackRotamer_5_1_float_ObjexxFCL_FArray2D_t method) (pyrosetta.rosetta.ObjexxFCL.FArrayInitializer_core_pack_dunbrack_PackedDunbrackRotamer_5_2_float_ObjexxFCL_FArray2D_t method) (pyrosetta.rosetta.ObjexxFCL.FArrayInitializer_core_pack_dunbrack_PackedDunbrackRotamer_5_3_float_ObjexxFCL_FArray2D_t method) (pyrosetta.rosetta.ObjexxFCL.FArrayInitializer_core_pack_dunbrack_PackedDunbrackRotamer_5_4_float_ObjexxFCL_FArray2D_t method) (pyrosetta.rosetta.ObjexxFCL.FArrayInitializer_core_pack_dunbrack_PackedDunbrackRotamer_5_5_float_ObjexxFCL_FArray2D_t method) (pyrosetta.rosetta.ObjexxFCL.FArrayInitializer_double_ObjexxFCL_FArray1D_t method) (pyrosetta.rosetta.ObjexxFCL.FArrayInitializer_double_ObjexxFCL_FArray2D_t method) (pyrosetta.rosetta.ObjexxFCL.FArrayInitializer_double_ObjexxFCL_FArray3D_t method) (pyrosetta.rosetta.ObjexxFCL.FArrayInitializer_double_ObjexxFCL_FArray4D_t method) (pyrosetta.rosetta.ObjexxFCL.FArrayInitializer_double_ObjexxFCL_FArray5D_t method) (pyrosetta.rosetta.ObjexxFCL.FArrayInitializer_float_ObjexxFCL_FArray1D_t method) (pyrosetta.rosetta.ObjexxFCL.FArrayInitializer_float_ObjexxFCL_FArray2D_t method) (pyrosetta.rosetta.ObjexxFCL.FArrayInitializer_float_ObjexxFCL_FArray3D_t method) (pyrosetta.rosetta.ObjexxFCL.FArrayInitializer_float_ObjexxFCL_FArray5D_t method) (pyrosetta.rosetta.ObjexxFCL.FArrayInitializer_int_ObjexxFCL_FArray1D_t method) (pyrosetta.rosetta.ObjexxFCL.FArrayInitializer_int_ObjexxFCL_FArray2D_t method) (pyrosetta.rosetta.ObjexxFCL.FArrayInitializer_int_ObjexxFCL_FArray3D_t method) (pyrosetta.rosetta.ObjexxFCL.FArrayInitializer_int_ObjexxFCL_FArray4D_t method) (pyrosetta.rosetta.ObjexxFCL.FArrayInitializer_int_ObjexxFCL_FArray5D_t method) (pyrosetta.rosetta.ObjexxFCL.FArrayInitializer_numeric_xyzVector_double_ObjexxFCL_FArray2D_t method) (pyrosetta.rosetta.ObjexxFCL.FArrayInitializer_ObjexxFCL_FArray1D_int_ObjexxFCL_FArray1D_t method) (pyrosetta.rosetta.ObjexxFCL.FArrayInitializer_ObjexxFCL_FArray2D_float__star__ObjexxFCL_FArray2D_t method) (pyrosetta.rosetta.ObjexxFCL.FArrayInitializer_ObjexxFCL_ubyte_ObjexxFCL_FArray2D_t method) (pyrosetta.rosetta.ObjexxFCL.FArrayInitializer_std_complex_double_ObjexxFCL_FArray3D_t method) (pyrosetta.rosetta.ObjexxFCL.FArrayInitializer_std_string_ObjexxFCL_FArray1D_t method) (pyrosetta.rosetta.ObjexxFCL.FArrayInitializer_std_string_ObjexxFCL_FArray2D_t method) (pyrosetta.rosetta.ObjexxFCL.FArrayInitializer_std_vector_unsigned_long_std_allocator_unsigned_long_ObjexxFCL_FArray3D_t method) (pyrosetta.rosetta.ObjexxFCL.FArrayInitializer_unsigned_char_ObjexxFCL_FArray2D_t method) (pyrosetta.rosetta.ObjexxFCL.FArrayInitializer_unsigned_char_ObjexxFCL_FArray3D_t method) (pyrosetta.rosetta.ObjexxFCL.FArrayInitializer_unsigned_char_ObjexxFCL_FArray4D_t method) (pyrosetta.rosetta.ObjexxFCL.FArrayInitializer_unsigned_long_ObjexxFCL_FArray1D_t method) (pyrosetta.rosetta.ObjexxFCL.FArrayInitializer_unsigned_long_ObjexxFCL_FArray2D_t method) (pyrosetta.rosetta.ObjexxFCL.FArrayInitializer_unsigned_long_ObjexxFCL_FArray3D_t method) (pyrosetta.rosetta.ObjexxFCL.FArrayInitializer_utility_vector1_core_pack_dunbrack_cenrot_CentroidRotamerSampleData_std_allocator_core_pack_dunbrack_cenrot_CentroidRotamerSampleData_ObjexxFCL_FArray2D_t method) (pyrosetta.rosetta.ObjexxFCL.FArrayInitializer_utility_vector1_double_std_allocator_double_ObjexxFCL_FArray2D_t method) (pyrosetta.rosetta.ObjexxFCL.FArrayInitializer_utility_vector1_double_std_allocator_double_ObjexxFCL_FArray3D_t method) (pyrosetta.rosetta.ObjexxFCL.FArrayInitializer_utility_vector1_numeric_xyzVector_double_std_allocator_numeric_xyzVector_double_ObjexxFCL_FArray3D_t method) (pyrosetta.rosetta.ObjexxFCL.FArrayInitializer_utility_vector1_unsigned_int_std_allocator_unsigned_int_ObjexxFCL_FArray3D_t method) is_acyclic() (pyrosetta.rosetta.core.chemical.carbohydrates.CarbohydrateInfo method) is_adduct() (pyrosetta.rosetta.core.chemical.ResidueType method) is_aldose() (pyrosetta.rosetta.core.chemical.carbohydrates.CarbohydrateInfo method) is_allowed_type() (pyrosetta.rosetta.core.energy_methods.RamaPreProEnergy method) is_alpha_aa() (pyrosetta.rosetta.core.chemical.ResidueType method) is_alpha_helical() (pyrosetta.rosetta.protocols.membrane.MPLipidAccessibility method) is_alpha_sugar() (pyrosetta.rosetta.core.chemical.carbohydrates.CarbohydrateInfo method) is_amino_sugar() (pyrosetta.rosetta.core.chemical.carbohydrates.CarbohydrateInfo method) is_ancestor_virtual() (pyrosetta.rosetta.core.conformation.symmetry.SymmData method) is_anti() (pyrosetta.rosetta.core.scoring.dssp.Pairing method) is_any_atom() (in module pyrosetta.rosetta.core.scoring) is_any_of() (in module pyrosetta.rosetta.ObjexxFCL) is_apolar() (pyrosetta.rosetta.core.conformation.Residue method) is_applicable() (pyrosetta.rosetta.core.fragment.AnnotatedFragData method) (pyrosetta.rosetta.core.fragment.BBTorsionAndAnglesSRFD method) (pyrosetta.rosetta.core.fragment.BBTorsionSRFD method) (pyrosetta.rosetta.core.fragment.DownJumpSRFD method) (pyrosetta.rosetta.core.fragment.FragData method) (pyrosetta.rosetta.core.fragment.Frame method) (pyrosetta.rosetta.core.fragment.IndependentBBTorsionSRFD method) (pyrosetta.rosetta.core.fragment.JumpingFrame method) (pyrosetta.rosetta.core.fragment.NonContinuousFrame method) (pyrosetta.rosetta.core.fragment.SecstructSRFD method) (pyrosetta.rosetta.core.fragment.SingleResidueFragData method) (pyrosetta.rosetta.core.fragment.UpJumpSRFD method) (pyrosetta.rosetta.protocols.enzdes.EnzdesFlexibleRegion method) is_approximately_equal() (pyrosetta.rosetta.core.scoring.func.SplineFunc method) is_aramid() (pyrosetta.rosetta.core.chemical.ResidueType method) (pyrosetta.rosetta.core.conformation.Residue method) is_archive_rank() (pyrosetta.rosetta.protocols.jd2.archive.MPIArchiveJobDistributor method) is_arg() (pyrosetta.rosetta.core.energy_methods.ArgCationPiEnergy method) is_aromatic() (pyrosetta.rosetta.core.chemical.AtomType method) (pyrosetta.rosetta.core.chemical.ResidueType method) (pyrosetta.rosetta.core.conformation.Residue method) is_asymmetric_seqpos() (pyrosetta.rosetta.core.conformation.symmetry.SymmetryInfo method) is_atom_axial_or_equatorial() (in module pyrosetta.rosetta.core.conformation) is_atom_axial_or_equatorial_to_ring() (in module pyrosetta.rosetta.core.chemical.rings) (in module pyrosetta.rosetta.core.conformation) (in module pyrosetta.rosetta.core.pose) is_atom_bin_in_range() (in module pyrosetta.rosetta.core.pose.rna) is_attached() (pyrosetta.rosetta.core.conformation.carbohydrates.GlycanTreeSetObserver method) (pyrosetta.rosetta.core.pose.datacache.CacheableObserver method) (pyrosetta.rosetta.core.pose.datacache.LengthEventCollector method) (pyrosetta.rosetta.core.pose.datacache.ObserverCache method) (pyrosetta.rosetta.core.pose.datacache.SpecialSegmentsObserver method) (pyrosetta.rosetta.protocols.denovo_design.components.StructureDataObserver method) (pyrosetta.rosetta.protocols.moves.PyMOLObserver method) (pyrosetta.rosetta.protocols.network.UIObserver method) (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.EnzdesCacheableObserver method) is_backbone() (pyrosetta.rosetta.core.chemical.Atom method) (pyrosetta.rosetta.core.scoring.hbonds.graph.AtomInfo method) (pyrosetta.rosetta.core.scoring.hbonds.hbtrie.HBAtom method) (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.EnzCstTemplateRes method) (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.MatchConstraintFileInfo method) is_backbone_heavyatom() (pyrosetta.rosetta.core.chemical.MutableResidueType method) is_backbone_only_cst() (pyrosetta.rosetta.protocols.forge.remodel.RemodelEnzdesCstModule method) (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.EnzConstraintIO method) is_barrel() (pyrosetta.rosetta.protocols.fldsgn.topology.Sheet method) is_base_paired() (pyrosetta.rosetta.protocols.dna.DNAParameters method) is_base_phosphate_atom_pair() (in module pyrosetta.rosetta.core.chemical.rna) is_base_type() (pyrosetta.rosetta.core.chemical.MutableResidueType method) (pyrosetta.rosetta.core.chemical.ResidueType method) (pyrosetta.rosetta.core.chemical.ResidueTypeBase method) is_bb (pyrosetta.rosetta.core.pack.guidance_scoreterms.lk_dome.MyWaterHolder property) is_been_accessed() (pyrosetta.rosetta.utility.options.BooleanOption method) (pyrosetta.rosetta.utility.options.BooleanVectorOption method) (pyrosetta.rosetta.utility.options.FileOption method) (pyrosetta.rosetta.utility.options.FileVectorOption method) (pyrosetta.rosetta.utility.options.IntegerOption method) (pyrosetta.rosetta.utility.options.IntegerVectorOption method) (pyrosetta.rosetta.utility.options.Option method) (pyrosetta.rosetta.utility.options.PathOption method) (pyrosetta.rosetta.utility.options.PathVectorOption method) (pyrosetta.rosetta.utility.options.RealOption method) (pyrosetta.rosetta.utility.options.RealVectorOption method) (pyrosetta.rosetta.utility.options.ResidueChainVectorOption method) (pyrosetta.rosetta.utility.options.ScalarOption method) (pyrosetta.rosetta.utility.options.ScalarOption_T_utility_options_BooleanOptionKey_bool_t method) (pyrosetta.rosetta.utility.options.ScalarOption_T_utility_options_FileOptionKey_utility_file_FileName_t method) (pyrosetta.rosetta.utility.options.ScalarOption_T_utility_options_IntegerOptionKey_int_t method) (pyrosetta.rosetta.utility.options.ScalarOption_T_utility_options_PathOptionKey_utility_file_PathName_t method) (pyrosetta.rosetta.utility.options.ScalarOption_T_utility_options_RealOptionKey_double_t method) (pyrosetta.rosetta.utility.options.ScalarOption_T_utility_options_StringOptionKey_std_string_t method) (pyrosetta.rosetta.utility.options.StringOption method) (pyrosetta.rosetta.utility.options.StringVectorOption method) (pyrosetta.rosetta.utility.options.VectorOption method) (pyrosetta.rosetta.utility.options.VectorOption_T_utility_options_BooleanVectorOptionKey_bool_t method) (pyrosetta.rosetta.utility.options.VectorOption_T_utility_options_FileVectorOptionKey_utility_file_FileName_t method) (pyrosetta.rosetta.utility.options.VectorOption_T_utility_options_IntegerVectorOptionKey_int_t method) (pyrosetta.rosetta.utility.options.VectorOption_T_utility_options_PathVectorOptionKey_utility_file_PathName_t method) (pyrosetta.rosetta.utility.options.VectorOption_T_utility_options_RealVectorOptionKey_double_t method) (pyrosetta.rosetta.utility.options.VectorOption_T_utility_options_ResidueChainVectorOptionKey_int_t method) (pyrosetta.rosetta.utility.options.VectorOption_T_utility_options_StringVectorOptionKey_std_string_t method) is_beta() (pyrosetta.rosetta.protocols.loop_grower.LoopGrower method) is_beta_aa() (pyrosetta.rosetta.core.chemical.ResidueType method) is_beta_aminoacid() (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.KinematicMover method) is_beta_sugar() (pyrosetta.rosetta.core.chemical.carbohydrates.CarbohydrateInfo method) is_blank() (in module pyrosetta.rosetta.ObjexxFCL) (pyrosetta.rosetta.ObjexxFCL.Cstring method) (pyrosetta.rosetta.ObjexxFCL.Fstring method) (pyrosetta.rosetta.ObjexxFCL.Fsubstring method) is_blank_seq() (in module pyrosetta.rosetta.core.import_pose) is_blank_string() (in module pyrosetta.rosetta.ObjexxFCL.format) is_bonded() (pyrosetta.rosetta.core.conformation.Conformation method) (pyrosetta.rosetta.core.conformation.Residue method) (pyrosetta.rosetta.core.conformation.symmetry.MirrorSymmetricConformation method) (pyrosetta.rosetta.core.conformation.symmetry.SymmetricConformation method) (pyrosetta.rosetta.protocols.environment.ProtectedConformation method) is_bool() (in module pyrosetta.rosetta.ObjexxFCL) (pyrosetta.rosetta.ObjexxFCL.Fstring method) (pyrosetta.rosetta.ObjexxFCL.Fsubstring method) is_branch_point() (pyrosetta.rosetta.core.chemical.ResidueType method) (pyrosetta.rosetta.core.conformation.Residue method) is_bulge() (pyrosetta.rosetta.core.scoring.dssp.StrandPairing method) (pyrosetta.rosetta.protocols.fldsgn.topology.StrandPairing method) is_bulged() (pyrosetta.rosetta.core.scoring.rna.data.RNA_DMS_LowResolutionPotential method) is_buried() (pyrosetta.rosetta.core.scoring.rna.RNA_ScoringInfo method) is_buried_ring() (pyrosetta.rosetta.protocols.pockets.GenPharmacophore method) is_c_terminus_fixed() (pyrosetta.rosetta.protocols.sewing.data_storage.LigandSegment method) (pyrosetta.rosetta.protocols.sewing.data_storage.SmartSegment method) is_camelid() (pyrosetta.rosetta.protocols.antibody.Ab_TemplateInfo method) (pyrosetta.rosetta.protocols.antibody.AntibodyInfo method) is_cancelled() (pyrosetta.rosetta.protocols.jd2.archive.Batch method) is_canonical() (in module pyrosetta.rosetta.protocols.cyclic_peptide_predict) (pyrosetta.rosetta.core.chemical.ResidueType method) is_canonical_aa() (pyrosetta.rosetta.core.chemical.ResidueType method) is_canonical_beta3_aa() (in module pyrosetta.rosetta.core.chemical) is_canonical_D_aa() (in module pyrosetta.rosetta.core.chemical) is_canonical_d_aminoacid() (pyrosetta.rosetta.core.scoring.Ramachandran method) is_canonical_L_aa_excluding_gly() (in module pyrosetta.rosetta.core.chemical) is_canonical_L_aa_or_gly() (in module pyrosetta.rosetta.core.chemical) is_canonical_nucleic() (pyrosetta.rosetta.core.chemical.ResidueType method) is_carbohydrate() (pyrosetta.rosetta.core.chemical.ResidueType method) (pyrosetta.rosetta.core.conformation.Residue method) is_carbohydrate_ring_atom() (in module pyrosetta.rosetta.core.scoring) is_catalytic_position() (pyrosetta.rosetta.protocols.enzdes.EnzdesBaseProtocol method) (pyrosetta.rosetta.protocols.enzdes.EnzdesFixBBProtocol method) (pyrosetta.rosetta.protocols.enzdes.EnzdesFlexBBProtocol method) (pyrosetta.rosetta.protocols.enzdes.SecondaryMatchProtocol method) is_catalytic_seqpos() (in module pyrosetta.rosetta.protocols.enzdes.enzutil) is_centroid() (pyrosetta.rosetta.core.conformation.Conformation method) (pyrosetta.rosetta.core.conformation.symmetry.MirrorSymmetricConformation method) (pyrosetta.rosetta.core.conformation.symmetry.SymmetricConformation method) (pyrosetta.rosetta.core.pose.Pose method) (pyrosetta.rosetta.protocols.environment.ProtectedConformation method) is_changed() (pyrosetta.rosetta.core.scoring.facts.FACTSPoseInfo method) is_char() (in module pyrosetta.rosetta.ObjexxFCL) (pyrosetta.rosetta.ObjexxFCL.Fstring method) (pyrosetta.rosetta.ObjexxFCL.Fsubstring method) is_charged() (pyrosetta.rosetta.core.chemical.ResidueType method) (pyrosetta.rosetta.core.conformation.Residue method) is_chargedH() (pyrosetta.rosetta.core.scoring.facts.FACTSRsdTypeInfo method) is_chemical_bond() (pyrosetta.rosetta.core.kinematics.Edge method) is_chimaeric() (pyrosetta.rosetta.protocols.sewing.data_storage.LigandSegment method) (pyrosetta.rosetta.protocols.sewing.data_storage.SmartSegment method) is_cl_value() (pyrosetta.rosetta.utility.options.BooleanOption method) (pyrosetta.rosetta.utility.options.BooleanVectorOption method) (pyrosetta.rosetta.utility.options.FileOption method) (pyrosetta.rosetta.utility.options.FileVectorOption method) (pyrosetta.rosetta.utility.options.IntegerOption method) (pyrosetta.rosetta.utility.options.IntegerVectorOption method) (pyrosetta.rosetta.utility.options.Option method) (pyrosetta.rosetta.utility.options.PathOption method) (pyrosetta.rosetta.utility.options.PathVectorOption method) (pyrosetta.rosetta.utility.options.RealOption method) (pyrosetta.rosetta.utility.options.RealVectorOption method) (pyrosetta.rosetta.utility.options.ResidueChainVectorOption method) (pyrosetta.rosetta.utility.options.ScalarOption method) (pyrosetta.rosetta.utility.options.ScalarOption_T_utility_options_BooleanOptionKey_bool_t method) (pyrosetta.rosetta.utility.options.ScalarOption_T_utility_options_FileOptionKey_utility_file_FileName_t method) (pyrosetta.rosetta.utility.options.ScalarOption_T_utility_options_IntegerOptionKey_int_t method) (pyrosetta.rosetta.utility.options.ScalarOption_T_utility_options_PathOptionKey_utility_file_PathName_t method) (pyrosetta.rosetta.utility.options.ScalarOption_T_utility_options_RealOptionKey_double_t method) (pyrosetta.rosetta.utility.options.ScalarOption_T_utility_options_StringOptionKey_std_string_t method) (pyrosetta.rosetta.utility.options.StringOption method) (pyrosetta.rosetta.utility.options.StringVectorOption method) (pyrosetta.rosetta.utility.options.VectorOption method) (pyrosetta.rosetta.utility.options.VectorOption_T_utility_options_BooleanVectorOptionKey_bool_t method) (pyrosetta.rosetta.utility.options.VectorOption_T_utility_options_FileVectorOptionKey_utility_file_FileName_t method) (pyrosetta.rosetta.utility.options.VectorOption_T_utility_options_IntegerVectorOptionKey_int_t method) (pyrosetta.rosetta.utility.options.VectorOption_T_utility_options_PathVectorOptionKey_utility_file_PathName_t method) (pyrosetta.rosetta.utility.options.VectorOption_T_utility_options_RealVectorOptionKey_double_t method) (pyrosetta.rosetta.utility.options.VectorOption_T_utility_options_ResidueChainVectorOptionKey_int_t method) (pyrosetta.rosetta.utility.options.VectorOption_T_utility_options_StringVectorOptionKey_std_string_t method) is_claim() (pyrosetta.rosetta.protocols.environment.claims.CutBiasClaim static method) (pyrosetta.rosetta.protocols.environment.claims.EnvClaim static method) (pyrosetta.rosetta.protocols.environment.claims.JumpClaim static method) (pyrosetta.rosetta.protocols.environment.claims.TorsionClaim static method) (pyrosetta.rosetta.protocols.environment.claims.VirtResClaim static method) (pyrosetta.rosetta.protocols.environment.claims.XYZClaim static method) is_clashing() (pyrosetta.rosetta.core.simple_metrics.per_residue_metrics.PerResidueClashMetric method) is_close() (pyrosetta.rosetta.numeric.HomogeneousTransform_Double method) (pyrosetta.rosetta.numeric.HomogeneousTransform_double_t method) (pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.Pharmacophore method) is_close_chain_break() (in module pyrosetta.rosetta.protocols.stepwise.legacy.modeler.protein) is_closer_to_tgt() (pyrosetta.rosetta.protocols.constel.OrientCommon static method) is_coarse() (pyrosetta.rosetta.core.chemical.ResidueType method) (pyrosetta.rosetta.core.conformation.Residue method) is_collinear() (in module pyrosetta.rosetta.core.kinematics.tree) is_compatible() (pyrosetta.rosetta.core.fragment.AnnotatedFragData method) (pyrosetta.rosetta.core.fragment.BBTorsionAndAnglesSRFD method) (pyrosetta.rosetta.core.fragment.BBTorsionSRFD method) (pyrosetta.rosetta.core.fragment.DownJumpSRFD method) (pyrosetta.rosetta.core.fragment.FragData method) (pyrosetta.rosetta.core.fragment.IndependentBBTorsionSRFD method) (pyrosetta.rosetta.core.fragment.SecstructSRFD method) (pyrosetta.rosetta.core.fragment.SingleResidueFragData method) (pyrosetta.rosetta.core.fragment.UpJumpSRFD method) is_compliant() (pyrosetta.rosetta.protocols.noesy_assign.CovalentCompliance method) is_conjugatable() (pyrosetta.rosetta.core.chemical.Element method) is_conjugated() (pyrosetta.rosetta.core.chemical.gasteiger.GasteigerAtomTypeData method) is_connect() (pyrosetta.rosetta.core.chemical.ICoorAtomID method) is_connected() (pyrosetta.rosetta.core.conformation.carbohydrates.GlycanTree method) is_conserved() (pyrosetta.rosetta.core.pose.datacache.PositionConservedResiduesStore method) is_constel_valid() (pyrosetta.rosetta.protocols.constel.MasterFilter static method) is_continuous() (pyrosetta.rosetta.core.fragment.Frame method) (pyrosetta.rosetta.core.fragment.JumpingFrame method) (pyrosetta.rosetta.core.fragment.NonContinuousFrame method) (pyrosetta.rosetta.protocols.enzdes.EnzdesFlexibleRegion method) (pyrosetta.rosetta.protocols.sewing.data_storage.HashedSmartAssembly method) (pyrosetta.rosetta.protocols.sewing.data_storage.SmartAssembly method) is_converged() (pyrosetta.rosetta.protocols.ddg.CartesianddG.MutationSet method) is_counted() (pyrosetta.rosetta.core.pack.guidance_scoreterms.buried_unsat_penalty.graph.BuriedUnsatPenaltyGraphHbondDonorAcceptorGroup method) (pyrosetta.rosetta.protocols.simple_filters.LongestContinuousApolarSegmentFilter method) (pyrosetta.rosetta.protocols.simple_filters.LongestContinuousPolarSegmentFilter method) is_covalent() (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.EnzConstraintParameters method) (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.MatchConstraintFileInfo method) is_cutpoint() (pyrosetta.rosetta.core.kinematics.FoldTree method) is_cutpoint_closed() (in module pyrosetta.rosetta.protocols.stepwise.modeler) is_cutpoint_closed_atom() (in module pyrosetta.rosetta.core.pose.rna) is_cutpoint_closed_torsion() (in module pyrosetta.rosetta.core.pose.rna) is_cutpoint_open() (in module pyrosetta.rosetta.core.pose.rna) is_cyclic() (pyrosetta.rosetta.core.chemical.carbohydrates.CarbohydrateInfo method) (pyrosetta.rosetta.core.chemical.ResidueType method) is_cyclizable (pyrosetta.rosetta.protocols.peptide_deriver.CyclizedPeptideInfo property) is_d_aa() (pyrosetta.rosetta.core.chemical.MutableResidueType method) (pyrosetta.rosetta.core.chemical.ResidueType method) (pyrosetta.rosetta.core.chemical.ResidueTypeBase method) is_d_aminoacid() (pyrosetta.rosetta.core.energy_methods.ReferenceEnergy method) is_d_rna() (pyrosetta.rosetta.core.chemical.MutableResidueType method) (pyrosetta.rosetta.core.chemical.ResidueType method) (pyrosetta.rosetta.core.chemical.ResidueTypeBase method) (pyrosetta.rosetta.core.conformation.Residue method) is_D_sugar() (pyrosetta.rosetta.core.chemical.carbohydrates.CarbohydrateInfo method) is_data_type() (pyrosetta.rosetta.core.io.mmtf.ExtraDataEnumManager method) is_db_partitioned() (pyrosetta.rosetta.utility.sql_database.session method) is_default() (pyrosetta.rosetta.core.scoring.mhc_epitope_energy.MHCEpitopeEnergySetup method) is_deriv_type() (pyrosetta.rosetta.core.scoring.hbonds.HBondTypeManager static method) is_designed() (pyrosetta.rosetta.protocols.mean_field.RotMatrix method) is_diagonal() (pyrosetta.rosetta.numeric.MathMatrix_double_t method) (pyrosetta.rosetta.numeric.MathMatrix_float_t method) is_directory() (in module pyrosetta.rosetta.utility.file) is_disulfide() (pyrosetta.rosetta.core.scoring.disulfides.CentroidDisulfidePotential method) is_disulfide_bond() (in module pyrosetta.rosetta.core.conformation) is_disulfide_bonded() (pyrosetta.rosetta.core.chemical.ResidueType method) is_DNA() (pyrosetta.rosetta.core.chemical.MutableResidueType method) (pyrosetta.rosetta.core.chemical.ResidueType method) (pyrosetta.rosetta.core.chemical.ResidueTypeBase method) (pyrosetta.rosetta.core.conformation.Residue method) is_dna() (pyrosetta.rosetta.core.scoring.hbonds.hbtrie.HBAtom method) is_don_chem_type() (pyrosetta.rosetta.core.scoring.hbonds.HBondTypeManager static method) is_donor() (pyrosetta.rosetta.core.chemical.AtomType method) (pyrosetta.rosetta.core.pack.guidance_scoreterms.buried_unsat_penalty.graph.BuriedUnsatPenaltyGraphHbondDonorAcceptorGroup method) (pyrosetta.rosetta.core.scoring.hbonds.graph.AtomInfo method) (pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.Pharmacophore method) is_double() (in module pyrosetta.rosetta.ObjexxFCL) (pyrosetta.rosetta.ObjexxFCL.Fstring method) (pyrosetta.rosetta.ObjexxFCL.Fsubstring method) is_edge_file_loaded() (pyrosetta.rosetta.protocols.sewing.hashing.EdgeMapGenerator method) is_elimination_candidate() (pyrosetta.rosetta.protocols.noesy_assign.CrossPeak method) (pyrosetta.rosetta.protocols.noesy_assign.CrossPeak3D method) (pyrosetta.rosetta.protocols.noesy_assign.CrossPeak4D method) is_empty() (pyrosetta.rosetta.core.scoring.constraints.ConstraintSet method) (pyrosetta.rosetta.protocols.comparative_modeling.IgnoreSubsetConstraintSet method) (pyrosetta.rosetta.protocols.constraints_additional.MaxSeqSepConstraintSet method) (pyrosetta.rosetta.protocols.loop_grower.LoopPartialSolutionStore method) (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.EnzConstraintParameters method) is_end_element() (pyrosetta.rosetta.utility.graph.DirectedEdgeList method) (pyrosetta.rosetta.utility.graph.EdgeList method) is_equivalent() (pyrosetta.rosetta.core.kinematics.FoldTree method) is_excluded() (pyrosetta.rosetta.protocols.mpi_refinement.Scheduler method) is_experimental_technique() (pyrosetta.rosetta.core.io.HeaderInformation method) is_extended (pyrosetta.rosetta.protocols.hbnet.HBondNetStruct property) is_extended() (pyrosetta.rosetta.protocols.loops.Loop method) is_fake() (pyrosetta.rosetta.core.chemical.Atom method) (pyrosetta.rosetta.core.chemical.Bond method) (pyrosetta.rosetta.core.chemical.Element method) is_false_string() (in module pyrosetta.rosetta.utility) is_finite() (pyrosetta.rosetta.core.scoring.EMapVector method) (pyrosetta.rosetta.core.scoring.sc.Atom method) (pyrosetta.rosetta.numeric.xyzMatrix_double_t method) (pyrosetta.rosetta.numeric.xyzMatrix_float_t method) (pyrosetta.rosetta.numeric.xyzVector_double_t method) (pyrosetta.rosetta.numeric.xyzVector_float_t method) (pyrosetta.rosetta.numeric.xyzVector_int_t method) (pyrosetta.rosetta.numeric.xyzVector_unsigned_long_t method) is_flexible() (pyrosetta.rosetta.protocols.enzdes.EnzdesFlexBBProtocol method) is_float() (in module pyrosetta.rosetta.ObjexxFCL) (pyrosetta.rosetta.ObjexxFCL.Fstring method) (pyrosetta.rosetta.ObjexxFCL.Fsubstring method) is_flushed() (pyrosetta.logging_support.PythonLoggingSink method) (pyrosetta.rosetta.basic.basic_otstream_char_std_char_traits_char_t method) (pyrosetta.rosetta.basic.ComparingTracer method) (pyrosetta.rosetta.basic.MemTracerImpl method) (pyrosetta.rosetta.basic.MemTracerImpl.TracerProxyImpl method) (pyrosetta.rosetta.basic.PyTracer method) (pyrosetta.rosetta.basic.TracerImpl method) (pyrosetta.rosetta.basic.TracerImpl.TracerProxyImpl method) (pyrosetta.rosetta.basic.TracerToFile method) is_folded() (pyrosetta.rosetta.protocols.noesy_assign.FoldResonance method) is_folded_down() (pyrosetta.rosetta.protocols.noesy_assign.FoldResonance method) is_folded_up() (pyrosetta.rosetta.protocols.noesy_assign.FoldResonance method) is_foldtype() (pyrosetta.rosetta.protocols.fldsgn.topology.SheetFoldTypeManager method) is_freedof() (pyrosetta.rosetta.core.scoring.facts.FACTSRsdTypeInfo method) is_fullatom() (pyrosetta.rosetta.core.conformation.Conformation method) (pyrosetta.rosetta.core.conformation.symmetry.MirrorSymmetricConformation method) (pyrosetta.rosetta.core.conformation.symmetry.SymmetricConformation method) (pyrosetta.rosetta.core.fragment.rna.FullAtomRNA_Fragments method) (pyrosetta.rosetta.core.fragment.rna.RNA_Fragments method) (pyrosetta.rosetta.core.pose.Pose method) (pyrosetta.rosetta.protocols.environment.ProtectedConformation method) (pyrosetta.rosetta.protocols.rna.denovo.coarse.CoarseRNA_Fragments method) is_function() (pyrosetta.rosetta.ObjexxFCL.FArrayInitializer_bool_ObjexxFCL_FArray1D_t method) (pyrosetta.rosetta.ObjexxFCL.FArrayInitializer_bool_ObjexxFCL_FArray2D_t method) (pyrosetta.rosetta.ObjexxFCL.FArrayInitializer_char_ObjexxFCL_FArray1D_t method) (pyrosetta.rosetta.ObjexxFCL.FArrayInitializer_core_pack_dunbrack_BBDepNRChiSample_float_ObjexxFCL_FArray2D_t method) (pyrosetta.rosetta.ObjexxFCL.FArrayInitializer_core_pack_dunbrack_BBDepScoreInterpData_1_ObjexxFCL_FArray2D_t method) (pyrosetta.rosetta.ObjexxFCL.FArrayInitializer_core_pack_dunbrack_BBDepScoreInterpData_1_ObjexxFCL_FArray3D_t method) (pyrosetta.rosetta.ObjexxFCL.FArrayInitializer_core_pack_dunbrack_BBDepScoreInterpData_2_ObjexxFCL_FArray2D_t method) (pyrosetta.rosetta.ObjexxFCL.FArrayInitializer_core_pack_dunbrack_BBDepScoreInterpData_2_ObjexxFCL_FArray3D_t method) (pyrosetta.rosetta.ObjexxFCL.FArrayInitializer_core_pack_dunbrack_BBDepScoreInterpData_3_ObjexxFCL_FArray2D_t method) (pyrosetta.rosetta.ObjexxFCL.FArrayInitializer_core_pack_dunbrack_BBDepScoreInterpData_3_ObjexxFCL_FArray3D_t method) (pyrosetta.rosetta.ObjexxFCL.FArrayInitializer_core_pack_dunbrack_BBDepScoreInterpData_4_ObjexxFCL_FArray2D_t method) (pyrosetta.rosetta.ObjexxFCL.FArrayInitializer_core_pack_dunbrack_BBDepScoreInterpData_4_ObjexxFCL_FArray3D_t method) (pyrosetta.rosetta.ObjexxFCL.FArrayInitializer_core_pack_dunbrack_BBDepScoreInterpData_5_ObjexxFCL_FArray2D_t method) (pyrosetta.rosetta.ObjexxFCL.FArrayInitializer_core_pack_dunbrack_BBDepScoreInterpData_5_ObjexxFCL_FArray3D_t method) (pyrosetta.rosetta.ObjexxFCL.FArrayInitializer_core_pack_dunbrack_BBIndNRChiSample_float_ObjexxFCL_FArray2D_t method) (pyrosetta.rosetta.ObjexxFCL.FArrayInitializer_core_pack_dunbrack_PackedDunbrackRotamer_1_1_float_ObjexxFCL_FArray2D_t method) (pyrosetta.rosetta.ObjexxFCL.FArrayInitializer_core_pack_dunbrack_PackedDunbrackRotamer_1_2_float_ObjexxFCL_FArray2D_t method) (pyrosetta.rosetta.ObjexxFCL.FArrayInitializer_core_pack_dunbrack_PackedDunbrackRotamer_1_3_float_ObjexxFCL_FArray2D_t method) (pyrosetta.rosetta.ObjexxFCL.FArrayInitializer_core_pack_dunbrack_PackedDunbrackRotamer_1_4_float_ObjexxFCL_FArray2D_t method) (pyrosetta.rosetta.ObjexxFCL.FArrayInitializer_core_pack_dunbrack_PackedDunbrackRotamer_1_5_float_ObjexxFCL_FArray2D_t method) (pyrosetta.rosetta.ObjexxFCL.FArrayInitializer_core_pack_dunbrack_PackedDunbrackRotamer_2_1_float_ObjexxFCL_FArray2D_t method) (pyrosetta.rosetta.ObjexxFCL.FArrayInitializer_core_pack_dunbrack_PackedDunbrackRotamer_2_2_float_ObjexxFCL_FArray2D_t method) (pyrosetta.rosetta.ObjexxFCL.FArrayInitializer_core_pack_dunbrack_PackedDunbrackRotamer_2_3_float_ObjexxFCL_FArray2D_t method) (pyrosetta.rosetta.ObjexxFCL.FArrayInitializer_core_pack_dunbrack_PackedDunbrackRotamer_2_4_float_ObjexxFCL_FArray2D_t method) (pyrosetta.rosetta.ObjexxFCL.FArrayInitializer_core_pack_dunbrack_PackedDunbrackRotamer_2_5_float_ObjexxFCL_FArray2D_t method) (pyrosetta.rosetta.ObjexxFCL.FArrayInitializer_core_pack_dunbrack_PackedDunbrackRotamer_3_1_float_ObjexxFCL_FArray2D_t method) (pyrosetta.rosetta.ObjexxFCL.FArrayInitializer_core_pack_dunbrack_PackedDunbrackRotamer_3_2_float_ObjexxFCL_FArray2D_t method) (pyrosetta.rosetta.ObjexxFCL.FArrayInitializer_core_pack_dunbrack_PackedDunbrackRotamer_3_3_float_ObjexxFCL_FArray2D_t method) (pyrosetta.rosetta.ObjexxFCL.FArrayInitializer_core_pack_dunbrack_PackedDunbrackRotamer_3_4_float_ObjexxFCL_FArray2D_t method) (pyrosetta.rosetta.ObjexxFCL.FArrayInitializer_core_pack_dunbrack_PackedDunbrackRotamer_3_5_float_ObjexxFCL_FArray2D_t method) (pyrosetta.rosetta.ObjexxFCL.FArrayInitializer_core_pack_dunbrack_PackedDunbrackRotamer_4_1_float_ObjexxFCL_FArray2D_t method) (pyrosetta.rosetta.ObjexxFCL.FArrayInitializer_core_pack_dunbrack_PackedDunbrackRotamer_4_2_float_ObjexxFCL_FArray2D_t method) (pyrosetta.rosetta.ObjexxFCL.FArrayInitializer_core_pack_dunbrack_PackedDunbrackRotamer_4_3_float_ObjexxFCL_FArray2D_t method) (pyrosetta.rosetta.ObjexxFCL.FArrayInitializer_core_pack_dunbrack_PackedDunbrackRotamer_4_4_float_ObjexxFCL_FArray2D_t method) (pyrosetta.rosetta.ObjexxFCL.FArrayInitializer_core_pack_dunbrack_PackedDunbrackRotamer_4_5_float_ObjexxFCL_FArray2D_t method) (pyrosetta.rosetta.ObjexxFCL.FArrayInitializer_core_pack_dunbrack_PackedDunbrackRotamer_5_1_float_ObjexxFCL_FArray2D_t method) (pyrosetta.rosetta.ObjexxFCL.FArrayInitializer_core_pack_dunbrack_PackedDunbrackRotamer_5_2_float_ObjexxFCL_FArray2D_t method) (pyrosetta.rosetta.ObjexxFCL.FArrayInitializer_core_pack_dunbrack_PackedDunbrackRotamer_5_3_float_ObjexxFCL_FArray2D_t method) (pyrosetta.rosetta.ObjexxFCL.FArrayInitializer_core_pack_dunbrack_PackedDunbrackRotamer_5_4_float_ObjexxFCL_FArray2D_t method) (pyrosetta.rosetta.ObjexxFCL.FArrayInitializer_core_pack_dunbrack_PackedDunbrackRotamer_5_5_float_ObjexxFCL_FArray2D_t method) (pyrosetta.rosetta.ObjexxFCL.FArrayInitializer_double_ObjexxFCL_FArray1D_t method) (pyrosetta.rosetta.ObjexxFCL.FArrayInitializer_double_ObjexxFCL_FArray2D_t method) (pyrosetta.rosetta.ObjexxFCL.FArrayInitializer_double_ObjexxFCL_FArray3D_t method) (pyrosetta.rosetta.ObjexxFCL.FArrayInitializer_double_ObjexxFCL_FArray4D_t method) (pyrosetta.rosetta.ObjexxFCL.FArrayInitializer_double_ObjexxFCL_FArray5D_t method) (pyrosetta.rosetta.ObjexxFCL.FArrayInitializer_float_ObjexxFCL_FArray1D_t method) (pyrosetta.rosetta.ObjexxFCL.FArrayInitializer_float_ObjexxFCL_FArray2D_t method) (pyrosetta.rosetta.ObjexxFCL.FArrayInitializer_float_ObjexxFCL_FArray3D_t method) (pyrosetta.rosetta.ObjexxFCL.FArrayInitializer_float_ObjexxFCL_FArray5D_t method) (pyrosetta.rosetta.ObjexxFCL.FArrayInitializer_int_ObjexxFCL_FArray1D_t method) (pyrosetta.rosetta.ObjexxFCL.FArrayInitializer_int_ObjexxFCL_FArray2D_t method) (pyrosetta.rosetta.ObjexxFCL.FArrayInitializer_int_ObjexxFCL_FArray3D_t method) (pyrosetta.rosetta.ObjexxFCL.FArrayInitializer_int_ObjexxFCL_FArray4D_t method) (pyrosetta.rosetta.ObjexxFCL.FArrayInitializer_int_ObjexxFCL_FArray5D_t method) (pyrosetta.rosetta.ObjexxFCL.FArrayInitializer_numeric_xyzVector_double_ObjexxFCL_FArray2D_t method) (pyrosetta.rosetta.ObjexxFCL.FArrayInitializer_ObjexxFCL_FArray1D_int_ObjexxFCL_FArray1D_t method) (pyrosetta.rosetta.ObjexxFCL.FArrayInitializer_ObjexxFCL_FArray2D_float__star__ObjexxFCL_FArray2D_t method) (pyrosetta.rosetta.ObjexxFCL.FArrayInitializer_ObjexxFCL_ubyte_ObjexxFCL_FArray2D_t method) (pyrosetta.rosetta.ObjexxFCL.FArrayInitializer_std_complex_double_ObjexxFCL_FArray3D_t method) (pyrosetta.rosetta.ObjexxFCL.FArrayInitializer_std_string_ObjexxFCL_FArray1D_t method) (pyrosetta.rosetta.ObjexxFCL.FArrayInitializer_std_string_ObjexxFCL_FArray2D_t method) (pyrosetta.rosetta.ObjexxFCL.FArrayInitializer_std_vector_unsigned_long_std_allocator_unsigned_long_ObjexxFCL_FArray3D_t method) (pyrosetta.rosetta.ObjexxFCL.FArrayInitializer_unsigned_char_ObjexxFCL_FArray2D_t method) (pyrosetta.rosetta.ObjexxFCL.FArrayInitializer_unsigned_char_ObjexxFCL_FArray3D_t method) (pyrosetta.rosetta.ObjexxFCL.FArrayInitializer_unsigned_char_ObjexxFCL_FArray4D_t method) (pyrosetta.rosetta.ObjexxFCL.FArrayInitializer_unsigned_long_ObjexxFCL_FArray1D_t method) (pyrosetta.rosetta.ObjexxFCL.FArrayInitializer_unsigned_long_ObjexxFCL_FArray2D_t method) (pyrosetta.rosetta.ObjexxFCL.FArrayInitializer_unsigned_long_ObjexxFCL_FArray3D_t method) (pyrosetta.rosetta.ObjexxFCL.FArrayInitializer_utility_vector1_core_pack_dunbrack_cenrot_CentroidRotamerSampleData_std_allocator_core_pack_dunbrack_cenrot_CentroidRotamerSampleData_ObjexxFCL_FArray2D_t method) (pyrosetta.rosetta.ObjexxFCL.FArrayInitializer_utility_vector1_double_std_allocator_double_ObjexxFCL_FArray2D_t method) (pyrosetta.rosetta.ObjexxFCL.FArrayInitializer_utility_vector1_double_std_allocator_double_ObjexxFCL_FArray3D_t method) (pyrosetta.rosetta.ObjexxFCL.FArrayInitializer_utility_vector1_numeric_xyzVector_double_std_allocator_numeric_xyzVector_double_ObjexxFCL_FArray3D_t method) (pyrosetta.rosetta.ObjexxFCL.FArrayInitializer_utility_vector1_unsigned_int_std_allocator_unsigned_int_ObjexxFCL_FArray3D_t method) is_furanose() (pyrosetta.rosetta.core.chemical.carbohydrates.CarbohydrateInfo method) is_gamma_aa() (pyrosetta.rosetta.core.chemical.ResidueType method) is_gap() (pyrosetta.rosetta.core.sequence.ChemicalShiftSequence method) (pyrosetta.rosetta.core.sequence.CompositeSequence method) (pyrosetta.rosetta.core.sequence.Sequence method) (pyrosetta.rosetta.core.sequence.SequenceCoupling method) (pyrosetta.rosetta.core.sequence.SequenceProfile method) is_gapped() (pyrosetta.rosetta.core.sequence.SequenceAlignment method) is_gasteiger_atom_type() (pyrosetta.rosetta.core.chemical.gasteiger.GasteigerAtomTypeData method) is_geo_dim_type() (pyrosetta.rosetta.core.scoring.hbonds.HBondTypeManager static method) is_geometry_initialized() (pyrosetta.rosetta.protocols.fldsgn.topology.Helix method) (pyrosetta.rosetta.protocols.fldsgn.topology.Loop method) (pyrosetta.rosetta.protocols.fldsgn.topology.SS_Base method) (pyrosetta.rosetta.protocols.fldsgn.topology.Strand method) is_glob() (pyrosetta.rosetta.core.scoring.saxs.FormFactor method) is_glycoside() (pyrosetta.rosetta.core.chemical.carbohydrates.CarbohydrateInfo method) is_glycosidic_omega2_torsion() (in module pyrosetta.rosetta.core.pose.carbohydrates) is_glycosidic_omega3_torsion() (in module pyrosetta.rosetta.core.pose.carbohydrates) is_glycosidic_omega_torsion() (in module pyrosetta.rosetta.core.conformation.carbohydrates) (in module pyrosetta.rosetta.core.pose.carbohydrates) is_glycosidic_phi_torsion() (in module pyrosetta.rosetta.core.conformation.carbohydrates) (in module pyrosetta.rosetta.core.pose.carbohydrates) is_glycosidic_psi_torsion() (in module pyrosetta.rosetta.core.conformation.carbohydrates) (in module pyrosetta.rosetta.core.pose.carbohydrates) is_glycosidic_torsion() (in module pyrosetta.rosetta.core.pose.carbohydrates) is_good() (pyrosetta.rosetta.core.sequence.ChemicalShiftScoringScheme method) (pyrosetta.rosetta.core.sequence.CompassScoringScheme method) (pyrosetta.rosetta.core.sequence.CompositeScoringScheme method) (pyrosetta.rosetta.core.sequence.DPScoringScheme method) (pyrosetta.rosetta.core.sequence.L1ScoringScheme method) (pyrosetta.rosetta.core.sequence.MatrixScoringScheme method) (pyrosetta.rosetta.core.sequence.PairScoringScheme method) (pyrosetta.rosetta.core.sequence.ProfSimScoringScheme method) (pyrosetta.rosetta.core.sequence.ScoringScheme method) (pyrosetta.rosetta.core.sequence.SimpleScoringScheme method) (pyrosetta.rosetta.protocols.abinitio.Template method) (pyrosetta.rosetta.protocols.abinitio.Templates method) is_group() (pyrosetta.rosetta.utility.options.BooleanOption method) (pyrosetta.rosetta.utility.options.BooleanVectorOption method) (pyrosetta.rosetta.utility.options.FileOption method) (pyrosetta.rosetta.utility.options.FileVectorOption method) (pyrosetta.rosetta.utility.options.IntegerOption method) (pyrosetta.rosetta.utility.options.IntegerVectorOption method) (pyrosetta.rosetta.utility.options.Option method) (pyrosetta.rosetta.utility.options.PathOption method) (pyrosetta.rosetta.utility.options.PathVectorOption method) (pyrosetta.rosetta.utility.options.RealOption method) (pyrosetta.rosetta.utility.options.RealVectorOption method) (pyrosetta.rosetta.utility.options.ResidueChainVectorOption method) (pyrosetta.rosetta.utility.options.ScalarOption method) (pyrosetta.rosetta.utility.options.ScalarOption_T_utility_options_BooleanOptionKey_bool_t method) (pyrosetta.rosetta.utility.options.ScalarOption_T_utility_options_FileOptionKey_utility_file_FileName_t method) (pyrosetta.rosetta.utility.options.ScalarOption_T_utility_options_IntegerOptionKey_int_t method) (pyrosetta.rosetta.utility.options.ScalarOption_T_utility_options_PathOptionKey_utility_file_PathName_t method) (pyrosetta.rosetta.utility.options.ScalarOption_T_utility_options_RealOptionKey_double_t method) (pyrosetta.rosetta.utility.options.ScalarOption_T_utility_options_StringOptionKey_std_string_t method) (pyrosetta.rosetta.utility.options.StringOption method) (pyrosetta.rosetta.utility.options.StringVectorOption method) (pyrosetta.rosetta.utility.options.VectorOption method) (pyrosetta.rosetta.utility.options.VectorOption_T_utility_options_BooleanVectorOptionKey_bool_t method) (pyrosetta.rosetta.utility.options.VectorOption_T_utility_options_FileVectorOptionKey_utility_file_FileName_t method) (pyrosetta.rosetta.utility.options.VectorOption_T_utility_options_IntegerVectorOptionKey_int_t method) (pyrosetta.rosetta.utility.options.VectorOption_T_utility_options_PathVectorOptionKey_utility_file_PathName_t method) (pyrosetta.rosetta.utility.options.VectorOption_T_utility_options_RealVectorOptionKey_double_t method) (pyrosetta.rosetta.utility.options.VectorOption_T_utility_options_ResidueChainVectorOptionKey_int_t method) (pyrosetta.rosetta.utility.options.VectorOption_T_utility_options_StringVectorOptionKey_std_string_t method) is_h2o() (pyrosetta.rosetta.core.chemical.AtomType method) is_H3_rama_kinked() (in module pyrosetta.rosetta.protocols.antibody) is_haro() (pyrosetta.rosetta.core.chemical.AtomType method) is_hashable() (pyrosetta.rosetta.protocols.sewing.data_storage.LigandSegment method) (pyrosetta.rosetta.protocols.sewing.data_storage.SmartSegment method) is_hb_satisfied() (in module pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock) is_head_node() (pyrosetta.rosetta.protocols.jd3.JobDirectedEdge method) (pyrosetta.rosetta.utility.graph.DirectedEdge method) is_heavy() (pyrosetta.rosetta.core.scoring.packing.PoseBalls method) is_heavyatom() (in module pyrosetta.rosetta.core.scoring) (pyrosetta.rosetta.core.chemical.AtomType method) is_helical() (pyrosetta.rosetta.core.conformation.membrane.ImplicitLipidInfo method) (pyrosetta.rosetta.core.conformation.membrane.MembraneInfo method) is_helix() (pyrosetta.rosetta.protocols.features.SecondaryStructureSegmentFeatures method) is_helix_jump() (pyrosetta.rosetta.protocols.abinitio.FixTemplateJumpSetup method) (pyrosetta.rosetta.protocols.abinitio.TemplateJumpSetup method) is_heptose() (pyrosetta.rosetta.core.chemical.carbohydrates.CarbohydrateInfo method) is_het() (pyrosetta.rosetta.core.pose.PDBInfo method) is_hexose() (pyrosetta.rosetta.core.chemical.carbohydrates.CarbohydrateInfo method) is_his() (pyrosetta.rosetta.core.energy_methods.ArgCationPiEnergy method) is_hit() (pyrosetta.rosetta.core.scoring.mhc_epitope_energy.AlleleMatrix method) is_homog_xform() (in module pyrosetta.bindings.homogeneous_transform) is_hybridization_type() (pyrosetta.rosetta.core.scoring.hbonds.HBondTypeManager static method) is_hydrogen() (pyrosetta.rosetta.core.chemical.Atom method) (pyrosetta.rosetta.core.chemical.AtomType method) (pyrosetta.rosetta.core.scoring.elec.electrie.ElecAtom method) (pyrosetta.rosetta.core.scoring.etable.etrie.EtableAtom method) (pyrosetta.rosetta.core.scoring.hbonds.graph.AtomInfo method) (pyrosetta.rosetta.core.scoring.hbonds.hbtrie.HBAtom method) (pyrosetta.rosetta.core.scoring.lkball.lkbtrie.LKBAtom method) (pyrosetta.rosetta.core.scoring.mm.mmtrie.MMEnergyTableAtom method) (pyrosetta.rosetta.core.scoring.vdwaals.VDWAtom method) is_hydroxyl() (pyrosetta.rosetta.core.scoring.hbonds.graph.AtomInfo method) is_ideal_pose() (in module pyrosetta.rosetta.core.pose) is_ideal_position() (in module pyrosetta.rosetta.core.conformation) (in module pyrosetta.rosetta.core.pose) is_identity() (pyrosetta.rosetta.core.id.SequenceMapping method) (pyrosetta.rosetta.core.sequence.DerivedSequenceMapping method) (pyrosetta.rosetta.numeric.xyzMatrix_double_t method) (pyrosetta.rosetta.numeric.xyzMatrix_float_t method) is_identity_ignore_gaps() (pyrosetta.rosetta.core.id.SequenceMapping method) (pyrosetta.rosetta.core.sequence.DerivedSequenceMapping method) is_in_Assembly() (pyrosetta.rosetta.protocols.sewing.data_storage.LigandSegment method) (pyrosetta.rosetta.protocols.sewing.data_storage.SmartSegment method) is_in_bin() (pyrosetta.rosetta.core.scoring.bin_transitions.BinTransitionCalculator method) is_in_grid() (pyrosetta.rosetta.core.grid.CartGrid_double_t method) (pyrosetta.rosetta.core.grid.CartGrid_int_t method) (pyrosetta.rosetta.protocols.qsar.scoring_grid.AtrGrid method) (pyrosetta.rosetta.protocols.qsar.scoring_grid.ChargeGrid method) (pyrosetta.rosetta.protocols.qsar.scoring_grid.ClassicGrid method) (pyrosetta.rosetta.protocols.qsar.scoring_grid.ConstantScoreBase method) (pyrosetta.rosetta.protocols.qsar.scoring_grid.GridBase method) (pyrosetta.rosetta.protocols.qsar.scoring_grid.GridSet method) (pyrosetta.rosetta.protocols.qsar.scoring_grid.HbaGrid method) (pyrosetta.rosetta.protocols.qsar.scoring_grid.HbdGrid method) (pyrosetta.rosetta.protocols.qsar.scoring_grid.LigandPropertyScore method) (pyrosetta.rosetta.protocols.qsar.scoring_grid.LipidMemGrid method) (pyrosetta.rosetta.protocols.qsar.scoring_grid.PCSMultiGrid method) (pyrosetta.rosetta.protocols.qsar.scoring_grid.PCSSingleGrid method) (pyrosetta.rosetta.protocols.qsar.scoring_grid.RepGrid method) (pyrosetta.rosetta.protocols.qsar.scoring_grid.ShapeGrid method) (pyrosetta.rosetta.protocols.qsar.scoring_grid.SingleGrid method) (pyrosetta.rosetta.protocols.qsar.scoring_grid.SiteGrid method) (pyrosetta.rosetta.protocols.qsar.scoring_grid.SolvationGrid method) (pyrosetta.rosetta.protocols.qsar.scoring_grid.SolvationMetaGrid method) (pyrosetta.rosetta.protocols.qsar.scoring_grid.VdwGrid method) is_in_helix() (pyrosetta.rosetta.protocols.helical_bundle_predict.HBPHelix method) (pyrosetta.rosetta.protocols.helical_bundle_predict.HBPHelixAssignments method) is_in_list() (in module pyrosetta.rosetta.protocols.generalized_kinematic_closure) is_in_taboo_map() (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.KinematicMover method) is_initialized() (pyrosetta.rosetta.core.pack.rotamer_set.UnboundRotamersOperation method) (pyrosetta.rosetta.core.pack.task.PackerTask method) (pyrosetta.rosetta.core.pack.task.PackerTask_ method) (pyrosetta.rosetta.protocols.features.ProteinSilentReport method) (pyrosetta.rosetta.protocols.fldsgn.BluePrintBDR method) (pyrosetta.rosetta.protocols.simple_moves.WaterRotsDB method) is_inside() (in module pyrosetta.rosetta.protocols.hydrate) (pyrosetta.rosetta.numeric.IntervalSet_Double method) (pyrosetta.rosetta.numeric.IntervalSet_double_t method) is_int() (in module pyrosetta.rosetta.ObjexxFCL) (pyrosetta.rosetta.ObjexxFCL.Fstring method) (pyrosetta.rosetta.ObjexxFCL.Fsubstring method) is_interface (pyrosetta.rosetta.protocols.ligand_docking.ligand_options.InterfaceInfo attribute) (pyrosetta.rosetta.protocols.ligand_docking.ligand_options.InterfaceInfo.Type attribute) is_interface() (pyrosetta.rosetta.core.scoring.rna.RNA_ScoringInfo method) (pyrosetta.rosetta.protocols.scoring.Interface method) (pyrosetta.rosetta.protocols.scoring.InterfaceInfo method) is_interface_ddg() (pyrosetta.rosetta.protocols.ddg.ddGMover method) is_interface_vector() (in module pyrosetta.rosetta.protocols.ligand_docking.ligand_options) is_internal() (pyrosetta.rosetta.core.chemical.AtomICoor method) (pyrosetta.rosetta.core.chemical.ICoorAtomID method) (pyrosetta.rosetta.protocols.stepwise.modeler.working_parameters.StepWiseBasicWorkingParameters method) (pyrosetta.rosetta.protocols.stepwise.modeler.working_parameters.StepWiseWorkingParameters method) is_ints() (in module pyrosetta.rosetta.ObjexxFCL) is_inverted() (pyrosetta.rosetta.core.pack.task.residue_selector.ClashBasedShellSelector method) is_inverted_virtual_residue() (pyrosetta.rosetta.core.chemical.ResidueType method) is_inwards() (pyrosetta.rosetta.core.scoring.dssp.Pairing method) is_jump() (pyrosetta.rosetta.core.kinematics.Edge method) (pyrosetta.rosetta.core.kinematics.tree.Atom method) (pyrosetta.rosetta.core.kinematics.tree.Atom_ method) (pyrosetta.rosetta.core.kinematics.tree.BondedAtom method) (pyrosetta.rosetta.core.kinematics.tree.JumpAtom method) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.mover.StepWiseMove method) is_jump_point() (pyrosetta.rosetta.core.kinematics.FoldTree method) is_ketose() (pyrosetta.rosetta.core.chemical.carbohydrates.CarbohydrateInfo method) is_known_atom() (pyrosetta.rosetta.core.scoring.saxs.FormFactorManager method) is_l_aa() (pyrosetta.rosetta.core.chemical.MutableResidueType method) (pyrosetta.rosetta.core.chemical.ResidueType method) (pyrosetta.rosetta.core.chemical.ResidueTypeBase method) is_l_rna() (pyrosetta.rosetta.core.chemical.MutableResidueType method) (pyrosetta.rosetta.core.chemical.ResidueType method) (pyrosetta.rosetta.core.chemical.ResidueTypeBase method) (pyrosetta.rosetta.core.conformation.Residue method) is_L_sugar() (pyrosetta.rosetta.core.chemical.carbohydrates.CarbohydrateInfo method) is_ladder() (pyrosetta.rosetta.core.scoring.dssp.StrandPairing method) is_leaf() (pyrosetta.rosetta.numeric.kdtree.KDNode method) is_lefthanded() (pyrosetta.rosetta.protocols.fldsgn.topology.BetaAlphaBetaMotif method) is_legal_greater_than() (in module pyrosetta.rosetta.numeric.kdtree) is_legal_kdtree_below_node() (in module pyrosetta.rosetta.numeric.kdtree) is_legal_less_than() (in module pyrosetta.rosetta.numeric.kdtree) is_ligand (pyrosetta.rosetta.protocols.hbnet.HBondResStruct property) is_ligand() (pyrosetta.rosetta.core.chemical.ResidueType method) (pyrosetta.rosetta.core.conformation.Residue method) is_ligand_bb_frozen() (pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.LigandConformer method) is_ligand_frozen() (pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.LigandConformer method) is_ligand_heavyatom() (in module pyrosetta.rosetta.core.scoring) is_ligand_heavyatom_residues() (in module pyrosetta.rosetta.core.scoring) is_ligand_present() (pyrosetta.rosetta.protocols.flexpep_docking.FlexPepDockingFlags method) is_ligand_terminal() (pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.LigandConformer method) is_lipid() (pyrosetta.rosetta.core.chemical.ResidueType method) is_literal() (pyrosetta.rosetta.numeric.expression_parser.ArithmeticASTValue method) is_loaded() (pyrosetta.rosetta.core.scoring.methods.dfire.DFIRE_Potential method) is_long() (in module pyrosetta.rosetta.ObjexxFCL) (pyrosetta.rosetta.ObjexxFCL.Fstring method) (pyrosetta.rosetta.ObjexxFCL.Fsubstring method) is_longdouble() (in module pyrosetta.rosetta.ObjexxFCL) (pyrosetta.rosetta.ObjexxFCL.Fstring method) (pyrosetta.rosetta.ObjexxFCL.Fsubstring method) is_loop() (pyrosetta.rosetta.core.pack.guidance_scoreterms.buried_unsat_penalty.graph.BuriedUnsatPenaltyEdge method) (pyrosetta.rosetta.core.pack.interaction_graph.NPDHBSimpleEdge method) (pyrosetta.rosetta.core.pack.interaction_graph.SimpleEdge method) (pyrosetta.rosetta.core.scoring.constraints.ConstraintEdge method) (pyrosetta.rosetta.core.scoring.EnergyEdge method) (pyrosetta.rosetta.core.scoring.MinimizationEdge method) (pyrosetta.rosetta.core.scoring.TenANeighborEdge method) (pyrosetta.rosetta.core.scoring.TwelveANeighborEdge method) (pyrosetta.rosetta.protocols.features.HelixCapFeatures method) (pyrosetta.rosetta.protocols.features.SecondaryStructureSegmentFeatures method) (pyrosetta.rosetta.protocols.legacy_sewing.HashEdge method) (pyrosetta.rosetta.utility.graph.Edge method) is_loop_residue() (pyrosetta.rosetta.protocols.loops.Loops method) is_lower_cutpoint() (in module pyrosetta.rosetta.core.scoring.methods) is_lower_terminus() (in module pyrosetta.rosetta.core.pose) (pyrosetta.rosetta.core.chemical.ResidueType method) (pyrosetta.rosetta.core.conformation.Residue method) is_magnesium() (pyrosetta.rosetta.core.scoring.rna.RNA_ScoringInfo method) is_mainchain_torsion_also_ring_torsion() (in module pyrosetta.rosetta.core.chemical) is_member() (pyrosetta.rosetta.protocols.fldsgn.topology.Sheet method) (pyrosetta.rosetta.protocols.fldsgn.topology.StrandPairing method) is_membrane() (pyrosetta.rosetta.core.chemical.ResidueType method) (pyrosetta.rosetta.core.conformation.Conformation method) (pyrosetta.rosetta.core.conformation.symmetry.MirrorSymmetricConformation method) (pyrosetta.rosetta.core.conformation.symmetry.SymmetricConformation method) (pyrosetta.rosetta.protocols.environment.ProtectedConformation method) is_membrane_fixed() (in module pyrosetta.rosetta.protocols.membrane) is_membrane_moveable_by_itself() (in module pyrosetta.rosetta.protocols.membrane) is_mergeable() (pyrosetta.rosetta.core.fragment.Frame method) (pyrosetta.rosetta.core.fragment.JumpingFrame method) (pyrosetta.rosetta.core.fragment.NonContinuousFrame method) (pyrosetta.rosetta.protocols.enzdes.EnzdesFlexibleRegion method) is_meta_aramid() (pyrosetta.rosetta.core.chemical.ResidueType method) (pyrosetta.rosetta.core.conformation.Residue method) is_metal() (pyrosetta.rosetta.core.chemical.ResidueType method) (pyrosetta.rosetta.core.conformation.Residue method) (pyrosetta.rosetta.core.io.NomenclatureManager static method) is_metalbinding() (pyrosetta.rosetta.core.chemical.ResidueType method) (pyrosetta.rosetta.core.conformation.Residue method) is_metapatch() (pyrosetta.rosetta.core.chemical.Patch method) is_metapatched() (pyrosetta.rosetta.core.chemical.MutableResidueType method) (pyrosetta.rosetta.core.chemical.ResidueType method) (pyrosetta.rosetta.core.chemical.ResidueTypeBase method) is_methylated_cterminus() (pyrosetta.rosetta.core.chemical.ResidueType method) is_mirror_symmetric() (in module pyrosetta.rosetta.core.conformation.symmetry) (in module pyrosetta.rosetta.core.pose.symmetry) is_mirrored_type() (pyrosetta.rosetta.core.chemical.ResidueType method) is_mixed_mode() (pyrosetta.rosetta.core.conformation.Conformation method) (pyrosetta.rosetta.core.conformation.symmetry.MirrorSymmetricConformation method) (pyrosetta.rosetta.core.conformation.symmetry.SymmetricConformation method) (pyrosetta.rosetta.protocols.environment.ProtectedConformation method) is_mover (pyrosetta.rosetta.protocols.multistage_rosetta_scripts.mover_or_filter property) is_moving_res() (pyrosetta.rosetta.protocols.stepwise.modeler.working_parameters.StepWiseWorkingParameters method) is_multi_trial() (pyrosetta.rosetta.protocols.backrub.BackrubMover method) (pyrosetta.rosetta.protocols.backrub.BackrubSidechainMover method) (pyrosetta.rosetta.protocols.canonical_sampling.ThermodynamicMover method) (pyrosetta.rosetta.protocols.enzdes.PredesignPerturbMover method) (pyrosetta.rosetta.protocols.kinematic_closure.BalancedKicMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyDeterministicSpinMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofPerturbMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofRandomizeMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofRandomTransMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofSeqPerturbMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofSeqRandomizeMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofSeqTransMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofTransMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyPerturbMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyPerturbNoCenterMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyPerturbRandomJumpMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyRandomizeMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodySpinMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyTiltMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyTransMover method) (pyrosetta.rosetta.protocols.rigid.UniformRigidBodyMover method) (pyrosetta.rosetta.protocols.rigid.UniformSphereTransMover method) (pyrosetta.rosetta.protocols.simple_moves.BackboneMover method) (pyrosetta.rosetta.protocols.simple_moves.BBConRotMover method) (pyrosetta.rosetta.protocols.simple_moves.BBG8T3AMover method) (pyrosetta.rosetta.protocols.simple_moves.BBGaussianMover method) (pyrosetta.rosetta.protocols.simple_moves.ShearMover method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.JumpRotamerSidechainMover method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.PerturbChiSidechainMover method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.PerturbRotamerSidechainMover method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SidechainMCMover method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SidechainMover method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SidechainMoverBase method) (pyrosetta.rosetta.protocols.simple_moves.SmallMover method) (pyrosetta.rosetta.protocols.topology_broker.RigidBodyRandomTMHMover method) is_multicomponent() (in module pyrosetta.rosetta.core.pose.symmetry) is_multisegment() (pyrosetta.rosetta.protocols.fold_from_loops.utils.Nub method) is_mutant_calc_complete() (pyrosetta.rosetta.protocols.ddg.ddGMover method) is_N_acetylated() (pyrosetta.rosetta.core.chemical.carbohydrates.CarbohydrateInfo method) is_n_methylated() (pyrosetta.rosetta.core.chemical.ResidueType method) is_N_substituted() (pyrosetta.rosetta.core.chemical.ResidueType method) is_n_terminus_fixed() (pyrosetta.rosetta.protocols.sewing.data_storage.LigandSegment method) (pyrosetta.rosetta.protocols.sewing.data_storage.SmartSegment method) is_NA() (pyrosetta.rosetta.core.chemical.ResidueType method) (pyrosetta.rosetta.core.conformation.Residue method) (pyrosetta.rosetta.core.io.NomenclatureManager static method) is_native (pyrosetta.rosetta.protocols.hbnet.HBondNetStruct property) is_native_pairing() (pyrosetta.rosetta.protocols.abinitio.PairingStatistics method) is_nbr_atom() (in module pyrosetta.rosetta.core.scoring) is_neigh_tree() (pyrosetta.rosetta.protocols.constel.NeighTeller method) is_non_peptide_heavy_atom() (in module pyrosetta.rosetta.core.scoring) is_nonempty_input_silent_file() (in module pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna) is_nonose() (pyrosetta.rosetta.core.chemical.carbohydrates.CarbohydrateInfo method) is_nonpivot_residue() (pyrosetta.rosetta.protocols.kinematic_closure.ClosureProblem method) is_normalization_enabled() (pyrosetta.rosetta.protocols.qsar.scoring_grid.GridSet method) is_normalized() (pyrosetta.rosetta.core.scoring.sc.Atom method) (pyrosetta.rosetta.numeric.Quaternion_double_t method) (pyrosetta.rosetta.numeric.xyzTriple_unsigned_long_t method) (pyrosetta.rosetta.numeric.xyzVector_double_t method) (pyrosetta.rosetta.numeric.xyzVector_float_t method) (pyrosetta.rosetta.numeric.xyzVector_int_t method) (pyrosetta.rosetta.numeric.xyzVector_unsigned_long_t method) is_normally_connected() (pyrosetta.rosetta.core.scoring.Ramachandran method) is_null() (pyrosetta.rosetta.core.scoring.GenTorsionParams method) (pyrosetta.rosetta.core.scoring.methods.BBDepCartBondedParameters method) (pyrosetta.rosetta.core.scoring.methods.BBIndepCartBondedParameters method) (pyrosetta.rosetta.core.scoring.methods.CartBondedParameters method) (pyrosetta.rosetta.core.scoring.SpringParams method) (pyrosetta.rosetta.cppdb.backend.result method) (pyrosetta.rosetta.cppdb.result method) (pyrosetta.rosetta.utility.json_spirit.Value_impl_utility_json_spirit_Config_map_std_basic_string_wchar_t_t method) (pyrosetta.rosetta.utility.json_spirit.Value_impl_utility_json_spirit_Config_map_std_string_t method) (pyrosetta.rosetta.utility.json_spirit.Value_impl_utility_json_spirit_Config_vector_std_basic_string_wchar_t_t method) (pyrosetta.rosetta.utility.json_spirit.Value_impl_utility_json_spirit_Config_vector_std_string_t method) is_num_in_list() (in module pyrosetta.rosetta.protocols.rna.denovo) is_O_acetylated() (pyrosetta.rosetta.core.chemical.carbohydrates.CarbohydrateInfo method) is_observing() (pyrosetta.rosetta.core.pose.metrics.PoseMetricContainer method) (pyrosetta.rosetta.core.pose.PDBInfo method) is_occupied() (pyrosetta.rosetta.core.pose.rna.VDW_Grid method) is_octose() (pyrosetta.rosetta.core.chemical.carbohydrates.CarbohydrateInfo method) is_old_DNA() (pyrosetta.rosetta.core.io.NomenclatureManager static method) is_old_RNA() (pyrosetta.rosetta.core.io.NomenclatureManager static method) is_oligourea() (pyrosetta.rosetta.core.chemical.ResidueType method) is_on() (pyrosetta.rosetta.protocols.checkpoint.Timer static method) is_open() (pyrosetta.rosetta.cppdb.session method) (pyrosetta.rosetta.std.filebuf method) (pyrosetta.rosetta.std.ifstream method) (pyrosetta.rosetta.std.ofstream method) (pyrosetta.rosetta.utility.sql_database.session method) is_optE_type_name() (pyrosetta.rosetta.protocols.optimize_weights.OptEPositionDataFactory static method) is_original_type() (pyrosetta.rosetta.core.pack.task.ResidueLevelTask method) (pyrosetta.rosetta.core.pack.task.ResidueLevelTask_ method) is_ortho_aramid() (pyrosetta.rosetta.core.chemical.ResidueType method) (pyrosetta.rosetta.core.conformation.Residue method) is_orthogonal() (pyrosetta.rosetta.core.kinematics.Stub method) is_orthonormal() (in module pyrosetta.rosetta.core.scoring.dna) is_outwards() (pyrosetta.rosetta.core.scoring.dssp.Pairing method) is_pair() (pyrosetta.rosetta.protocols.scoring.Interface method) (pyrosetta.rosetta.protocols.scoring.InterfaceInfo method) is_para_aramid() (pyrosetta.rosetta.core.chemical.ResidueType method) (pyrosetta.rosetta.core.conformation.Residue method) is_parallel() (pyrosetta.rosetta.core.scoring.dssp.Pairing method) (pyrosetta.rosetta.protocols.fldsgn.topology.DimerPairing method) (pyrosetta.rosetta.protocols.fldsgn.topology.HelixPairing method) (pyrosetta.rosetta.protocols.fldsgn.topology.StrandPairing method) is_pass_through() (pyrosetta.rosetta.core.chemical.ResidueTypeSetCache method) is_patched() (pyrosetta.rosetta.core.sequence.AnnotatedSequence method) is_pcs_tensor_diagonalized() (pyrosetta.rosetta.core.scoring.nmr.pcs.PCSTensor method) is_pcs_tensor_in_arbitrary_frame() (pyrosetta.rosetta.core.scoring.nmr.pcs.PCSTensor method) is_pcs_tensor_in_pas() (pyrosetta.rosetta.core.scoring.nmr.pcs.PCSTensor method) is_pcs_tensor_reconfigured() (pyrosetta.rosetta.core.scoring.nmr.pcs.PCSTensor method) is_pentose() (pyrosetta.rosetta.core.chemical.carbohydrates.CarbohydrateInfo method) is_peptide() (pyrosetta.rosetta.core.kinematics.Edge method) is_peptoid() (pyrosetta.rosetta.core.chemical.MutableResidueType method) (pyrosetta.rosetta.core.chemical.ResidueType method) (pyrosetta.rosetta.core.chemical.ResidueTypeBase method) (pyrosetta.rosetta.core.conformation.Residue method) is_permissible_length() (pyrosetta.rosetta.protocols.pose_sewing.data_storage.SegmentEnvelope method) is_permissible_secondary_structure() (pyrosetta.rosetta.protocols.pose_sewing.data_storage.SegmentEnvelope method) is_phe() (pyrosetta.rosetta.core.energy_methods.ArgCationPiEnergy method) is_phosphate() (pyrosetta.rosetta.core.chemical.rna.RNA_Info method) is_phosphate_ (pyrosetta.rosetta.core.chemical.rna.RNA_Info property) is_pi() (pyrosetta.rosetta.core.energy_methods.ArgCationPiEnergy method) is_pivot_residue() (pyrosetta.rosetta.protocols.kinematic_closure.ClosureProblem method) is_PNA() (pyrosetta.rosetta.core.chemical.ResidueType method) is_point_in_grid() (pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.GridScorer method) is_polar() (pyrosetta.rosetta.core.chemical.ResidueType method) (pyrosetta.rosetta.core.conformation.Residue method) is_polar_atom() (pyrosetta.rosetta.core.scoring.sasa.LeGrandSasa static method) (pyrosetta.rosetta.core.scoring.sasa.SasaMethod static method) is_polar_hydrogen() (pyrosetta.rosetta.core.chemical.AtomType method) is_polarH() (pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.Pharmacophore method) is_polymer() (pyrosetta.rosetta.core.chemical.MutableResidueType method) (pyrosetta.rosetta.core.chemical.ResidueType method) (pyrosetta.rosetta.core.chemical.ResidueTypeBase method) (pyrosetta.rosetta.core.conformation.Residue method) (pyrosetta.rosetta.core.kinematics.Edge method) is_polymer_bonded() (pyrosetta.rosetta.core.conformation.Residue method) is_polymer_heavyatom() (in module pyrosetta.rosetta.core.scoring) is_polymer_lower() (pyrosetta.rosetta.core.chemical.ICoorAtomID method) is_polymer_upper() (pyrosetta.rosetta.core.chemical.ICoorAtomID method) is_position_conserved_residue() (in module pyrosetta.rosetta.core.pose) is_positive_state() (pyrosetta.rosetta.protocols.multistate_design.PackingState method) (pyrosetta.rosetta.protocols.multistate_design.SingleState method) is_post_methylene_meta_aramid() (pyrosetta.rosetta.core.chemical.ResidueType method) (pyrosetta.rosetta.core.conformation.Residue method) is_post_methylene_ortho_aramid() (pyrosetta.rosetta.core.chemical.ResidueType method) (pyrosetta.rosetta.core.conformation.Residue method) is_post_methylene_para_aramid() (pyrosetta.rosetta.core.chemical.ResidueType method) (pyrosetta.rosetta.core.conformation.Residue method) is_pre_methylene_meta_aramid() (pyrosetta.rosetta.core.chemical.ResidueType method) (pyrosetta.rosetta.core.conformation.Residue method) is_pre_methylene_ortho_aramid() (pyrosetta.rosetta.core.chemical.ResidueType method) (pyrosetta.rosetta.core.conformation.Residue method) is_pre_methylene_para_aramid() (pyrosetta.rosetta.core.chemical.ResidueType method) (pyrosetta.rosetta.core.conformation.Residue method) is_pre_methylene_post_methylene_meta_aramid() (pyrosetta.rosetta.core.chemical.ResidueType method) (pyrosetta.rosetta.core.conformation.Residue method) is_pre_methylene_post_methylene_ortho_aramid() (pyrosetta.rosetta.core.chemical.ResidueType method) (pyrosetta.rosetta.core.conformation.Residue method) is_pre_methylene_post_methylene_para_aramid() (pyrosetta.rosetta.core.chemical.ResidueType method) (pyrosetta.rosetta.core.conformation.Residue method) is_pre_proline() (pyrosetta.rosetta.protocols.stepwise.modeler.working_parameters.StepWiseWorkingParameters method) is_prepend (pyrosetta.rosetta.protocols.stepwise.modeler.rna.sugar.SugarModeling property) is_prepend() (pyrosetta.rosetta.protocols.stepwise.modeler.working_parameters.StepWiseBasicWorkingParameters method) (pyrosetta.rosetta.protocols.stepwise.modeler.working_parameters.StepWiseWorkingParameters method) is_prepend_map() (pyrosetta.rosetta.protocols.stepwise.modeler.working_parameters.StepWiseWorkingParameters method) is_prohibited() (pyrosetta.rosetta.core.chemical.ResidueTypeSetCache method) is_properly_initialized() (pyrosetta.rosetta.protocols.ddg.ddGMover method) is_protected() (pyrosetta.rosetta.core.conformation.Conformation method) (pyrosetta.rosetta.core.conformation.symmetry.MirrorSymmetricConformation method) (pyrosetta.rosetta.core.conformation.symmetry.SymmetricConformation method) (pyrosetta.rosetta.protocols.environment.ProtectedConformation method) is_protein (pyrosetta.rosetta.protocols.hbnet.HBondResStruct property) is_protein() (in module pyrosetta.rosetta.protocols.stepwise.modeler) (pyrosetta.rosetta.core.chemical.MutableResidueType method) (pyrosetta.rosetta.core.chemical.ResidueType method) (pyrosetta.rosetta.core.chemical.ResidueTypeBase method) (pyrosetta.rosetta.core.conformation.Residue method) (pyrosetta.rosetta.core.scoring.hbonds.hbtrie.HBAtom method) is_protein_backbone() (in module pyrosetta.rosetta.core.scoring) is_protein_backbone_including_O() (in module pyrosetta.rosetta.core.scoring) is_protein_CA() (in module pyrosetta.rosetta.core.scoring) is_protein_CA_or_CB() (in module pyrosetta.rosetta.core.scoring) is_protein_CA_or_equiv() (in module pyrosetta.rosetta.core.scoring) is_protein_sidechain_heavyatom() (in module pyrosetta.rosetta.core.scoring) is_proton() (pyrosetta.rosetta.protocols.noesy_assign.FloatingResonance method) (pyrosetta.rosetta.protocols.noesy_assign.LabelResonance method) (pyrosetta.rosetta.protocols.noesy_assign.ProtonResonance method) (pyrosetta.rosetta.protocols.noesy_assign.Resonance method) is_proton_chi() (pyrosetta.rosetta.core.chemical.MutableChiRecord method) (pyrosetta.rosetta.core.chemical.MutableResidueType method) (pyrosetta.rosetta.core.chemical.ResidueType method) is_pseudo_bonded() (pyrosetta.rosetta.core.conformation.Residue method) is_purine() (pyrosetta.rosetta.core.chemical.ResidueType method) (pyrosetta.rosetta.core.conformation.Residue method) is_pyranose() (pyrosetta.rosetta.core.chemical.carbohydrates.CarbohydrateInfo method) is_pyrimidine() (pyrosetta.rosetta.core.chemical.ResidueType method) (pyrosetta.rosetta.core.conformation.Residue method) is_qsar_map_attached() (pyrosetta.rosetta.protocols.qsar.scoring_grid.GridSet method) is_r_peptoid() (pyrosetta.rosetta.core.chemical.MutableResidueType method) (pyrosetta.rosetta.core.chemical.ResidueType method) (pyrosetta.rosetta.core.chemical.ResidueTypeBase method) is_rdc_tensor_in_arbitrary_frame() (pyrosetta.rosetta.core.scoring.nmr.rdc.RDCTensor method) is_rdc_tensor_in_pas() (pyrosetta.rosetta.core.scoring.nmr.rdc.RDCTensor method) is_reducing_sugar() (pyrosetta.rosetta.core.chemical.carbohydrates.CarbohydrateInfo method) is_referencepose_number() (in module pyrosetta.rosetta.core.pose) is_registered() (pyrosetta.rosetta.protocols.environment.Environment method) is_relevant() (pyrosetta.rosetta.utility.options.OptionCollection method) is_relevant_neighbor() (pyrosetta.rosetta.core.scoring.nmr.NMRDummySpinlabelAtom method) (pyrosetta.rosetta.core.scoring.nmr.VoxelGridPoint method) (pyrosetta.rosetta.core.scoring.nmr.VoxelGridPoint_AA method) (pyrosetta.rosetta.protocols.nmr.pcs.AtomGridPoint method) is_remodelable() (pyrosetta.rosetta.protocols.enzdes.EnzdesFlexBBProtocol method) is_repulsive() (pyrosetta.rosetta.core.chemical.AtomType method) (pyrosetta.rosetta.core.chemical.ResidueType method) (pyrosetta.rosetta.core.conformation.Residue method) is_required() (pyrosetta.rosetta.utility.tag.XMLSchemaAttribute method) is_res_exposed() (in module pyrosetta.rosetta.core.scoring.sasa) is_residue_allowed() (pyrosetta.rosetta.protocols.splice.SampleRotamersFromPDB_RotamerSetOperation method) is_residue_in_grid() (pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.GridScorer method) is_residue_in_tree() (pyrosetta.rosetta.core.conformation.carbohydrates.GlycanTreeSet method) is_residues_in_contact() (in module pyrosetta.rosetta.protocols.stepwise.modeler.rna) is_reversible() (pyrosetta.rosetta.core.scoring.motif.ResPairMotif method) is_ring_atom() (pyrosetta.rosetta.core.chemical.ResidueType method) is_rmoi_hbonded() (pyrosetta.rosetta.protocols.constel.HBondCommon static method) is_RNA() (pyrosetta.rosetta.core.chemical.MutableResidueType method) (pyrosetta.rosetta.core.chemical.ResidueType method) (pyrosetta.rosetta.core.chemical.ResidueTypeBase method) (pyrosetta.rosetta.core.conformation.Residue method) is_rna_and_protein() (pyrosetta.rosetta.core.import_pose.RNA_DeNovoParameters method) is_RNA_base() (pyrosetta.rosetta.core.chemical.rna.RNA_Info method) is_RNA_base_ (pyrosetta.rosetta.core.chemical.rna.RNA_Info property) is_RNA_base_atom() (pyrosetta.rosetta.core.chemical.rna.RNA_Info method) is_rna_chainbreak() (in module pyrosetta.rosetta.core.pose.rna) is_root() (pyrosetta.rosetta.core.kinematics.FoldTree method) (pyrosetta.rosetta.numeric.kdtree.KDNode method) is_rot_sample_name() (in module pyrosetta.rosetta.core.pack.task) is_s_peptoid() (pyrosetta.rosetta.core.chemical.MutableResidueType method) (pyrosetta.rosetta.core.chemical.ResidueType method) (pyrosetta.rosetta.core.chemical.ResidueTypeBase method) is_same() (pyrosetta.rosetta.protocols.ddg.CartesianddG.MutationSet method) is_same_sugar_pucker() (in module pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna) is_satisfied() (pyrosetta.rosetta.protocols.constel.FilterByAmphetamine static method) (pyrosetta.rosetta.protocols.constel.FilterByHistamine static method) (pyrosetta.rosetta.protocols.constel.FilterByIndoleCOO static method) (pyrosetta.rosetta.protocols.constel.FilterByProxTerm static method) (pyrosetta.rosetta.protocols.constel.FilterByTryptamine static method) is_sc() (pyrosetta.rosetta.core.scoring.hbonds.hbtrie.HBCPData method) is_sc_bb_clash() (in module pyrosetta.rosetta.core.pack.task.residue_selector) is_sc_sc_clash() (in module pyrosetta.rosetta.core.pack.task.residue_selector) is_scatom() (in module pyrosetta.rosetta.core.scoring) is_scofx_cstfied() (in module pyrosetta.rosetta.protocols.enzdes.enzutil) is_score_precomputed() (pyrosetta.rosetta.core.scoring.electron_density_atomwise.ElectronDensityAtomwise method) is_score_type() (pyrosetta.rosetta.core.scoring.ScoreTypeManager static method) is_selection_initialized() (pyrosetta.rosetta.core.select.util.SelectResiduesByLayer method) is_septanose() (pyrosetta.rosetta.core.chemical.carbohydrates.CarbohydrateInfo method) is_seq_sep_type() (pyrosetta.rosetta.core.scoring.hbonds.HBondTypeManager static method) is_set_s_kk() (pyrosetta.rosetta.protocols.cluster.DataPoint method) is_short() (in module pyrosetta.rosetta.ObjexxFCL) (pyrosetta.rosetta.ObjexxFCL.Fstring method) (pyrosetta.rosetta.ObjexxFCL.Fsubstring method) is_sidechain_amine() (pyrosetta.rosetta.core.chemical.ResidueType method) is_sidechain_thiol() (pyrosetta.rosetta.core.chemical.ResidueType method) is_similar_aa() (pyrosetta.rosetta.core.conformation.Residue method) is_similar_rotamer() (pyrosetta.rosetta.core.conformation.Residue method) is_simple_full_length_job_params() (pyrosetta.rosetta.protocols.stepwise.modeler.working_parameters.StepWiseWorkingParameters method) is_simple_tree() (pyrosetta.rosetta.core.kinematics.FoldTree method) is_singlecomponent() (in module pyrosetta.rosetta.core.pose.symmetry) is_solution_trivial() (pyrosetta.rosetta.protocols.kinematic_closure.BalancedKicMover static method) is_solvent (pyrosetta.rosetta.protocols.hbnet.HBondResStruct property) is_solvent() (pyrosetta.rosetta.core.chemical.ResidueType method) is_sp2_proton_chi() (in module pyrosetta.rosetta.core.chemical) is_sparis_foldtype() (pyrosetta.rosetta.protocols.fldsgn.topology.SheetFoldTypeManager method) is_square() (pyrosetta.rosetta.numeric.MathMatrix_double_t method) (pyrosetta.rosetta.numeric.MathMatrix_float_t method) is_sri() (pyrosetta.rosetta.core.chemical.ResidueType method) (pyrosetta.rosetta.core.conformation.Residue method) is_string() (in module pyrosetta.rosetta.ObjexxFCL) (pyrosetta.rosetta.ObjexxFCL.Fstring method) (pyrosetta.rosetta.ObjexxFCL.Fsubstring method) is_string_constructible_char__star__t (class in pyrosetta.rosetta.utility.type_traits) is_string_constructible_const_char__star__t (class in pyrosetta.rosetta.utility.type_traits) is_string_constructible_const_std_string__ref__t (class in pyrosetta.rosetta.utility.type_traits) is_string_constructible_const_std_string_t (class in pyrosetta.rosetta.utility.type_traits) is_string_constructible_const_utility_tag_XMLSchemaType__ref__t (class in pyrosetta.rosetta.utility.type_traits) is_string_constructible_std_string__ref__t (class in pyrosetta.rosetta.utility.type_traits) is_string_constructible_std_string_t (class in pyrosetta.rosetta.utility.type_traits) is_string_constructible_utility_tag_XMLSchemaType_t (class in pyrosetta.rosetta.utility.type_traits) is_string_numeric() (in module pyrosetta.rosetta.utility) is_sugar() (pyrosetta.rosetta.core.io.NomenclatureManager static method) is_sugar_virtual() (in module pyrosetta.rosetta.protocols.stepwise.modeler.rna.sugar) is_surface() (pyrosetta.rosetta.core.chemical.ResidueType method) (pyrosetta.rosetta.core.conformation.Residue method) is_symmetric() (in module pyrosetta.rosetta.core.conformation.symmetry) (in module pyrosetta.rosetta.core.pose.symmetry) (pyrosetta.rosetta.core.io.silent.BinarySilentStruct method) (pyrosetta.rosetta.core.io.silent.RigidBodySilentStruct method) is_symmetric_partner_of() (pyrosetta.rosetta.protocols.noesy_assign.PeakAssignment method) is_tail_node() (pyrosetta.rosetta.protocols.jd3.JobDirectedEdge method) (pyrosetta.rosetta.utility.graph.DirectedEdge method) is_tensor_diagonalized() (pyrosetta.rosetta.core.scoring.nmr.rdc.RDCTensor method) is_tensor_reconfigured() (pyrosetta.rosetta.core.scoring.nmr.rdc.RDCTensor method) is_terminal() (pyrosetta.rosetta.protocols.loops.Loop method) is_terminus() (pyrosetta.rosetta.core.chemical.ResidueType method) (pyrosetta.rosetta.core.conformation.Residue method) is_tetrose() (pyrosetta.rosetta.core.chemical.carbohydrates.CarbohydrateInfo method) is_this_strand_at_edge() (in module pyrosetta.rosetta.protocols.features.strand_assembly) is_this_strand_at_edge_by_looking_db() (in module pyrosetta.rosetta.protocols.features.strand_assembly) is_TNA() (pyrosetta.rosetta.core.chemical.ResidueType method) (pyrosetta.rosetta.core.conformation.Residue method) is_tna_chainbreak() (in module pyrosetta.rosetta.core.pose.rna) is_top() (pyrosetta.rosetta.protocols.dna.DnaChains method) is_torsion_exists() (pyrosetta.rosetta.core.pose.rna.RNA_IdealCoord method) is_torsion_valid() (in module pyrosetta.rosetta.core.pose.rna) is_TP3() (pyrosetta.rosetta.core.chemical.ResidueType method) is_tri_diagonal() (pyrosetta.rosetta.numeric.MathMatrix_double_t method) (pyrosetta.rosetta.numeric.MathMatrix_float_t method) is_triazolemer() (pyrosetta.rosetta.core.chemical.ResidueType method) (pyrosetta.rosetta.core.conformation.Residue method) is_triose() (pyrosetta.rosetta.core.chemical.carbohydrates.CarbohydrateInfo method) is_trp() (pyrosetta.rosetta.core.energy_methods.ArgCationPiEnergy method) is_true_string() (in module pyrosetta.rosetta.utility) is_type() (in module pyrosetta.rosetta.ObjexxFCL) (pyrosetta.rosetta.ObjexxFCL.Fstring method) (pyrosetta.rosetta.ObjexxFCL.Fsubstring method) is_tyr() (pyrosetta.rosetta.core.energy_methods.ArgCationPiEnergy method) is_uint() (in module pyrosetta.rosetta.ObjexxFCL) (pyrosetta.rosetta.ObjexxFCL.Fstring method) (pyrosetta.rosetta.ObjexxFCL.Fsubstring method) is_uint64() (pyrosetta.rosetta.utility.json_spirit.Value_impl_utility_json_spirit_Config_map_std_basic_string_wchar_t_t method) (pyrosetta.rosetta.utility.json_spirit.Value_impl_utility_json_spirit_Config_map_std_string_t method) (pyrosetta.rosetta.utility.json_spirit.Value_impl_utility_json_spirit_Config_vector_std_basic_string_wchar_t_t method) (pyrosetta.rosetta.utility.json_spirit.Value_impl_utility_json_spirit_Config_vector_std_string_t method) is_ulong() (in module pyrosetta.rosetta.ObjexxFCL) (pyrosetta.rosetta.ObjexxFCL.Fstring method) (pyrosetta.rosetta.ObjexxFCL.Fsubstring method) is_ulose() (pyrosetta.rosetta.core.chemical.carbohydrates.CarbohydrateInfo method) is_undefined() (in module pyrosetta.rosetta.utility) is_under_memory_limit() (pyrosetta.rosetta.protocols.wum.WorkUnitQueue method) (pyrosetta.rosetta.protocols.wum.WorkUnitQueue_Swapped method) is_unit() (pyrosetta.rosetta.core.scoring.sc.Atom method) (pyrosetta.rosetta.numeric.xyzTriple_unsigned_long_t method) (pyrosetta.rosetta.numeric.xyzVector_double_t method) (pyrosetta.rosetta.numeric.xyzVector_float_t method) (pyrosetta.rosetta.numeric.xyzVector_int_t method) (pyrosetta.rosetta.numeric.xyzVector_unsigned_long_t method) is_upper_cutpoint() (in module pyrosetta.rosetta.core.scoring.methods) is_upper_terminus() (in module pyrosetta.rosetta.core.pose) (pyrosetta.rosetta.core.chemical.ResidueType method) (pyrosetta.rosetta.core.conformation.Residue method) is_uronic_acid() (pyrosetta.rosetta.core.chemical.carbohydrates.CarbohydrateInfo method) is_ushort() (in module pyrosetta.rosetta.ObjexxFCL) (pyrosetta.rosetta.ObjexxFCL.Fstring method) (pyrosetta.rosetta.ObjexxFCL.Fsubstring method) is_using() (pyrosetta.rosetta.core.energy_methods.GoapRsdType method) is_valid() (pyrosetta.rosetta.core.conformation.membrane.Span method) (pyrosetta.rosetta.core.conformation.membrane.SpanningTopology method) (pyrosetta.rosetta.core.fragment.AnnotatedFragData method) (pyrosetta.rosetta.core.fragment.FragData method) (pyrosetta.rosetta.core.fragment.FragID method) (pyrosetta.rosetta.core.fragment.Frame method) (pyrosetta.rosetta.core.fragment.JumpingFrame method) (pyrosetta.rosetta.core.fragment.NonContinuousFrame method) (pyrosetta.rosetta.core.scoring.PolymerBondedEnergyContainer method) (pyrosetta.rosetta.protocols.enzdes.EnzdesFlexibleRegion method) (pyrosetta.rosetta.protocols.jumping.JumpSample method) (pyrosetta.rosetta.protocols.noesy_assign.FragsToAtomDist.DistanceRecord method) (pyrosetta.rosetta.protocols.pose_sewing.data_storage.SegmentEnvelope method) is_valid_chunk() (pyrosetta.rosetta.protocols.frag_picker.FragmentPicker method) is_valid_modification_affix() (pyrosetta.rosetta.core.chemical.carbohydrates.CarbohydrateInfoManager static method) is_valid_position() (pyrosetta.rosetta.numeric.MathNTensor_bool_3_t method) (pyrosetta.rosetta.numeric.MathNTensor_double_1_t method) (pyrosetta.rosetta.numeric.MathNTensor_double_2_t method) (pyrosetta.rosetta.numeric.MathNTensor_double_3_t method) (pyrosetta.rosetta.numeric.MathNTensor_double_4_t method) (pyrosetta.rosetta.numeric.MathNTensor_double_5_t method) (pyrosetta.rosetta.numeric.MathNTensor_double_6_t method) (pyrosetta.rosetta.numeric.MathNTensorBase_bool_t method) (pyrosetta.rosetta.numeric.MathNTensorBase_double_t method) (pyrosetta.rosetta.numeric.MathTensor_double_t method) is_valid_quota_pool_name() (pyrosetta.rosetta.protocols.frag_picker.quota.ABEGO_SS_Config method) (pyrosetta.rosetta.protocols.frag_picker.quota.QuotaConfig method) is_valid_record_type() (pyrosetta.rosetta.core.io.pdb.RecordCollection static method) is_valid_ring_affix() (pyrosetta.rosetta.core.chemical.carbohydrates.CarbohydrateInfoManager static method) is_valid_sugar_code() (pyrosetta.rosetta.core.chemical.carbohydrates.CarbohydrateInfoManager static method) is_value() (pyrosetta.rosetta.ObjexxFCL.FArrayInitializer_bool_ObjexxFCL_FArray1D_t method) (pyrosetta.rosetta.ObjexxFCL.FArrayInitializer_bool_ObjexxFCL_FArray2D_t method) (pyrosetta.rosetta.ObjexxFCL.FArrayInitializer_char_ObjexxFCL_FArray1D_t method) (pyrosetta.rosetta.ObjexxFCL.FArrayInitializer_core_pack_dunbrack_BBDepNRChiSample_float_ObjexxFCL_FArray2D_t method) (pyrosetta.rosetta.ObjexxFCL.FArrayInitializer_core_pack_dunbrack_BBDepScoreInterpData_1_ObjexxFCL_FArray2D_t method) (pyrosetta.rosetta.ObjexxFCL.FArrayInitializer_core_pack_dunbrack_BBDepScoreInterpData_1_ObjexxFCL_FArray3D_t method) (pyrosetta.rosetta.ObjexxFCL.FArrayInitializer_core_pack_dunbrack_BBDepScoreInterpData_2_ObjexxFCL_FArray2D_t method) (pyrosetta.rosetta.ObjexxFCL.FArrayInitializer_core_pack_dunbrack_BBDepScoreInterpData_2_ObjexxFCL_FArray3D_t method) (pyrosetta.rosetta.ObjexxFCL.FArrayInitializer_core_pack_dunbrack_BBDepScoreInterpData_3_ObjexxFCL_FArray2D_t method) (pyrosetta.rosetta.ObjexxFCL.FArrayInitializer_core_pack_dunbrack_BBDepScoreInterpData_3_ObjexxFCL_FArray3D_t method) (pyrosetta.rosetta.ObjexxFCL.FArrayInitializer_core_pack_dunbrack_BBDepScoreInterpData_4_ObjexxFCL_FArray2D_t method) (pyrosetta.rosetta.ObjexxFCL.FArrayInitializer_core_pack_dunbrack_BBDepScoreInterpData_4_ObjexxFCL_FArray3D_t method) (pyrosetta.rosetta.ObjexxFCL.FArrayInitializer_core_pack_dunbrack_BBDepScoreInterpData_5_ObjexxFCL_FArray2D_t method) (pyrosetta.rosetta.ObjexxFCL.FArrayInitializer_core_pack_dunbrack_BBDepScoreInterpData_5_ObjexxFCL_FArray3D_t method) (pyrosetta.rosetta.ObjexxFCL.FArrayInitializer_core_pack_dunbrack_BBIndNRChiSample_float_ObjexxFCL_FArray2D_t method) (pyrosetta.rosetta.ObjexxFCL.FArrayInitializer_core_pack_dunbrack_PackedDunbrackRotamer_1_1_float_ObjexxFCL_FArray2D_t method) (pyrosetta.rosetta.ObjexxFCL.FArrayInitializer_core_pack_dunbrack_PackedDunbrackRotamer_1_2_float_ObjexxFCL_FArray2D_t method) (pyrosetta.rosetta.ObjexxFCL.FArrayInitializer_core_pack_dunbrack_PackedDunbrackRotamer_1_3_float_ObjexxFCL_FArray2D_t method) (pyrosetta.rosetta.ObjexxFCL.FArrayInitializer_core_pack_dunbrack_PackedDunbrackRotamer_1_4_float_ObjexxFCL_FArray2D_t method) (pyrosetta.rosetta.ObjexxFCL.FArrayInitializer_core_pack_dunbrack_PackedDunbrackRotamer_1_5_float_ObjexxFCL_FArray2D_t method) (pyrosetta.rosetta.ObjexxFCL.FArrayInitializer_core_pack_dunbrack_PackedDunbrackRotamer_2_1_float_ObjexxFCL_FArray2D_t method) (pyrosetta.rosetta.ObjexxFCL.FArrayInitializer_core_pack_dunbrack_PackedDunbrackRotamer_2_2_float_ObjexxFCL_FArray2D_t method) (pyrosetta.rosetta.ObjexxFCL.FArrayInitializer_core_pack_dunbrack_PackedDunbrackRotamer_2_3_float_ObjexxFCL_FArray2D_t method) (pyrosetta.rosetta.ObjexxFCL.FArrayInitializer_core_pack_dunbrack_PackedDunbrackRotamer_2_4_float_ObjexxFCL_FArray2D_t method) (pyrosetta.rosetta.ObjexxFCL.FArrayInitializer_core_pack_dunbrack_PackedDunbrackRotamer_2_5_float_ObjexxFCL_FArray2D_t method) (pyrosetta.rosetta.ObjexxFCL.FArrayInitializer_core_pack_dunbrack_PackedDunbrackRotamer_3_1_float_ObjexxFCL_FArray2D_t method) (pyrosetta.rosetta.ObjexxFCL.FArrayInitializer_core_pack_dunbrack_PackedDunbrackRotamer_3_2_float_ObjexxFCL_FArray2D_t method) (pyrosetta.rosetta.ObjexxFCL.FArrayInitializer_core_pack_dunbrack_PackedDunbrackRotamer_3_3_float_ObjexxFCL_FArray2D_t method) (pyrosetta.rosetta.ObjexxFCL.FArrayInitializer_core_pack_dunbrack_PackedDunbrackRotamer_3_4_float_ObjexxFCL_FArray2D_t method) (pyrosetta.rosetta.ObjexxFCL.FArrayInitializer_core_pack_dunbrack_PackedDunbrackRotamer_3_5_float_ObjexxFCL_FArray2D_t method) (pyrosetta.rosetta.ObjexxFCL.FArrayInitializer_core_pack_dunbrack_PackedDunbrackRotamer_4_1_float_ObjexxFCL_FArray2D_t method) (pyrosetta.rosetta.ObjexxFCL.FArrayInitializer_core_pack_dunbrack_PackedDunbrackRotamer_4_2_float_ObjexxFCL_FArray2D_t method) (pyrosetta.rosetta.ObjexxFCL.FArrayInitializer_core_pack_dunbrack_PackedDunbrackRotamer_4_3_float_ObjexxFCL_FArray2D_t method) (pyrosetta.rosetta.ObjexxFCL.FArrayInitializer_core_pack_dunbrack_PackedDunbrackRotamer_4_4_float_ObjexxFCL_FArray2D_t method) (pyrosetta.rosetta.ObjexxFCL.FArrayInitializer_core_pack_dunbrack_PackedDunbrackRotamer_4_5_float_ObjexxFCL_FArray2D_t method) (pyrosetta.rosetta.ObjexxFCL.FArrayInitializer_core_pack_dunbrack_PackedDunbrackRotamer_5_1_float_ObjexxFCL_FArray2D_t method) (pyrosetta.rosetta.ObjexxFCL.FArrayInitializer_core_pack_dunbrack_PackedDunbrackRotamer_5_2_float_ObjexxFCL_FArray2D_t method) (pyrosetta.rosetta.ObjexxFCL.FArrayInitializer_core_pack_dunbrack_PackedDunbrackRotamer_5_3_float_ObjexxFCL_FArray2D_t method) (pyrosetta.rosetta.ObjexxFCL.FArrayInitializer_core_pack_dunbrack_PackedDunbrackRotamer_5_4_float_ObjexxFCL_FArray2D_t method) (pyrosetta.rosetta.ObjexxFCL.FArrayInitializer_core_pack_dunbrack_PackedDunbrackRotamer_5_5_float_ObjexxFCL_FArray2D_t method) (pyrosetta.rosetta.ObjexxFCL.FArrayInitializer_double_ObjexxFCL_FArray1D_t method) (pyrosetta.rosetta.ObjexxFCL.FArrayInitializer_double_ObjexxFCL_FArray2D_t method) (pyrosetta.rosetta.ObjexxFCL.FArrayInitializer_double_ObjexxFCL_FArray3D_t method) (pyrosetta.rosetta.ObjexxFCL.FArrayInitializer_double_ObjexxFCL_FArray4D_t method) (pyrosetta.rosetta.ObjexxFCL.FArrayInitializer_double_ObjexxFCL_FArray5D_t method) (pyrosetta.rosetta.ObjexxFCL.FArrayInitializer_float_ObjexxFCL_FArray1D_t method) (pyrosetta.rosetta.ObjexxFCL.FArrayInitializer_float_ObjexxFCL_FArray2D_t method) (pyrosetta.rosetta.ObjexxFCL.FArrayInitializer_float_ObjexxFCL_FArray3D_t method) (pyrosetta.rosetta.ObjexxFCL.FArrayInitializer_float_ObjexxFCL_FArray5D_t method) (pyrosetta.rosetta.ObjexxFCL.FArrayInitializer_int_ObjexxFCL_FArray1D_t method) (pyrosetta.rosetta.ObjexxFCL.FArrayInitializer_int_ObjexxFCL_FArray2D_t method) (pyrosetta.rosetta.ObjexxFCL.FArrayInitializer_int_ObjexxFCL_FArray3D_t method) (pyrosetta.rosetta.ObjexxFCL.FArrayInitializer_int_ObjexxFCL_FArray4D_t method) (pyrosetta.rosetta.ObjexxFCL.FArrayInitializer_int_ObjexxFCL_FArray5D_t method) (pyrosetta.rosetta.ObjexxFCL.FArrayInitializer_numeric_xyzVector_double_ObjexxFCL_FArray2D_t method) (pyrosetta.rosetta.ObjexxFCL.FArrayInitializer_ObjexxFCL_FArray1D_int_ObjexxFCL_FArray1D_t method) (pyrosetta.rosetta.ObjexxFCL.FArrayInitializer_ObjexxFCL_FArray2D_float__star__ObjexxFCL_FArray2D_t method) (pyrosetta.rosetta.ObjexxFCL.FArrayInitializer_ObjexxFCL_ubyte_ObjexxFCL_FArray2D_t method) (pyrosetta.rosetta.ObjexxFCL.FArrayInitializer_std_complex_double_ObjexxFCL_FArray3D_t method) (pyrosetta.rosetta.ObjexxFCL.FArrayInitializer_std_string_ObjexxFCL_FArray1D_t method) (pyrosetta.rosetta.ObjexxFCL.FArrayInitializer_std_string_ObjexxFCL_FArray2D_t method) (pyrosetta.rosetta.ObjexxFCL.FArrayInitializer_std_vector_unsigned_long_std_allocator_unsigned_long_ObjexxFCL_FArray3D_t method) (pyrosetta.rosetta.ObjexxFCL.FArrayInitializer_unsigned_char_ObjexxFCL_FArray2D_t method) (pyrosetta.rosetta.ObjexxFCL.FArrayInitializer_unsigned_char_ObjexxFCL_FArray3D_t method) (pyrosetta.rosetta.ObjexxFCL.FArrayInitializer_unsigned_char_ObjexxFCL_FArray4D_t method) (pyrosetta.rosetta.ObjexxFCL.FArrayInitializer_unsigned_long_ObjexxFCL_FArray1D_t method) (pyrosetta.rosetta.ObjexxFCL.FArrayInitializer_unsigned_long_ObjexxFCL_FArray2D_t method) (pyrosetta.rosetta.ObjexxFCL.FArrayInitializer_unsigned_long_ObjexxFCL_FArray3D_t method) (pyrosetta.rosetta.ObjexxFCL.FArrayInitializer_utility_vector1_core_pack_dunbrack_cenrot_CentroidRotamerSampleData_std_allocator_core_pack_dunbrack_cenrot_CentroidRotamerSampleData_ObjexxFCL_FArray2D_t method) (pyrosetta.rosetta.ObjexxFCL.FArrayInitializer_utility_vector1_double_std_allocator_double_ObjexxFCL_FArray2D_t method) (pyrosetta.rosetta.ObjexxFCL.FArrayInitializer_utility_vector1_double_std_allocator_double_ObjexxFCL_FArray3D_t method) (pyrosetta.rosetta.ObjexxFCL.FArrayInitializer_utility_vector1_numeric_xyzVector_double_std_allocator_numeric_xyzVector_double_ObjexxFCL_FArray3D_t method) (pyrosetta.rosetta.ObjexxFCL.FArrayInitializer_utility_vector1_unsigned_int_std_allocator_unsigned_int_ObjexxFCL_FArray3D_t method) (pyrosetta.rosetta.utility.options.BooleanOption method) (pyrosetta.rosetta.utility.options.BooleanVectorOption method) (pyrosetta.rosetta.utility.options.FileOption method) (pyrosetta.rosetta.utility.options.FileVectorOption method) (pyrosetta.rosetta.utility.options.IntegerOption method) (pyrosetta.rosetta.utility.options.IntegerVectorOption method) (pyrosetta.rosetta.utility.options.Option method) (pyrosetta.rosetta.utility.options.PathOption method) (pyrosetta.rosetta.utility.options.PathVectorOption method) (pyrosetta.rosetta.utility.options.RealOption method) (pyrosetta.rosetta.utility.options.RealVectorOption method) (pyrosetta.rosetta.utility.options.ResidueChainVectorOption method) (pyrosetta.rosetta.utility.options.ScalarOption method) (pyrosetta.rosetta.utility.options.ScalarOption_T_utility_options_BooleanOptionKey_bool_t method) (pyrosetta.rosetta.utility.options.ScalarOption_T_utility_options_FileOptionKey_utility_file_FileName_t method) (pyrosetta.rosetta.utility.options.ScalarOption_T_utility_options_IntegerOptionKey_int_t method) (pyrosetta.rosetta.utility.options.ScalarOption_T_utility_options_PathOptionKey_utility_file_PathName_t method) (pyrosetta.rosetta.utility.options.ScalarOption_T_utility_options_RealOptionKey_double_t method) (pyrosetta.rosetta.utility.options.ScalarOption_T_utility_options_StringOptionKey_std_string_t method) (pyrosetta.rosetta.utility.options.StringOption method) (pyrosetta.rosetta.utility.options.StringVectorOption method) (pyrosetta.rosetta.utility.options.VectorOption method) (pyrosetta.rosetta.utility.options.VectorOption_T_utility_options_BooleanVectorOptionKey_bool_t method) (pyrosetta.rosetta.utility.options.VectorOption_T_utility_options_FileVectorOptionKey_utility_file_FileName_t method) (pyrosetta.rosetta.utility.options.VectorOption_T_utility_options_IntegerVectorOptionKey_int_t method) (pyrosetta.rosetta.utility.options.VectorOption_T_utility_options_PathVectorOptionKey_utility_file_PathName_t method) (pyrosetta.rosetta.utility.options.VectorOption_T_utility_options_RealVectorOptionKey_double_t method) (pyrosetta.rosetta.utility.options.VectorOption_T_utility_options_ResidueChainVectorOptionKey_int_t method) (pyrosetta.rosetta.utility.options.VectorOption_T_utility_options_StringVectorOptionKey_std_string_t method) is_variant_type() (pyrosetta.rosetta.core.chemical.ResidueProperties method) is_virtual() (pyrosetta.rosetta.core.chemical.Atom method) (pyrosetta.rosetta.core.chemical.AtomType method) (pyrosetta.rosetta.core.chemical.ResidueType method) (pyrosetta.rosetta.core.chemical.rna.RNA_Info method) (pyrosetta.rosetta.core.conformation.Residue method) (pyrosetta.rosetta.core.conformation.symmetry.SymmetryInfo method) is_virtual_ (pyrosetta.rosetta.core.chemical.rna.RNA_Info property) is_virtual_base() (in module pyrosetta.rosetta.protocols.stepwise.modeler.rna) is_virtual_residue() (pyrosetta.rosetta.core.chemical.ResidueType method) (pyrosetta.rosetta.core.conformation.Residue method) is_virtualizable_by_packer() (pyrosetta.rosetta.core.chemical.ResidueType method) is_vital() (pyrosetta.rosetta.protocols.sewing.data_storage.LigandSegment method) (pyrosetta.rosetta.protocols.sewing.data_storage.SmartSegment method) is_VRT1() (pyrosetta.rosetta.core.chemical.ResidueType method) is_wat() (pyrosetta.rosetta.core.scoring.elec.electrie.ElecAtom method) (pyrosetta.rosetta.core.scoring.etable.etrie.EtableAtom method) (pyrosetta.rosetta.core.scoring.hbonds.hbtrie.HBAtom method) (pyrosetta.rosetta.core.scoring.mm.mmtrie.MMEnergyTableAtom method) (pyrosetta.rosetta.core.scoring.vdwaals.VDWAtom method) is_water() (pyrosetta.rosetta.core.chemical.ResidueType method) (pyrosetta.rosetta.core.conformation.Residue method) is_weight_type() (pyrosetta.rosetta.core.scoring.hbonds.HBondTypeManager static method) is_whitespace() (in module pyrosetta.rosetta.ObjexxFCL) (pyrosetta.rosetta.ObjexxFCL.Fstring method) (pyrosetta.rosetta.ObjexxFCL.Fsubstring method) is_working_res() (pyrosetta.rosetta.protocols.stepwise.modeler.working_parameters.StepWiseBasicWorkingParameters method) (pyrosetta.rosetta.protocols.stepwise.modeler.working_parameters.StepWiseWorkingParameters method) is_wt_calc_complete() (pyrosetta.rosetta.protocols.ddg.ddGMover method) is_zero() (pyrosetta.rosetta.core.scoring.sc.Atom method) (pyrosetta.rosetta.numeric.xyzMatrix_double_t method) (pyrosetta.rosetta.numeric.xyzMatrix_float_t method) (pyrosetta.rosetta.numeric.xyzTriple_unsigned_long_t method) (pyrosetta.rosetta.numeric.xyzVector_double_t method) (pyrosetta.rosetta.numeric.xyzVector_float_t method) (pyrosetta.rosetta.numeric.xyzVector_int_t method) (pyrosetta.rosetta.numeric.xyzVector_unsigned_long_t method) isAcceptor() (pyrosetta.rosetta.protocols.sparta.PDB method) IsAromaticBond (pyrosetta.rosetta.core.chemical.BondAromaticity attribute) isAtomInRingOfSize() (pyrosetta.rosetta.RDKit.RingInfo method) isbb() (pyrosetta.rosetta.core.scoring.elec.electrie.ElecAtom method) IsBondInRing() (pyrosetta.rosetta.core.chemical.Bond method) isBondInRingOfSize() (pyrosetta.rosetta.RDKit.RingInfo method) IsBondOrderKnown() (pyrosetta.rosetta.core.chemical.Bond method) isbound (pyrosetta.rosetta.core.scoring.atomic_depth.volumepixel property) isClose() (pyrosetta.rosetta.protocols.pockets.CCluster method) (pyrosetta.rosetta.protocols.pockets.PCluster method) isCompound() (pyrosetta.rosetta.protocols.rbsegment_relax.RBSegment method) isDesignable (pyrosetta.rosetta.protocols.forge.remodel.LineObject property) isDigit() (in module pyrosetta.rosetta.protocols.sparta) isDirExists() (in module pyrosetta.rosetta.protocols.sparta) isdisjoint() (pyrosetta.bindings.pose.ResidueLabelAccessor method) isdone (pyrosetta.rosetta.core.scoring.atomic_depth.volumepixel property) isDonor() (pyrosetta.rosetta.protocols.sparta.PDB method) ISECT (pyrosetta.rosetta.core.scoring.packstat.EventType attribute) isEmpty() (pyrosetta.rosetta.core.grid.CartGrid_double_t method) (pyrosetta.rosetta.core.grid.CartGrid_int_t method) (pyrosetta.rosetta.protocols.rbsegment_relax.RBSegment method) isFiberDataLoaded() (pyrosetta.rosetta.core.scoring.fiber_diffraction.FiberDiffraction method) isfinite() (in module pyrosetta.rosetta.utility) isFullyOccupied() (pyrosetta.rosetta.core.grid.CartGrid_double_t method) (pyrosetta.rosetta.core.grid.CartGrid_int_t method) isGenericRB() (pyrosetta.rosetta.protocols.rbsegment_relax.RBSegment method) IsHeavyAtomPredicate (class in pyrosetta.rosetta.core.scoring) isHelix() (pyrosetta.rosetta.protocols.rbsegment_relax.RBSegment method) isHet (pyrosetta.rosetta.core.io.AtomInformation property) (pyrosetta.rosetta.core.pose.PDBInfo.AtomRecord property) isInContact() (pyrosetta.rosetta.protocols.flexpep_docking.FlexPepDockingPoseMetrics method) isinf() (in module pyrosetta.rosetta.utility) isInitialized() (pyrosetta.rosetta.RDKit.RingInfo method) IsMainAtomPredicate (class in pyrosetta.rosetta.core.scoring) isMapLoaded() (pyrosetta.rosetta.core.scoring.electron_density.ElectronDensity method) (pyrosetta.rosetta.core.scoring.electron_density_atomwise.ElectronDensityAtomwise method) isnan() (in module pyrosetta.rosetta.utility) isneigh() (pyrosetta.rosetta.protocols.constel.NeighTeller method) isolate() (pyrosetta.rosetta.protocols.sewing.data_storage.LigandSegment method) (pyrosetta.rosetta.protocols.sewing.data_storage.SmartSegment method) isometry() (pyrosetta.rosetta.core.chemical.Bond method) isPowerOfTwo() (in module pyrosetta.rosetta.core.scoring.fiber_diffraction) IsProteinBackboneIncludingOPredicate (class in pyrosetta.rosetta.core.scoring) IsProteinBackbonePredicate (class in pyrosetta.rosetta.core.scoring) IsProteinCAPredicate (class in pyrosetta.rosetta.core.scoring) IsRelevantItem() (pyrosetta.rosetta.core.scoring.nmr.NMRDummySpinlabelVoxelGrid method) (pyrosetta.rosetta.protocols.nmr.pcs.AtomGrid method) IsSameItem() (pyrosetta.rosetta.core.scoring.nmr.NMRDummySpinlabelVoxelGrid method) (pyrosetta.rosetta.protocols.nmr.pcs.AtomGrid method) isSheet() (pyrosetta.rosetta.protocols.rbsegment_relax.RBSegment method) isSimple() (pyrosetta.rosetta.protocols.rbsegment_relax.RBSegment method) isSolventExposed() (pyrosetta.rosetta.protocols.pockets.CCluster method) (pyrosetta.rosetta.protocols.pockets.PCluster method) isSpace() (in module pyrosetta.rosetta.protocols.sparta) IsSpecificAtomsPredicate (class in pyrosetta.rosetta.core.scoring) isSSBonded() (pyrosetta.rosetta.protocols.sparta.PDB method) isTarget() (pyrosetta.rosetta.protocols.pockets.CCluster method) (pyrosetta.rosetta.protocols.pockets.PCluster method) istart (pyrosetta.rosetta.protocols.mpi_refinement.MethodParams property) isTooSmall() (pyrosetta.rosetta.protocols.pockets.EggshellGrid method) (pyrosetta.rosetta.protocols.pockets.ElectrostaticpotentialGrid method) (pyrosetta.rosetta.protocols.pockets.PocketGrid method) (pyrosetta.rosetta.protocols.pockets.TargetPocketGrid method) istream (class in pyrosetta.rosetta.std) istream.sentry (class in pyrosetta.rosetta.std) istringstream (class in pyrosetta.rosetta.std) istringstream.sentry (class in pyrosetta.rosetta.std) IsValidPosition() (pyrosetta.rosetta.numeric.MathMatrix_double_t method) (pyrosetta.rosetta.numeric.MathMatrix_float_t method) isVarFloat() (pyrosetta.rosetta.protocols.sparta.GDB method) isVarInt() (pyrosetta.rosetta.protocols.sparta.GDB method) isVarString() (pyrosetta.rosetta.protocols.sparta.GDB method) ITEExpression (class in pyrosetta.rosetta.numeric.expression_parser) items() (pyrosetta.bindings.pose.PoseResidueLabelMaskAccessor method) (pyrosetta.bindings.pose.PoseScoreAccessor method) (pyrosetta.io.silent_file_map.SilentFileEnergyAccessor method) (pyrosetta.io.silent_file_map.SilentFileMap method) (pyrosetta.io.silent_file_map.SilentFilePoseAccessor method) (pyrosetta.rosetta.core.scoring.motif.MotifHitStats method) (pyrosetta.rosetta.protocols.indexed_structure_store._map_string_vector_Real method) (pyrosetta.rosetta.protocols.indexed_structure_store._map_string_vector_Size method) (pyrosetta.rosetta.protocols.indexed_structure_store._map_string_vector_vector_Real method) (pyrosetta.rosetta.std.map_char_double method) (pyrosetta.rosetta.std.map_char_protocols_pose_sewing_movers_SeedSettings method) (pyrosetta.rosetta.std.map_char_std_pair_unsigned_long_unsigned_long_t_std_allocator_std_pair_const_char_std_pair_unsigned_long_unsigned_long_t method) (pyrosetta.rosetta.std.map_char_std_shared_ptr_protocols_ligand_docking_LigandArea_t_std_allocator_std_pair_const_char_std_shared_ptr_protocols_ligand_docking_LigandArea_t method) (pyrosetta.rosetta.std.map_char_utility_vector1_double_std_allocator_double_t_std_allocator_std_pair_const_char_utility_vector1_double_std_allocator_double_t method) (pyrosetta.rosetta.std.map_char_utility_vector1_std_string_std_allocator_std_string_t_std_allocator_std_pair_const_char_utility_vector1_std_string_std_allocator_std_string_t method) (pyrosetta.rosetta.std.map_core_chemical_AA_double method) (pyrosetta.rosetta.std.map_core_chemical_AA_std_pair_double_double_t_std_allocator_std_pair_const_core_chemical_AA_std_pair_double_double_t method) (pyrosetta.rosetta.std.map_core_chemical_AA_utility_vector1_double_std_allocator_double_t_std_allocator_std_pair_const_core_chemical_AA_utility_vector1_double_std_allocator_double_t method) (pyrosetta.rosetta.std.map_core_environment_LocalPosition_double method) (pyrosetta.rosetta.std.map_core_id_AtomID_bool method) (pyrosetta.rosetta.std.map_core_id_AtomID_core_id_AtomID method) (pyrosetta.rosetta.std.map_core_id_AtomID_double method) (pyrosetta.rosetta.std.map_core_id_AtomID_unsigned_long method) (pyrosetta.rosetta.std.map_core_id_AtomID_utility_vector1_double_std_allocator_double_t_std_allocator_std_pair_const_core_id_AtomID_utility_vector1_double_std_allocator_double_t method) (pyrosetta.rosetta.std.map_core_scoring_rmsd_atoms_utility_vector1_std_string_std_allocator_std_string_t_std_allocator_std_pair_const_core_scoring_rmsd_atoms_utility_vector1_std_string_std_allocator_std_string_t method) (pyrosetta.rosetta.std.map_core_scoring_ScoreType_double method) (pyrosetta.rosetta.std.map_int_int method) (pyrosetta.rosetta.std.map_int_protocols_legacy_sewing_Model method) (pyrosetta.rosetta.std.map_int_utility_vector0_float_std_allocator_float_t_std_allocator_std_pair_const_int_utility_vector0_float_std_allocator_float_t method) (pyrosetta.rosetta.std.map_protocols_antibody_CDRNameEnum_protocols_loops_Loop method) (pyrosetta.rosetta.std.map_protocols_antibody_CDRNameEnum_utility_vector1_core_chemical_AA_std_allocator_core_chemical_AA_t_std_allocator_std_pair_const_protocols_antibody_CDRNameEnum_utility_vector1_core_chemical_AA_std_allocator_core_chemical_AA_t method) (pyrosetta.rosetta.std.map_protocols_antibody_CDRNameEnum_utility_vector1_protocols_antibody_CDRDBPose_std_allocator_protocols_antibody_CDRDBPose_t_std_allocator_std_pair_const_protocols_antibody_CDRNameEnum_utility_vector1_protocols_antibody_CDRDBPose_std_allocator_protocols_antibody_CDRDBPose_t method) (pyrosetta.rosetta.std.map_protocols_antibody_CDRNameEnum_utility_vector1_protocols_antibody_CDRDBSequence_std_allocator_protocols_antibody_CDRDBSequence_t_std_allocator_std_pair_const_protocols_antibody_CDRNameEnum_utility_vector1_protocols_antibody_CDRDBSequence_std_allocator_protocols_antibody_CDRDBSequence_t method) (pyrosetta.rosetta.std.map_protocols_antibody_clusters_CDRClusterEnum_utility_vector1_protocols_antibody_design_MutantPosition_std_allocator_protocols_antibody_design_MutantPosition_t_std_allocator_std_pair_const_protocols_antibody_clusters_CDRClusterEnum_utility_vector1_protocols_antibody_design_MutantPosition_std_allocator_protocols_antibody_design_MutantPosition_t method) (pyrosetta.rosetta.std.map_protocols_carbohydrates_GlycanSequon_std_string method) (pyrosetta.rosetta.std.map_std_pair_core_chemical_AA_core_chemical_AA_t_double_std_less_std_pair_core_chemical_AA_core_chemical_AA_t_std_allocator_std_pair_const_std_pair_core_chemical_AA_core_chemical_AA_double_t method) (pyrosetta.rosetta.std.map_std_pair_core_id_AtomID_core_id_AtomID_t_utility_vector1_double_std_allocator_double_t_std_less_std_pair_core_id_AtomID_core_id_AtomID_t_std_allocator_std_pair_const_std_pair_core_id_AtomID_core_id_AtomID_utility_vector1_double_std_allocator_double_t method) (pyrosetta.rosetta.std.map_std_pair_protocols_legacy_sewing_Basis_protocols_legacy_sewing_Basis_t_protocols_legacy_sewing_HashResult_std_less_std_pair_protocols_legacy_sewing_Basis_protocols_legacy_sewing_Basis_t_std_allocator_std_pair_const_std_pair_protocols_legacy_sewing_Basis_protocols_legacy_sewing_Basis_protocols_legacy_sewing_HashResult_t method) (pyrosetta.rosetta.std.map_std_pair_std_string_std_string_t_utility_vector1_core_chemical_carbohydrates_LinkageConformerData_std_allocator_core_chemical_carbohydrates_LinkageConformerData_t_std_less_std_pair_std_string_std_string_t_std_allocator_std_pair_const_std_pair_std_string_std_string_utility_vector1_core_chemical_carbohydrates_LinkageConformerData_std_allocator_core_chemical_carbohydrates_LinkageConformerData_t method) (pyrosetta.rosetta.std.map_std_pair_unsigned_long_std_string_t_utility_vector1_std_pair_numeric_xyzVector_double_double_std_allocator_std_pair_numeric_xyzVector_double_double_t_std_less_std_pair_unsigned_long_std_string_t_std_allocator_std_pair_const_std_pair_unsigned_long_std_string_utility_vector1_std_pair_numeric_xyzVector_double_double_std_allocator_std_pair_numeric_xyzVector_double_double_t method) (pyrosetta.rosetta.std.map_std_pair_unsigned_long_unsigned_long_t_std_set_protocols_sewing_hashing_LigandCoordInfo_t_std_less_std_pair_unsigned_long_unsigned_long_t_std_allocator_std_pair_const_std_pair_unsigned_long_unsigned_long_std_set_protocols_sewing_hashing_LigandCoordInfo_t method) (pyrosetta.rosetta.std.map_std_pair_unsigned_long_unsigned_long_t_unsigned_long_std_less_std_pair_unsigned_long_unsigned_long_t_std_allocator_std_pair_const_std_pair_unsigned_long_unsigned_long_unsigned_long_t method) (pyrosetta.rosetta.std.map_std_shared_ptr_const_protocols_toolbox_match_enzdes_util_InvrotTreeNodeBase_t_unsigned_long_std_less_std_shared_ptr_const_protocols_toolbox_match_enzdes_util_InvrotTreeNodeBase_t_std_allocator_std_pair_const_std_shared_ptr_const_protocols_toolbox_match_enzdes_util_InvrotTreeNodeBase_unsigned_long_t method) (pyrosetta.rosetta.std.map_std_string_bool method) (pyrosetta.rosetta.std.map_std_string_char method) (pyrosetta.rosetta.std.map_std_string_core_chemical_AA method) (pyrosetta.rosetta.std.map_std_string_core_chemical_carbohydrates_RootData method) (pyrosetta.rosetta.std.map_std_string_core_chemical_carbohydrates_SugarModificationsNomenclatureTableRow method) (pyrosetta.rosetta.std.map_std_string_core_conformation_symmetry_VirtualCoordinate method) (pyrosetta.rosetta.std.map_std_string_core_id_NamedAtomID method) (pyrosetta.rosetta.std.map_std_string_core_io_CisPeptideInformation method) (pyrosetta.rosetta.std.map_std_string_core_io_ModifiedResidueInformation method) (pyrosetta.rosetta.std.map_std_string_core_io_nmr_ParaIon method) (pyrosetta.rosetta.std.map_std_string_core_io_nmr_SpinlabelDatabaseEntry method) (pyrosetta.rosetta.std.map_std_string_core_io_pdb_RecordType method) (pyrosetta.rosetta.std.map_std_string_core_pose_Pose method) (pyrosetta.rosetta.std.map_std_string_core_scoring_rmsd_atoms method) (pyrosetta.rosetta.std.map_std_string_double method) (pyrosetta.rosetta.std.map_std_string_float method) (pyrosetta.rosetta.std.map_std_string_int method) (pyrosetta.rosetta.std.map_std_string_numeric_interpolation_spline_LinearFunction method) (pyrosetta.rosetta.std.map_std_string_numeric_xyzVector_double_t_std_allocator_std_pair_const_std_string_numeric_xyzVector_double_t method) (pyrosetta.rosetta.std.map_std_string_protocols_denovo_design_components_Alias method) (pyrosetta.rosetta.std.map_std_string_protocols_scoring_methods_pcs2_PcsInputFile method) (pyrosetta.rosetta.std.map_std_string_protocols_scoring_methods_pcs_PCS_file_data method) (pyrosetta.rosetta.std.map_std_string_protocols_scoring_methods_pcsTs1_PCS_file_data_Ts1 method) (pyrosetta.rosetta.std.map_std_string_protocols_scoring_methods_pcsTs2_PCS_file_data_Ts2 method) (pyrosetta.rosetta.std.map_std_string_protocols_scoring_methods_pcsTs3_PCS_file_data_Ts3 method) (pyrosetta.rosetta.std.map_std_string_protocols_scoring_methods_pcsTs4_PCS_file_data_Ts4 method) (pyrosetta.rosetta.std.map_std_string_std_map_std_string_bool_std_less_std_string_std_allocator_std_pair_const_std_string_bool_t_std_allocator_std_pair_const_std_string_std_map_std_string_bool_std_less_std_string_std_allocator_std_pair_const_std_string_bool_t method) (pyrosetta.rosetta.std.map_std_string_std_map_std_string_double_std_less_std_string_std_allocator_std_pair_const_std_string_double_t_std_allocator_std_pair_const_std_string_std_map_std_string_double_std_less_std_string_std_allocator_std_pair_const_std_string_double_t method) (pyrosetta.rosetta.std.map_std_string_std_map_std_string_std_map_std_string_double_std_less_std_string_std_allocator_std_pair_const_std_string_double_std_less_std_string_std_allocator_std_pair_const_std_string_std_map_std_string_double_std_less_std_string_std_allocator_std_pair_const_std_string_double_t_std_allocator_std_pair_const_std_string_std_map_std_string_std_map_std_string_double_std_less_std_string_std_allocator_std_pair_const_std_string_double_std_less_std_string_std_allocator_std_pair_const_std_string_std_map_std_string_double_std_less_std_string_std_allocator_std_pair_const_std_string_double_t method) (pyrosetta.rosetta.std.map_std_string_std_map_std_string_std_pair_std_string_std_string_std_less_std_string_std_allocator_std_pair_const_std_string_std_pair_std_string_std_string_t_std_allocator_std_pair_const_std_string_std_map_std_string_std_pair_std_string_std_string_std_less_std_string_std_allocator_std_pair_const_std_string_std_pair_std_string_std_string_t method) (pyrosetta.rosetta.std.map_std_string_std_map_std_string_std_string_std_less_std_string_std_allocator_std_pair_const_std_string_std_string_t_std_allocator_std_pair_const_std_string_std_map_std_string_std_string_std_less_std_string_std_allocator_std_pair_const_std_string_std_string_t method) (pyrosetta.rosetta.std.map_std_string_std_map_unsigned_long_double_std_less_unsigned_long_std_allocator_std_pair_const_unsigned_long_double_t_std_allocator_std_pair_const_std_string_std_map_unsigned_long_double_std_less_unsigned_long_std_allocator_std_pair_const_unsigned_long_double_t method) (pyrosetta.rosetta.std.map_std_string_std_map_unsigned_long_std_map_core_chemical_AA_double_std_less_core_chemical_AA_std_allocator_std_pair_const_core_chemical_AA_double_std_less_unsigned_long_std_allocator_std_pair_const_unsigned_long_std_map_core_chemical_AA_double_std_less_core_chemical_AA_std_allocator_std_pair_const_core_chemical_AA_double_t_std_allocator_std_pair_const_std_string_std_map_unsigned_long_std_map_core_chemical_AA_double_std_less_core_chemical_AA_std_allocator_std_pair_const_core_chemical_AA_double_std_less_unsigned_long_std_allocator_std_pair_const_unsigned_long_std_map_core_chemical_AA_double_std_less_core_chemical_AA_std_allocator_std_pair_const_core_chemical_AA_double_t method) (pyrosetta.rosetta.std.map_std_string_std_map_unsigned_long_std_string_std_less_unsigned_long_std_allocator_std_pair_const_unsigned_long_std_string_t_std_allocator_std_pair_const_std_string_std_map_unsigned_long_std_string_std_less_unsigned_long_std_allocator_std_pair_const_unsigned_long_std_string_t method) (pyrosetta.rosetta.std.map_std_string_std_pair_core_chemical_io_merge_residue_behavior_std_map_std_string_std_string_std_less_std_string_std_allocator_std_pair_const_std_string_std_string_t_std_allocator_std_pair_const_std_string_std_pair_core_chemical_io_merge_residue_behavior_std_map_std_string_std_string_std_less_std_string_std_allocator_std_pair_const_std_string_std_string_t method) (pyrosetta.rosetta.std.map_std_string_std_pair_std_string_std_string_t_std_allocator_std_pair_const_std_string_std_pair_std_string_std_string_t method) (pyrosetta.rosetta.std.map_std_string_std_pair_utility_vector1_std_pair_std_string_std_string_std_allocator_std_pair_std_string_std_string_utility_vector1_std_map_std_string_std_string_std_less_std_string_std_allocator_std_pair_const_std_string_std_string_std_allocator_std_map_std_string_std_string_std_less_std_string_std_allocator_std_pair_const_std_string_std_string_t_std_allocator_std_pair_const_std_string_std_pair_utility_vector1_std_pair_std_string_std_string_std_allocator_std_pair_std_string_std_string_utility_vector1_std_map_std_string_std_string_std_less_std_string_std_allocator_std_pair_const_std_string_std_string_std_allocator_std_map_std_string_std_string_std_less_std_string_std_allocator_std_pair_const_std_string_std_string_t method) (pyrosetta.rosetta.std.map_std_string_std_set_std_shared_ptr_basic_datacache_WriteableCacheableData_t_std_allocator_std_pair_const_std_string_std_set_std_shared_ptr_basic_datacache_WriteableCacheableData_t method) (pyrosetta.rosetta.std.map_std_string_std_set_std_string_t_std_allocator_std_pair_const_std_string_std_set_std_string_t method) (pyrosetta.rosetta.std.map_std_string_std_shared_ptr_basic_MetricValueBase_t_std_allocator_std_pair_const_std_string_std_shared_ptr_basic_MetricValueBase_t method) (pyrosetta.rosetta.std.map_std_string_std_shared_ptr_basic_resource_manager_ResourceLoaderCreator_t_std_allocator_std_pair_const_std_string_std_shared_ptr_basic_resource_manager_ResourceLoaderCreator_t method) (pyrosetta.rosetta.std.map_std_string_std_shared_ptr_basic_resource_manager_ResourceLocatorCreator_t_std_allocator_std_pair_const_std_string_std_shared_ptr_basic_resource_manager_ResourceLocatorCreator_t method) (pyrosetta.rosetta.std.map_std_string_std_shared_ptr_const_core_chemical_Metapatch_t_std_allocator_std_pair_const_std_string_std_shared_ptr_const_core_chemical_Metapatch_t method) (pyrosetta.rosetta.std.map_std_string_std_shared_ptr_const_protocols_evaluation_PoseEvaluator_t_std_allocator_std_pair_const_std_string_std_shared_ptr_const_protocols_evaluation_PoseEvaluator_t method) (pyrosetta.rosetta.std.map_std_string_std_shared_ptr_const_protocols_pack_daemon_VectorExpression_t_std_allocator_std_pair_const_std_string_std_shared_ptr_const_protocols_pack_daemon_VectorExpression_t method) (pyrosetta.rosetta.std.map_std_string_std_shared_ptr_const_utility_tag_Tag_t_std_allocator_std_pair_const_std_string_std_shared_ptr_const_utility_tag_Tag_t method) (pyrosetta.rosetta.std.map_std_string_std_shared_ptr_core_pack_palette_PackerPaletteCreator_t_std_allocator_std_pair_const_std_string_std_shared_ptr_core_pack_palette_PackerPaletteCreator_t method) (pyrosetta.rosetta.std.map_std_string_std_shared_ptr_core_pack_task_operation_ResLvlTaskOperationCreator_t_std_allocator_std_pair_const_std_string_std_shared_ptr_core_pack_task_operation_ResLvlTaskOperationCreator_t method) (pyrosetta.rosetta.std.map_std_string_std_shared_ptr_core_pack_task_operation_TaskOperationCreator_t_std_allocator_std_pair_const_std_string_std_shared_ptr_core_pack_task_operation_TaskOperationCreator_t method) (pyrosetta.rosetta.std.map_std_string_std_shared_ptr_core_pack_task_ResfileCommand_t_std_allocator_std_pair_const_std_string_std_shared_ptr_core_pack_task_ResfileCommand_t method) (pyrosetta.rosetta.std.map_std_string_std_shared_ptr_core_pose_Pose_t_std_allocator_std_pair_const_std_string_std_shared_ptr_core_pose_Pose_t method) (pyrosetta.rosetta.std.map_std_string_std_shared_ptr_core_scoring_motif_MotifHash_t_std_allocator_std_pair_const_std_string_std_shared_ptr_core_scoring_motif_MotifHash_t method) (pyrosetta.rosetta.std.map_std_string_std_shared_ptr_core_select_jump_selector_JumpSelectorCreator_t_std_allocator_std_pair_const_std_string_std_shared_ptr_core_select_jump_selector_JumpSelectorCreator_t method) (pyrosetta.rosetta.std.map_std_string_std_shared_ptr_core_select_residue_selector_ResidueSelector_t_std_allocator_std_pair_const_std_string_std_shared_ptr_core_select_residue_selector_ResidueSelector_t method) (pyrosetta.rosetta.std.map_std_string_std_shared_ptr_core_select_residue_selector_ResidueSelectorCreator_t_std_allocator_std_pair_const_std_string_std_shared_ptr_core_select_residue_selector_ResidueSelectorCreator_t method) (pyrosetta.rosetta.std.map_std_string_std_shared_ptr_core_simple_metrics_SimpleMetricCreator_t_std_allocator_std_pair_const_std_string_std_shared_ptr_core_simple_metrics_SimpleMetricCreator_t method) (pyrosetta.rosetta.std.map_std_string_std_shared_ptr_numeric_expression_parser_VariableExpression_t_std_allocator_std_pair_const_std_string_std_shared_ptr_numeric_expression_parser_VariableExpression_t method) (pyrosetta.rosetta.std.map_std_string_std_shared_ptr_protocols_filters_FilterCreator_t_std_allocator_std_pair_const_std_string_std_shared_ptr_protocols_filters_FilterCreator_t method) (pyrosetta.rosetta.std.map_std_string_std_shared_ptr_protocols_moves_MoverCreator_t_std_allocator_std_pair_const_std_string_std_shared_ptr_protocols_moves_MoverCreator_t method) (pyrosetta.rosetta.std.map_std_string_std_shared_ptr_protocols_multistage_rosetta_scripts_cluster_ClusterMetricCreator_t_std_allocator_std_pair_const_std_string_std_shared_ptr_protocols_multistage_rosetta_scripts_cluster_ClusterMetricCreator_t method) (pyrosetta.rosetta.std.map_std_string_std_shared_ptr_protocols_parser_DataLoaderCreator_t_std_allocator_std_pair_const_std_string_std_shared_ptr_protocols_parser_DataLoaderCreator_t method) (pyrosetta.rosetta.std.map_std_string_std_shared_ptr_protocols_splice_SpliceSegment_t_std_allocator_std_pair_const_std_string_std_shared_ptr_protocols_splice_SpliceSegment_t method) (pyrosetta.rosetta.std.map_std_string_std_string method) (pyrosetta.rosetta.std.map_std_string_std_tuple_std_string_std_string_char_utility_vector1_std_string_std_allocator_std_string_t_std_allocator_std_pair_const_std_string_std_tuple_std_string_std_string_char_utility_vector1_std_string_std_allocator_std_string_t method) (pyrosetta.rosetta.std.map_std_string_std_vector_double_t_std_allocator_std_pair_const_std_string_std_vector_double_t method) (pyrosetta.rosetta.std.map_std_string_std_vector_std_string_t_std_allocator_std_pair_const_std_string_std_vector_std_string_t method) (pyrosetta.rosetta.std.map_std_string_std_vector_std_vector_double_t_std_allocator_std_pair_const_std_string_std_vector_std_vector_double_t method) (pyrosetta.rosetta.std.map_std_string_std_vector_unsigned_long_t_std_allocator_std_pair_const_std_string_std_vector_unsigned_long_t method) (pyrosetta.rosetta.std.map_std_string_unsigned_long method) (pyrosetta.rosetta.std.map_std_string_utility_json_spirit_Value_impl_utility_json_spirit_Config_map_std_string_t_std_allocator_std_pair_const_std_string_utility_json_spirit_Value_impl_utility_json_spirit_Config_map_std_string_t method) (pyrosetta.rosetta.std.map_std_string_utility_vector1_char_std_allocator_char_t_std_allocator_std_pair_const_std_string_utility_vector1_char_std_allocator_char_t method) (pyrosetta.rosetta.std.map_std_string_utility_vector1_core_io_LinkInformation_std_allocator_core_io_LinkInformation_t_std_allocator_std_pair_const_std_string_utility_vector1_core_io_LinkInformation_std_allocator_core_io_LinkInformation_t method) (pyrosetta.rosetta.std.map_std_string_utility_vector1_core_io_SSBondInformation_std_allocator_core_io_SSBondInformation_t_std_allocator_std_pair_const_std_string_utility_vector1_core_io_SSBondInformation_std_allocator_core_io_SSBondInformation_t method) (pyrosetta.rosetta.std.map_std_string_utility_vector1_std_shared_ptr_const_core_chemical_Patch_std_allocator_std_shared_ptr_const_core_chemical_Patch_t_std_allocator_std_pair_const_std_string_utility_vector1_std_shared_ptr_const_core_chemical_Patch_std_allocator_std_shared_ptr_const_core_chemical_Patch_t method) (pyrosetta.rosetta.std.map_std_string_utility_vector1_std_shared_ptr_core_conformation_Residue_std_allocator_std_shared_ptr_core_conformation_Residue_t_std_allocator_std_pair_const_std_string_utility_vector1_std_shared_ptr_core_conformation_Residue_std_allocator_std_shared_ptr_core_conformation_Residue_t method) (pyrosetta.rosetta.std.map_std_string_utility_vector1_std_string_std_allocator_std_string_t_std_allocator_std_pair_const_std_string_utility_vector1_std_string_std_allocator_std_string_t method) (pyrosetta.rosetta.std.map_std_string_utility_vector1_unsigned_long_std_allocator_unsigned_long_t_std_allocator_std_pair_const_std_string_utility_vector1_unsigned_long_std_allocator_unsigned_long_t method) (pyrosetta.rosetta.std.map_unsigned_long_bool method) (pyrosetta.rosetta.std.map_unsigned_long_char method) (pyrosetta.rosetta.std.map_unsigned_long_core_conformation_symmetry_SymDof method) (pyrosetta.rosetta.std.map_unsigned_long_double method) (pyrosetta.rosetta.std.map_unsigned_long_numeric_xyzVector_double_t_std_allocator_std_pair_const_unsigned_long_numeric_xyzVector_double_t method) (pyrosetta.rosetta.std.map_unsigned_long_protocols_dna_DnaNeighbor method) (pyrosetta.rosetta.std.map_unsigned_long_protocols_dna_DnaPosition method) (pyrosetta.rosetta.std.map_unsigned_long_protocols_indexed_structure_store_FragmentLookupResult method) (pyrosetta.rosetta.std.map_unsigned_long_protocols_sewing_hashing_IdealContact method) (pyrosetta.rosetta.std.map_unsigned_long_std_map_core_chemical_AA_double_std_less_core_chemical_AA_std_allocator_std_pair_const_core_chemical_AA_double_t_std_allocator_std_pair_const_unsigned_long_std_map_core_chemical_AA_double_std_less_core_chemical_AA_std_allocator_std_pair_const_core_chemical_AA_double_t method) (pyrosetta.rosetta.std.map_unsigned_long_std_pair_char_std_string_t_std_allocator_std_pair_const_unsigned_long_std_pair_char_std_string_t method) (pyrosetta.rosetta.std.map_unsigned_long_std_pair_double_double_t_std_allocator_std_pair_const_unsigned_long_std_pair_double_double_t method) (pyrosetta.rosetta.std.map_unsigned_long_std_set_std_string_t_std_allocator_std_pair_const_unsigned_long_std_set_std_string_t method) (pyrosetta.rosetta.std.map_unsigned_long_std_shared_ptr_const_core_chemical_ResidueType_t_std_allocator_std_pair_const_unsigned_long_std_shared_ptr_const_core_chemical_ResidueType_t method) (pyrosetta.rosetta.std.map_unsigned_long_std_shared_ptr_const_core_conformation_PseudoBondCollection_t_std_allocator_std_pair_const_unsigned_long_std_shared_ptr_const_core_conformation_PseudoBondCollection_t method) (pyrosetta.rosetta.std.map_unsigned_long_std_shared_ptr_const_protocols_sewing_data_storage_LigandResidue_t_std_allocator_std_pair_const_unsigned_long_std_shared_ptr_const_protocols_sewing_data_storage_LigandResidue_t method) (pyrosetta.rosetta.std.map_unsigned_long_std_shared_ptr_core_conformation_carbohydrates_GlycanTree_t_std_allocator_std_pair_const_unsigned_long_std_shared_ptr_core_conformation_carbohydrates_GlycanTree_t method) (pyrosetta.rosetta.std.map_unsigned_long_std_shared_ptr_core_fragment_FragSet_t_std_allocator_std_pair_const_unsigned_long_std_shared_ptr_core_fragment_FragSet_t method) (pyrosetta.rosetta.std.map_unsigned_long_std_shared_ptr_core_io_PositionDdGInfo_PositionDdGInfo_t_std_allocator_std_pair_const_unsigned_long_std_shared_ptr_core_io_PositionDdGInfo_PositionDdGInfo_t method) (pyrosetta.rosetta.std.map_unsigned_long_std_shared_ptr_core_scoring_epr_deer_metrics_DEERData_t_std_allocator_std_pair_const_unsigned_long_std_shared_ptr_core_scoring_epr_deer_metrics_DEERData_t method) (pyrosetta.rosetta.std.map_unsigned_long_std_shared_ptr_protocols_frags_TorsionFragmentLibrary_t_std_allocator_std_pair_const_unsigned_long_std_shared_ptr_protocols_frags_TorsionFragmentLibrary_t method) (pyrosetta.rosetta.std.map_unsigned_long_std_shared_ptr_protocols_indexed_structure_store_FragmentStore_t_std_allocator_std_pair_const_unsigned_long_std_shared_ptr_protocols_indexed_structure_store_FragmentStore_t method) (pyrosetta.rosetta.std.map_unsigned_long_std_shared_ptr_protocols_sewing_data_storage_LigandResidue_t_std_allocator_std_pair_const_unsigned_long_std_shared_ptr_protocols_sewing_data_storage_LigandResidue_t method) (pyrosetta.rosetta.std.map_unsigned_long_std_shared_ptr_protocols_sewing_data_storage_SmartSegment_t_std_allocator_std_pair_const_unsigned_long_std_shared_ptr_protocols_sewing_data_storage_SmartSegment_t method) (pyrosetta.rosetta.std.map_unsigned_long_std_string method) (pyrosetta.rosetta.std.map_unsigned_long_unsigned_long method) (pyrosetta.rosetta.std.map_unsigned_long_utility_vector1_core_id_AtomID_std_allocator_core_id_AtomID_t_std_allocator_std_pair_const_unsigned_long_utility_vector1_core_id_AtomID_std_allocator_core_id_AtomID_t method) (pyrosetta.rosetta.std.map_unsigned_long_utility_vector1_double_std_allocator_double_t_std_allocator_std_pair_const_unsigned_long_utility_vector1_double_std_allocator_double_t method) (pyrosetta.rosetta.std.map_unsigned_long_utility_vector1_std_pair_bool_std_shared_ptr_core_conformation_Residue_std_allocator_std_pair_bool_std_shared_ptr_core_conformation_Residue_t_std_allocator_std_pair_const_unsigned_long_utility_vector1_std_pair_bool_std_shared_ptr_core_conformation_Residue_std_allocator_std_pair_bool_std_shared_ptr_core_conformation_Residue_t method) (pyrosetta.rosetta.std.map_unsigned_long_utility_vector1_std_pair_numeric_xyzVector_double_double_std_allocator_std_pair_numeric_xyzVector_double_double_t_std_allocator_std_pair_const_unsigned_long_utility_vector1_std_pair_numeric_xyzVector_double_double_std_allocator_std_pair_numeric_xyzVector_double_double_t method) (pyrosetta.rosetta.std.map_unsigned_long_utility_vector1_std_pair_unsigned_long_double_std_allocator_std_pair_unsigned_long_double_t_std_allocator_std_pair_const_unsigned_long_utility_vector1_std_pair_unsigned_long_double_std_allocator_std_pair_unsigned_long_double_t method) (pyrosetta.rosetta.std.map_unsigned_long_utility_vector1_std_shared_ptr_const_core_conformation_Residue_std_allocator_std_shared_ptr_const_core_conformation_Residue_t_std_allocator_std_pair_const_unsigned_long_utility_vector1_std_shared_ptr_const_core_conformation_Residue_std_allocator_std_shared_ptr_const_core_conformation_Residue_t method) (pyrosetta.rosetta.std.map_unsigned_long_utility_vector1_std_string_std_allocator_std_string_t_std_allocator_std_pair_const_unsigned_long_utility_vector1_std_string_std_allocator_std_string_t method) (pyrosetta.rosetta.std.map_unsigned_long_utility_vector1_unsigned_long_std_allocator_unsigned_long_t_std_allocator_std_pair_const_unsigned_long_utility_vector1_unsigned_long_std_allocator_unsigned_long_t method) iter() (pyrosetta.rosetta.protocols.mpi_refinement.Scheduler method) iter_over_labels() (pyrosetta.rosetta.core.energy_methods.DEEREnergy method) iterate_bump_selector() (pyrosetta.rosetta.core.pack.rotamer_set.BumpSelector method) iterate_over_basis_pairs() (pyrosetta.rosetta.protocols.sewing.data_storage.HashedSmartAssembly method) (pyrosetta.rosetta.protocols.sewing.data_storage.SmartAssembly method) iterate_tensor_weights() (pyrosetta.rosetta.core.scoring.ResidualDipolarCoupling method) IteratedConvergenceMover (class in pyrosetta.rosetta.protocols.moves) IteratedConvergenceMoverCreator (class in pyrosetta.rosetta.protocols.moves) iteration (pyrosetta.rosetta.protocols.canonical_sampling.DbTrajectoryRecorder.Frame property) (pyrosetta.rosetta.protocols.trajectory.DbTrajectoryWriter.Frame property) iteration() (pyrosetta.rosetta.protocols.monte_carlo.AcceptedScores method) (pyrosetta.rosetta.protocols.vip.VIP_Mover method) iterations() (pyrosetta.rosetta.protocols.ddg.CartesianddG.MutationSet method) (pyrosetta.rosetta.protocols.generalized_kinematic_closure.perturber.GeneralizedKICperturber method) IterativeAbrelax (class in pyrosetta.rosetta.protocols.abinitio) IterativeAbrelax.IterationStage (class in pyrosetta.rosetta.protocols.abinitio) IterativeBase (class in pyrosetta.rosetta.protocols.abinitio) IterativeBase.IterationStage (class in pyrosetta.rosetta.protocols.abinitio) IterativeCentroid (class in pyrosetta.rosetta.protocols.abinitio) IterativeCentroid.IterationStage (class in pyrosetta.rosetta.protocols.abinitio) IterativeFullatom (class in pyrosetta.rosetta.protocols.abinitio) IterativeFullatom.IterationStage (class in pyrosetta.rosetta.protocols.abinitio) IterativeOptEDriver (class in pyrosetta.rosetta.protocols.optimize_weights) IterativeVectorExpression (class in pyrosetta.rosetta.protocols.pack_daemon) itime() (in module pyrosetta.rosetta.ObjexxFCL) itoa() (in module pyrosetta.rosetta.protocols.sparta) (pyrosetta.rosetta.protocols.sparta.ANN method) itterative() (pyrosetta.rosetta.protocols.task_operations.DatabaseThread method) IVa (pyrosetta.rosetta.protocols.abinitio.abscript.StageID attribute) ivalue() (pyrosetta.rosetta.ObjexxFCL.DimensionExpression method) (pyrosetta.rosetta.ObjexxFCL.DimensionExpressionCon method) (pyrosetta.rosetta.ObjexxFCL.DimensionExpressionCube method) (pyrosetta.rosetta.ObjexxFCL.DimensionExpressionDiv method) (pyrosetta.rosetta.ObjexxFCL.DimensionExpressionMax method) (pyrosetta.rosetta.ObjexxFCL.DimensionExpressionMin method) (pyrosetta.rosetta.ObjexxFCL.DimensionExpressionMul method) (pyrosetta.rosetta.ObjexxFCL.DimensionExpressionPow method) (pyrosetta.rosetta.ObjexxFCL.DimensionExpressionRef method) (pyrosetta.rosetta.ObjexxFCL.DimensionExpressionSquare method) (pyrosetta.rosetta.ObjexxFCL.DimensionExpressionSub method) (pyrosetta.rosetta.ObjexxFCL.DimensionExpressionSum method) IVb (pyrosetta.rosetta.protocols.abinitio.abscript.StageID attribute) ivm() (pyrosetta.rosetta.protocols.toolbox.InteratomicVarianceMatrix method) iword() (pyrosetta.rosetta.std.ios_base method) ix (pyrosetta.rosetta.core.scoring.atomic_depth.voxel property) (pyrosetta.rosetta.core.scoring.atomic_depth.voxel2 property) iy (pyrosetta.rosetta.core.scoring.atomic_depth.voxel property) (pyrosetta.rosetta.core.scoring.atomic_depth.voxel2 property) iz (pyrosetta.rosetta.core.scoring.atomic_depth.voxel property) (pyrosetta.rosetta.core.scoring.atomic_depth.voxel2 property) izstream (class in pyrosetta.rosetta.utility.io)