pose_manipulation

Bindings for protocols::toolbox::pose_manipulation namespace

pyrosetta.rosetta.protocols.toolbox.pose_manipulation.add_chainbreaks_according_to_jumps(pose: pyrosetta.rosetta.core.pose.Pose) → None

Florian Richter( floric.washington.edu), nov 11

adds chainbreak residue types depending on fold tree jumps

C++: protocols::toolbox::pose_manipulation::add_chainbreaks_according_to_jumps(class core::pose::Pose &) –> void

pyrosetta.rosetta.protocols.toolbox.pose_manipulation.construct_poly_XXX_pose(*args, **kwargs)

Overloaded function.

  1. construct_poly_XXX_pose(aa: str, pose: pyrosetta.rosetta.core.pose.Pose, positions: pyrosetta.rosetta.utility.vector1_unsigned_long, keep_pro: bool, keep_gly: bool, keep_disulfide_cys: bool) -> None

Nobuyasu Koga ( nobuyasu.edu ), Oct 09

puts in XXX residues at the positions specified in the ‘positions’ input array

C++: protocols::toolbox::pose_manipulation::construct_poly_XXX_pose(const std::string &, class core::pose::Pose &, const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &, bool, bool, bool) –> void

  1. construct_poly_XXX_pose(aa: str, pose: pyrosetta.rosetta.core.pose.Pose, positions: pyrosetta.rosetta.utility.vector1_unsigned_long, restype_set: pyrosetta.rosetta.core.chemical.ResidueTypeSet, keep_pro: bool, keep_gly: bool, keep_disulfide_cys: bool) -> None

Nobuyasu Koga ( nobuyasu.edu ), Oct 09; Tom Linsky (tlinsky.edu), Nov 2014

puts in XXX residues at the positions from the given residue typeset specified in the ‘positions’ input array

C++: protocols::toolbox::pose_manipulation::construct_poly_XXX_pose(const std::string &, class core::pose::Pose &, const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &, class std::shared_ptr<const class core::chemical::ResidueTypeSet>, bool, bool, bool) –> void

pyrosetta.rosetta.protocols.toolbox.pose_manipulation.construct_poly_ala_pose(pose: pyrosetta.rosetta.core.pose.Pose, positions: pyrosetta.rosetta.utility.vector1_unsigned_long, keep_pro: bool, keep_gly: bool, keep_disulfide_cys: bool) → None

Florian Richter( floric.washington.edu) , june 08

puts in ala residues at the positions specified in the ‘positions’ input array

C++: protocols::toolbox::pose_manipulation::construct_poly_ala_pose(class core::pose::Pose &, const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &, const bool, const bool, const bool) –> void

pyrosetta.rosetta.protocols.toolbox.pose_manipulation.construct_poly_beta_ala_pose(pose: pyrosetta.rosetta.core.pose.Pose, positions: pyrosetta.rosetta.utility.vector1_unsigned_long, keep_pro: bool, keep_gly: bool, keep_disulfide_cys: bool) → None

Vikram K. Mulligan (vmullig.edu)

puts in beta-3-ala residues at the positions specified in the ‘positions’ input array.

C++: protocols::toolbox::pose_manipulation::construct_poly_beta_ala_pose(class core::pose::Pose &, const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &, const bool, const bool, const bool) –> void

pyrosetta.rosetta.protocols.toolbox.pose_manipulation.construct_poly_d_ala_pose(pose: pyrosetta.rosetta.core.pose.Pose, positions: pyrosetta.rosetta.utility.vector1_unsigned_long, keep_pro: bool, keep_gly: bool, keep_disulfide_cys: bool) → None

Vikram K. Mulligan (vmullig.edu)

puts in D-ala residues at the positions specified in the ‘positions’ input array

C++: protocols::toolbox::pose_manipulation::construct_poly_d_ala_pose(class core::pose::Pose &, const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &, const bool, const bool, const bool) –> void

pyrosetta.rosetta.protocols.toolbox.pose_manipulation.construct_poly_d_beta_ala_pose(pose: pyrosetta.rosetta.core.pose.Pose, positions: pyrosetta.rosetta.utility.vector1_unsigned_long, keep_pro: bool, keep_gly: bool, keep_disulfide_cys: bool) → None

Vikram K. Mulligan (vmullig.edu)

puts in D-beta-3-ala residues at the positions specified in the ‘positions’ input array

C++: protocols::toolbox::pose_manipulation::construct_poly_d_beta_ala_pose(class core::pose::Pose &, const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &, const bool, const bool, const bool) –> void

pyrosetta.rosetta.protocols.toolbox.pose_manipulation.construct_poly_uniq_restype_pose(pose: pyrosetta.rosetta.core.pose.Pose, positions: pyrosetta.rosetta.utility.vector1_unsigned_long, restype: pyrosetta.rosetta.core.chemical.ResidueType, keep_pro: bool, keep_gly: bool, keep_disulfide_cys: bool) → None

Possu Huang ( possu.edu)

allows construction of a polymer of any residue type

C++: protocols::toolbox::pose_manipulation::construct_poly_uniq_restype_pose(class core::pose::Pose &, const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &, const class core::chemical::ResidueType &, const bool, const bool, const bool) –> void

pyrosetta.rosetta.protocols.toolbox.pose_manipulation.remove_chainbreaks_according_to_jumps(pose: pyrosetta.rosetta.core.pose.Pose) → None

Florian Richter( floric.washington.edu), nov 11

removes chainbreak residue types depending on fold tree jumps

C++: protocols::toolbox::pose_manipulation::remove_chainbreaks_according_to_jumps(class core::pose::Pose &) –> void

pyrosetta.rosetta.protocols.toolbox.pose_manipulation.remove_non_protein_residues(pose: pyrosetta.rosetta.core.pose.Pose) → None

Florian Richter( floric.washington.edu) , aug 08

deletes all nonprotein residues from a pose

C++: protocols::toolbox::pose_manipulation::remove_non_protein_residues(class core::pose::Pose &) –> void

pyrosetta.rosetta.protocols.toolbox.pose_manipulation.repack_these_residues(*args, **kwargs)

Overloaded function.

  1. repack_these_residues(subset: pyrosetta.rosetta.utility.vector1_bool, pose: pyrosetta.rosetta.core.pose.Pose, scorefxn: pyrosetta.rosetta.core.scoring.ScoreFunction) -> None

  2. repack_these_residues(subset: pyrosetta.rosetta.utility.vector1_bool, pose: pyrosetta.rosetta.core.pose.Pose, scorefxn: pyrosetta.rosetta.core.scoring.ScoreFunction, include_current: bool) -> None

  3. repack_these_residues(subset: pyrosetta.rosetta.utility.vector1_bool, pose: pyrosetta.rosetta.core.pose.Pose, scorefxn: pyrosetta.rosetta.core.scoring.ScoreFunction, include_current: bool, name1s_if_design: str) -> None

Brian Coventry (bcov.edu)

Repack a subset of residues

Repacks a multiple residues using the command-line flags

A list of amino acid name1s may be provided if one wishes to design. Leaving this “” or default implies no design

C++: protocols::toolbox::pose_manipulation::repack_these_residues(const class utility::vector1<bool, class std::allocator<bool> > &, class core::pose::Pose &, class std::shared_ptr<class core::scoring::ScoreFunction>, bool, std::string) –> void

pyrosetta.rosetta.protocols.toolbox.pose_manipulation.repack_this_residue(*args, **kwargs)

Overloaded function.

  1. repack_this_residue(seq_pos: int, pose: pyrosetta.rosetta.core.pose.Pose, scorefxn: pyrosetta.rosetta.core.scoring.ScoreFunction) -> None

  2. repack_this_residue(seq_pos: int, pose: pyrosetta.rosetta.core.pose.Pose, scorefxn: pyrosetta.rosetta.core.scoring.ScoreFunction, include_current: bool) -> None

  3. repack_this_residue(seq_pos: int, pose: pyrosetta.rosetta.core.pose.Pose, scorefxn: pyrosetta.rosetta.core.scoring.ScoreFunction, include_current: bool, name1s_if_design: str) -> None

Brian Coventry (bcov.edu)

Repack a single residue

Repacks a single residue using the command-line flags

A list of amino acid name1s may be provided if one wishes to design. Leaving this “” or default implies no design

C++: protocols::toolbox::pose_manipulation::repack_this_residue(unsigned long, class core::pose::Pose &, class std::shared_ptr<class core::scoring::ScoreFunction>, bool, std::string) –> void

pyrosetta.rosetta.protocols.toolbox.pose_manipulation.rigid_body_move(*args, **kwargs)

Overloaded function.

  1. rigid_body_move(rotation_unit_vector: pyrosetta.rosetta.numeric.xyzVector_double_t, angle_deg: float, translation_vector: pyrosetta.rosetta.numeric.xyzVector_double_t, pose: pyrosetta.rosetta.core.pose.Pose, subset: pyrosetta.rosetta.utility.vector1_bool) -> None

  2. rigid_body_move(rotation_unit_vector: pyrosetta.rosetta.numeric.xyzVector_double_t, angle_deg: float, translation_vector: pyrosetta.rosetta.numeric.xyzVector_double_t, pose: pyrosetta.rosetta.core.pose.Pose, subset: pyrosetta.rosetta.utility.vector1_bool, center_of_rotation: pyrosetta.rosetta.numeric.xyzVector_double_t) -> None

Performs a rigid body rotation then translation of a section

of a pose given by a ResidueSubset. By default this routine will find the CA center of mass of the subset and use that as the center of rotation.

C++: protocols::toolbox::pose_manipulation::rigid_body_move(const class numeric::xyzVector<double> &, double, const class numeric::xyzVector<double> &, class core::pose::Pose &, const class utility::vector1<bool, class std::allocator<bool> > &, class numeric::xyzVector<double>) –> void

  1. rigid_body_move(rotation_unit_vector: pyrosetta.rosetta.numeric.xyzVector_double_t, angle_deg: float, translation_vector: pyrosetta.rosetta.numeric.xyzVector_double_t, translation_scalar: float, pose: pyrosetta.rosetta.core.pose.Pose, subset: pyrosetta.rosetta.utility.vector1_bool) -> None

  2. rigid_body_move(rotation_unit_vector: pyrosetta.rosetta.numeric.xyzVector_double_t, angle_deg: float, translation_vector: pyrosetta.rosetta.numeric.xyzVector_double_t, translation_scalar: float, pose: pyrosetta.rosetta.core.pose.Pose, subset: pyrosetta.rosetta.utility.vector1_bool, center_of_rotation: pyrosetta.rosetta.numeric.xyzVector_double_t) -> None

Performs a rigid body rotation then translation of a section

of a pose given by a ResidueSubset. By default this routine will find the CA center of mass of the subset and use that as the center of rotation.

C++: protocols::toolbox::pose_manipulation::rigid_body_move(const class numeric::xyzVector<double> &, double, const class numeric::xyzVector<double> &, double, class core::pose::Pose &, const class utility::vector1<bool, class std::allocator<bool> > &, class numeric::xyzVector<double>) –> void

  1. rigid_body_move(rotation: pyrosetta.rosetta.numeric.xyzMatrix_double_t, translation_vector: pyrosetta.rosetta.numeric.xyzVector_double_t, pose: pyrosetta.rosetta.core.pose.Pose, subset: pyrosetta.rosetta.utility.vector1_bool) -> None

  2. rigid_body_move(rotation: pyrosetta.rosetta.numeric.xyzMatrix_double_t, translation_vector: pyrosetta.rosetta.numeric.xyzVector_double_t, pose: pyrosetta.rosetta.core.pose.Pose, subset: pyrosetta.rosetta.utility.vector1_bool, center_of_rotation: pyrosetta.rosetta.numeric.xyzVector_double_t) -> None

Performs a rigid body rotation then translation of a section

of a pose given by a ResidueSubset. By default this routine will find the CA center of mass of the subset and use that as the center of rotation.

C++: protocols::toolbox::pose_manipulation::rigid_body_move(class numeric::xyzMatrix<double>, const class numeric::xyzVector<double> &, class core::pose::Pose &, const class utility::vector1<bool, class std::allocator<bool> > &, class numeric::xyzVector<double>) –> void

  1. rigid_body_move(rotation: pyrosetta.rosetta.numeric.xyzMatrix_double_t, translation_vector: pyrosetta.rosetta.numeric.xyzVector_double_t, translation_scalar: float, pose: pyrosetta.rosetta.core.pose.Pose, subset: pyrosetta.rosetta.utility.vector1_bool) -> None

  2. rigid_body_move(rotation: pyrosetta.rosetta.numeric.xyzMatrix_double_t, translation_vector: pyrosetta.rosetta.numeric.xyzVector_double_t, translation_scalar: float, pose: pyrosetta.rosetta.core.pose.Pose, subset: pyrosetta.rosetta.utility.vector1_bool, center_of_rotation: pyrosetta.rosetta.numeric.xyzVector_double_t) -> None

Performs a rigid body rotation then translation of a section

of a pose given by a ResidueSubset. By default this routine will find the CA center of mass of the subset and use that as the center of rotation.

C++: protocols::toolbox::pose_manipulation::rigid_body_move(class numeric::xyzMatrix<double>, const class numeric::xyzVector<double> &, double, class core::pose::Pose &, const class utility::vector1<bool, class std::allocator<bool> > &, class numeric::xyzVector<double>) –> void

pyrosetta.rosetta.protocols.toolbox.pose_manipulation.superimpose_pose_on_subset_CA(*args, **kwargs)

Overloaded function.

  1. superimpose_pose_on_subset_CA(pose: pyrosetta.rosetta.core.pose.Pose, ref_pose: pyrosetta.rosetta.core.pose.Pose, positions: pyrosetta.rosetta.utility.vector1_unsigned_long) -> float

  2. superimpose_pose_on_subset_CA(pose: pyrosetta.rosetta.core.pose.Pose, ref_pose: pyrosetta.rosetta.core.pose.Pose, positions: pyrosetta.rosetta.utility.vector1_unsigned_long, offset: int) -> float

Florian Richter( floric.washington.edu) , sep 08

superimposes one pose onto the other at the positions specified and

with the offset specified

C++: protocols::toolbox::pose_manipulation::superimpose_pose_on_subset_CA(class core::pose::Pose &, const class core::pose::Pose &, const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &, const int) –> double