import_pose¶

Bindings for core::import_pose namespace

class pyrosetta.rosetta.core.import_pose.FileType¶

Bases: pybind11_object

Enum for the file type.

If you add to this list, update the extension_from_filetype function!

Members:

PDB_file

CIF_file

MMTF_file

SRLZ_file

end_of_filetype_list

Unknown_file

CIF_file = <FileType.CIF_file: 2>¶

MMTF_file = <FileType.MMTF_file: 3>¶

PDB_file = <FileType.PDB_file: 1>¶

SRLZ_file = <FileType.SRLZ_file: 4>¶

Unknown_file = <FileType.end_of_filetype_list: 5>¶

end_of_filetype_list = <FileType.end_of_filetype_list: 5>¶

property name¶

property value¶

class pyrosetta.rosetta.core.import_pose.FullModelPoseBuilder¶

Bases: pybind11_object

assign(self: pyrosetta.rosetta.core.import_pose.FullModelPoseBuilder, : pyrosetta.rosetta.core.import_pose.FullModelPoseBuilder) → pyrosetta.rosetta.core.import_pose.FullModelPoseBuilder¶: C++: core::import_pose::FullModelPoseBuilder::operator=(const class core::import_pose::FullModelPoseBuilder &) –> class core::import_pose::FullModelPoseBuilder &

build(self: pyrosetta.rosetta.core.import_pose.FullModelPoseBuilder) → pyrosetta.rosetta.core.pose.Pose¶: C++: core::import_pose::FullModelPoseBuilder::build() –> class std::shared_ptr<class core::pose::Pose>

initialize_full_model_parameters(self: pyrosetta.rosetta.core.import_pose.FullModelPoseBuilder) → None¶: C++: core::import_pose::FullModelPoseBuilder::initialize_full_model_parameters() –> void

initialize_further_from_options(self: pyrosetta.rosetta.core.import_pose.FullModelPoseBuilder) → None¶: C++: core::import_pose::FullModelPoseBuilder::initialize_further_from_options() –> void

initialize_input_poses_from_options(self: pyrosetta.rosetta.core.import_pose.FullModelPoseBuilder, rsd_set: pyrosetta.rosetta.core.chemical.ResidueTypeSet) → None¶: C++: core::import_pose::FullModelPoseBuilder::initialize_input_poses_from_options(class std::shared_ptr<const class core::chemical::ResidueTypeSet>) –> void

set_alignment_anchor_res(self: pyrosetta.rosetta.core.import_pose.FullModelPoseBuilder, alignment_anchor_res: pyrosetta.rosetta.utility.vector1_unsigned_long) → None¶: C++: core::import_pose::FullModelPoseBuilder::set_alignment_anchor_res(const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &) –> void

set_block_stack_above_res(self: pyrosetta.rosetta.core.import_pose.FullModelPoseBuilder, block_stack_above_res: pyrosetta.rosetta.utility.vector1_unsigned_long) → None¶: C++: core::import_pose::FullModelPoseBuilder::set_block_stack_above_res(const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &) –> void

set_block_stack_below_res(self: pyrosetta.rosetta.core.import_pose.FullModelPoseBuilder, block_stack_below_res: pyrosetta.rosetta.utility.vector1_unsigned_long) → None¶: C++: core::import_pose::FullModelPoseBuilder::set_block_stack_below_res(const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &) –> void

set_bulge_res(self: pyrosetta.rosetta.core.import_pose.FullModelPoseBuilder, bulge_res: pyrosetta.rosetta.utility.vector1_unsigned_long) → None¶: C++: core::import_pose::FullModelPoseBuilder::set_bulge_res(const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &) –> void

set_calc_rms_res(self: pyrosetta.rosetta.core.import_pose.FullModelPoseBuilder, calc_rms_res: pyrosetta.rosetta.utility.vector1_unsigned_long) → None¶: C++: core::import_pose::FullModelPoseBuilder::set_calc_rms_res(const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &) –> void

set_constraint_file(self: pyrosetta.rosetta.core.import_pose.FullModelPoseBuilder, constraint_file: str) → None¶: C++: core::import_pose::FullModelPoseBuilder::set_constraint_file(const std::string &) –> void

set_cutpoint_closed(self: pyrosetta.rosetta.core.import_pose.FullModelPoseBuilder, cutpoint_closed: pyrosetta.rosetta.utility.vector1_unsigned_long) → None¶: C++: core::import_pose::FullModelPoseBuilder::set_cutpoint_closed(const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &) –> void

set_cutpoint_open_in_full_model(self: pyrosetta.rosetta.core.import_pose.FullModelPoseBuilder, cutpoint_open_in_full_model: pyrosetta.rosetta.utility.vector1_unsigned_long) → None¶: C++: core::import_pose::FullModelPoseBuilder::set_cutpoint_open_in_full_model(const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &) –> void

set_cyclize_res(self: pyrosetta.rosetta.core.import_pose.FullModelPoseBuilder, cyclize_res: pyrosetta.rosetta.utility.vector1_unsigned_long) → None¶: C++: core::import_pose::FullModelPoseBuilder::set_cyclize_res(const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &) –> void

set_disulfide_file(self: pyrosetta.rosetta.core.import_pose.FullModelPoseBuilder, disulfide_file: str) → None¶: C++: core::import_pose::FullModelPoseBuilder::set_disulfide_file(const std::string &) –> void

set_extra_minimize_jump_res(self: pyrosetta.rosetta.core.import_pose.FullModelPoseBuilder, extra_minimize_jump_res: pyrosetta.rosetta.utility.vector1_unsigned_long) → None¶: C++: core::import_pose::FullModelPoseBuilder::set_extra_minimize_jump_res(const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &) –> void

set_extra_minimize_res(self: pyrosetta.rosetta.core.import_pose.FullModelPoseBuilder, extra_minimize_res: pyrosetta.rosetta.utility.vector1_unsigned_long) → None¶: C++: core::import_pose::FullModelPoseBuilder::set_extra_minimize_res(const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &) –> void

set_fasta_file(self: pyrosetta.rosetta.core.import_pose.FullModelPoseBuilder, fasta_file: str) → None¶: C++: core::import_pose::FullModelPoseBuilder::set_fasta_file(const std::string &) –> void

set_fiveprime_res(self: pyrosetta.rosetta.core.import_pose.FullModelPoseBuilder, fiveprime_res: pyrosetta.rosetta.utility.vector1_unsigned_long) → None¶: C++: core::import_pose::FullModelPoseBuilder::set_fiveprime_res(const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &) –> void

set_full_model_parameters(self: pyrosetta.rosetta.core.import_pose.FullModelPoseBuilder, full_model_parameters: core::pose::full_model_info::FullModelParameters) → None¶: C++: core::import_pose::FullModelPoseBuilder::set_full_model_parameters(const class std::shared_ptr<class core::pose::full_model_info::FullModelParameters> &) –> void

set_global_seq_file(self: pyrosetta.rosetta.core.import_pose.FullModelPoseBuilder, global_seq_file: str) → None¶: C++: core::import_pose::FullModelPoseBuilder::set_global_seq_file(const std::string &) –> void

set_input_poses(self: pyrosetta.rosetta.core.import_pose.FullModelPoseBuilder, input_poses: pyrosetta.rosetta.utility.vector1_std_shared_ptr_core_pose_Pose_t) → None¶: C++: core::import_pose::FullModelPoseBuilder::set_input_poses(class utility::vector1<class std::shared_ptr<class core::pose::Pose>, class std::allocator<class std::shared_ptr<class core::pose::Pose> > >) –> void

set_input_resnum_and_chain_and_segid(self: pyrosetta.rosetta.core.import_pose.FullModelPoseBuilder, input_resnum_and_chain_and_segid: Tuple[pyrosetta.rosetta.utility.vector1_unsigned_long, pyrosetta.rosetta.utility.vector1_char, pyrosetta.rosetta.utility.vector1_std_string]) → None¶: C++: core::import_pose::FullModelPoseBuilder::set_input_resnum_and_chain_and_segid(const class std::tuple<class utility::vector1<unsigned long, class std::allocator<unsigned long> >, class utility::vector1<char, class std::allocator<char> >, class utility::vector1<std::string, class std::allocator<std::string > > > &) –> void

set_jump_res(self: pyrosetta.rosetta.core.import_pose.FullModelPoseBuilder, jump_res: pyrosetta.rosetta.utility.vector1_unsigned_long) → None¶: C++: core::import_pose::FullModelPoseBuilder::set_jump_res(const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &) –> void

set_options(self: pyrosetta.rosetta.core.import_pose.FullModelPoseBuilder, options: pyrosetta.rosetta.utility.options.OptionCollection) → None¶: C++: core::import_pose::FullModelPoseBuilder::set_options(const class utility::options::OptionCollection &) –> void

set_preferred_root_res(self: pyrosetta.rosetta.core.import_pose.FullModelPoseBuilder, preferred_root_res: pyrosetta.rosetta.utility.vector1_unsigned_long) → None¶: C++: core::import_pose::FullModelPoseBuilder::set_preferred_root_res(const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &) –> void

set_rna_anti_chi(self: pyrosetta.rosetta.core.import_pose.FullModelPoseBuilder, rna_anti_chi: pyrosetta.rosetta.utility.vector1_unsigned_long) → None¶: C++: core::import_pose::FullModelPoseBuilder::set_rna_anti_chi(const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &) –> void

set_rna_north_sugar(self: pyrosetta.rosetta.core.import_pose.FullModelPoseBuilder, rna_north_sugar: pyrosetta.rosetta.utility.vector1_unsigned_long) → None¶: C++: core::import_pose::FullModelPoseBuilder::set_rna_north_sugar(const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &) –> void

set_rna_sample_sugar(self: pyrosetta.rosetta.core.import_pose.FullModelPoseBuilder, rna_sample_sugar: pyrosetta.rosetta.utility.vector1_unsigned_long) → None¶: C++: core::import_pose::FullModelPoseBuilder::set_rna_sample_sugar(const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &) –> void

set_rna_south_sugar(self: pyrosetta.rosetta.core.import_pose.FullModelPoseBuilder, rna_south_sugar: pyrosetta.rosetta.utility.vector1_unsigned_long) → None¶: C++: core::import_pose::FullModelPoseBuilder::set_rna_south_sugar(const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &) –> void

set_rna_syn_chi(self: pyrosetta.rosetta.core.import_pose.FullModelPoseBuilder, rna_syn_chi: pyrosetta.rosetta.utility.vector1_unsigned_long) → None¶: C++: core::import_pose::FullModelPoseBuilder::set_rna_syn_chi(const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &) –> void

set_sample_res(self: pyrosetta.rosetta.core.import_pose.FullModelPoseBuilder, sample_res: pyrosetta.rosetta.utility.vector1_unsigned_long) → None¶: C++: core::import_pose::FullModelPoseBuilder::set_sample_res(const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &) –> void

set_terminal_res(self: pyrosetta.rosetta.core.import_pose.FullModelPoseBuilder, terminal_res: pyrosetta.rosetta.utility.vector1_unsigned_long) → None¶: C++: core::import_pose::FullModelPoseBuilder::set_terminal_res(const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &) –> void

set_twoprime_res(self: pyrosetta.rosetta.core.import_pose.FullModelPoseBuilder, twoprime_res: pyrosetta.rosetta.utility.vector1_unsigned_long) → None¶: C++: core::import_pose::FullModelPoseBuilder::set_twoprime_res(const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &) –> void

set_virtual_sugar_res(self: pyrosetta.rosetta.core.import_pose.FullModelPoseBuilder, virtual_sugar_res: pyrosetta.rosetta.utility.vector1_unsigned_long) → None¶: C++: core::import_pose::FullModelPoseBuilder::set_virtual_sugar_res(const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &) –> void

set_working_res(self: pyrosetta.rosetta.core.import_pose.FullModelPoseBuilder, working_res: pyrosetta.rosetta.utility.vector1_unsigned_long) → None¶: C++: core::import_pose::FullModelPoseBuilder::set_working_res(const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &) –> void

class pyrosetta.rosetta.core.import_pose.ImportPoseOptions¶

Bases: StructFileReaderOptions

This class contains all of the data which is used in the process of reading a PDB into a Pose. There is actually a substantial amount of data!

static append_schema_attributes(attrs: pyrosetta.rosetta.std.list_utility_tag_XMLSchemaAttribute_t) → None¶: C++: core::import_pose::ImportPoseOptions::append_schema_attributes(class std::list<class utility::tag::XMLSchemaAttribute, class std::allocator<class utility::tag::XMLSchemaAttribute> > &) –> void

assign(self: pyrosetta.rosetta.core.import_pose.ImportPoseOptions, : pyrosetta.rosetta.core.import_pose.ImportPoseOptions) → pyrosetta.rosetta.core.import_pose.ImportPoseOptions¶: C++: core::import_pose::ImportPoseOptions::operator=(const class core::import_pose::ImportPoseOptions &) –> class core::import_pose::ImportPoseOptions &

auto_detect_glycan_connections(self: pyrosetta.rosetta.core.io.StructFileRepOptions) → bool¶: C++: core::io::StructFileRepOptions::auto_detect_glycan_connections() const –> bool

centroid(self: pyrosetta.rosetta.core.import_pose.ImportPoseOptions) → bool¶: C++: core::import_pose::ImportPoseOptions::centroid() const –> bool

chains_whose_residues_are_separate_chemical_entities(self: pyrosetta.rosetta.core.io.StructFileRepOptions) → str¶: C++: core::io::StructFileRepOptions::chains_whose_residues_are_separate_chemical_entities() const –> const std::string &

check_if_residues_are_Ctermini(self: pyrosetta.rosetta.core.io.StructFileRepOptions) → str¶: C++: core::io::StructFileRepOptions::check_if_residues_are_Ctermini() const –> const std::string &

check_if_residues_are_Ntermini(self: pyrosetta.rosetta.core.io.StructFileRepOptions) → str¶: C++: core::io::StructFileRepOptions::check_if_residues_are_Ntermini() const –> const std::string &

clone(self: pyrosetta.rosetta.core.io.StructFileRepOptions) → pyrosetta.rosetta.core.io.StructFileRepOptions¶

Copy this object and return an owning pointer to the copy.

C++: core::io::StructFileRepOptions::clone() const –> class std::shared_ptr<class core::io::StructFileRepOptions>

connect_info_cutoff(self: pyrosetta.rosetta.core.io.StructFileRepOptions) → float¶: C++: core::io::StructFileRepOptions::connect_info_cutoff() const –> double

constraints_from_link_records(self: pyrosetta.rosetta.core.io.StructFileRepOptions) → bool¶: C++: core::io::StructFileRepOptions::constraints_from_link_records() const –> bool

do_not_autoassign_SS(self: pyrosetta.rosetta.core.io.StructFileRepOptions) → bool¶: C++: core::io::StructFileRepOptions::do_not_autoassign_SS() const –> bool

exit_if_missing_heavy_atoms(self: pyrosetta.rosetta.core.io.StructFileRepOptions) → bool¶: C++: core::io::StructFileRepOptions::exit_if_missing_heavy_atoms() const –> bool

fast_restyping(self: pyrosetta.rosetta.core.io.StructFileRepOptions) → bool¶: C++: core::io::StructFileRepOptions::fast_restyping() const –> bool

fold_tree_io(self: pyrosetta.rosetta.core.import_pose.ImportPoseOptions) → bool¶: C++: core::import_pose::ImportPoseOptions::fold_tree_io() const –> bool

glycam_pdb_format(self: pyrosetta.rosetta.core.io.StructFileReaderOptions) → bool¶: C++: core::io::StructFileReaderOptions::glycam_pdb_format() const –> bool

guarantee_no_DNA(self: pyrosetta.rosetta.core.io.StructFileRepOptions) → bool¶: C++: core::io::StructFileRepOptions::guarantee_no_DNA() const –> bool

ignore_sugars(self: pyrosetta.rosetta.core.io.StructFileRepOptions) → bool¶: C++: core::io::StructFileRepOptions::ignore_sugars() const –> bool

ignore_unrecognized_res(self: pyrosetta.rosetta.core.io.StructFileRepOptions) → bool¶: C++: core::io::StructFileRepOptions::ignore_unrecognized_res() const –> bool

ignore_waters(self: pyrosetta.rosetta.core.io.StructFileRepOptions) → bool¶: C++: core::io::StructFileRepOptions::ignore_waters() const –> bool

ignore_zero_occupancy(self: pyrosetta.rosetta.core.io.StructFileRepOptions) → bool¶: C++: core::io::StructFileRepOptions::ignore_zero_occupancy() const –> bool

integration_test_mode(self: pyrosetta.rosetta.core.io.StructFileRepOptions) → bool¶: C++: core::io::StructFileRepOptions::integration_test_mode() const –> bool

keep_input_protonation_state(self: pyrosetta.rosetta.core.io.StructFileRepOptions) → bool¶: C++: core::io::StructFileRepOptions::keep_input_protonation_state() const –> bool

static list_options_read(read_options: pyrosetta.rosetta.std.list_utility_keys_VariantKey_utility_options_OptionKey_t) → None¶: C++: core::import_pose::ImportPoseOptions::list_options_read(class std::list<class utility::keys::VariantKey<class utility::options::OptionKey>, class std::allocator<class utility::keys::VariantKey<class utility::options::OptionKey> > > &) –> void

maintain_links(self: pyrosetta.rosetta.core.io.StructFileRepOptions) → bool¶: C++: core::io::StructFileRepOptions::maintain_links() const –> bool

max_bond_length(self: pyrosetta.rosetta.core.io.StructFileRepOptions) → float¶: C++: core::io::StructFileRepOptions::max_bond_length() const –> double

membrane(self: pyrosetta.rosetta.core.import_pose.ImportPoseOptions) → bool¶: C++: core::import_pose::ImportPoseOptions::membrane() const –> bool

metal_bond_LJ_multiplier(self: pyrosetta.rosetta.core.import_pose.ImportPoseOptions) → float¶: C++: core::import_pose::ImportPoseOptions::metal_bond_LJ_multiplier() const –> double

metal_bond_angle_constraint_multiplier(self: pyrosetta.rosetta.core.import_pose.ImportPoseOptions) → float¶: C++: core::import_pose::ImportPoseOptions::metal_bond_angle_constraint_multiplier() const –> double

metal_bond_dist_constraint_multiplier(self: pyrosetta.rosetta.core.import_pose.ImportPoseOptions) → float¶: C++: core::import_pose::ImportPoseOptions::metal_bond_dist_constraint_multiplier() const –> double

min_bond_length(self: pyrosetta.rosetta.core.io.StructFileRepOptions) → float¶: C++: core::io::StructFileRepOptions::min_bond_length() const –> double

missing_dens_as_jump(self: pyrosetta.rosetta.core.io.StructFileRepOptions) → bool¶: C++: core::io::StructFileRepOptions::missing_dens_as_jump() const –> bool

mmtf_extra_data_io(self: pyrosetta.rosetta.core.io.StructFileReaderOptions) → bool¶: C++: core::io::StructFileReaderOptions::mmtf_extra_data_io() const –> bool

new_chain_order(self: pyrosetta.rosetta.core.io.StructFileReaderOptions) → bool¶: C++: core::io::StructFileReaderOptions::new_chain_order() const –> bool

no_chainend_ter(self: pyrosetta.rosetta.core.io.StructFileRepOptions) → bool¶: C++: core::io::StructFileRepOptions::no_chainend_ter() const –> bool

no_detect_pseudobonds(self: pyrosetta.rosetta.core.io.StructFileRepOptions) → bool¶: C++: core::io::StructFileRepOptions::no_detect_pseudobonds() const –> bool

no_optH(self: pyrosetta.rosetta.core.import_pose.ImportPoseOptions) → bool¶: C++: core::import_pose::ImportPoseOptions::no_optH() const –> bool

no_output_cen(self: pyrosetta.rosetta.core.io.StructFileRepOptions) → bool¶: C++: core::io::StructFileRepOptions::no_output_cen() const –> bool

normalize_to_thk(self: pyrosetta.rosetta.core.io.StructFileRepOptions) → bool¶: C++: core::io::StructFileRepOptions::normalize_to_thk() const –> bool

obey_ENDMDL(self: pyrosetta.rosetta.core.io.StructFileReaderOptions) → bool¶: C++: core::io::StructFileReaderOptions::obey_ENDMDL() const –> bool

output_alternate_atomids(self: pyrosetta.rosetta.core.io.StructFileRepOptions) → bool¶: C++: core::io::StructFileRepOptions::output_alternate_atomids() const –> bool

output_ligands_as_separate_chains(self: pyrosetta.rosetta.core.io.StructFileRepOptions) → bool¶: C++: core::io::StructFileRepOptions::output_ligands_as_separate_chains() const –> bool

output_only_asymmetric_unit(self: pyrosetta.rosetta.core.io.StructFileRepOptions) → bool¶: C++: core::io::StructFileRepOptions::output_only_asymmetric_unit() const –> bool

output_pose_cache(self: pyrosetta.rosetta.core.io.StructFileRepOptions) → bool¶: C++: core::io::StructFileRepOptions::output_pose_cache() const –> bool

output_pose_energies_table(self: pyrosetta.rosetta.core.io.StructFileRepOptions) → bool¶: C++: core::io::StructFileRepOptions::output_pose_energies_table() const –> bool

output_secondary_structure(self: pyrosetta.rosetta.core.io.StructFileRepOptions) → bool¶: C++: core::io::StructFileRepOptions::output_secondary_structure() const –> bool

output_torsions(self: pyrosetta.rosetta.core.io.StructFileRepOptions) → bool¶: C++: core::io::StructFileRepOptions::output_torsions() const –> bool

output_virtual(self: pyrosetta.rosetta.core.io.StructFileRepOptions) → bool¶: C++: core::io::StructFileRepOptions::output_virtual() const –> bool

output_virtual_zero_occ(self: pyrosetta.rosetta.core.io.StructFileRepOptions) → bool¶: C++: core::io::StructFileRepOptions::output_virtual_zero_occ() const –> bool

pack_missing_sidechains(self: pyrosetta.rosetta.core.import_pose.ImportPoseOptions) → bool¶: C++: core::import_pose::ImportPoseOptions::pack_missing_sidechains() const –> bool

parse_my_tag(self: pyrosetta.rosetta.core.import_pose.ImportPoseOptions, tag: utility::tag::Tag) → None¶: C++: core::import_pose::ImportPoseOptions::parse_my_tag(class std::shared_ptr<const class utility::tag::Tag>) –> void

pdb_author(self: pyrosetta.rosetta.core.io.StructFileRepOptions) → str¶: C++: core::io::StructFileRepOptions::pdb_author() const –> const std::string &

pdb_comments(self: pyrosetta.rosetta.core.io.StructFileRepOptions) → bool¶: C++: core::io::StructFileRepOptions::pdb_comments() const –> bool

pdb_parents(self: pyrosetta.rosetta.core.io.StructFileRepOptions) → bool¶: C++: core::io::StructFileRepOptions::pdb_parents() const –> bool

per_chain_renumbering(self: pyrosetta.rosetta.core.io.StructFileRepOptions) → bool¶: C++: core::io::StructFileRepOptions::per_chain_renumbering() const –> bool

preserve_crystinfo(self: pyrosetta.rosetta.core.io.StructFileRepOptions) → bool¶: C++: core::io::StructFileRepOptions::preserve_crystinfo() const –> bool

preserve_header(self: pyrosetta.rosetta.core.io.StructFileRepOptions) → bool¶: C++: core::io::StructFileRepOptions::preserve_header() const –> bool

randomize_missing_coords(self: pyrosetta.rosetta.core.io.StructFileRepOptions) → bool¶: C++: core::io::StructFileRepOptions::randomize_missing_coords() const –> bool

read_fold_tree(self: pyrosetta.rosetta.core.import_pose.ImportPoseOptions) → bool¶: C++: core::import_pose::ImportPoseOptions::read_fold_tree() const –> bool

read_only_ATOM_entries(self: pyrosetta.rosetta.core.io.StructFileRepOptions) → bool¶: C++: core::io::StructFileRepOptions::read_only_ATOM_entries() const –> bool

read_pdb_header(self: pyrosetta.rosetta.core.io.StructFileReaderOptions) → bool¶: C++: core::io::StructFileReaderOptions::read_pdb_header() const –> bool

remember_unrecognized_res(self: pyrosetta.rosetta.core.io.StructFileRepOptions) → bool¶: C++: core::io::StructFileRepOptions::remember_unrecognized_res() const –> bool

remember_unrecognized_water(self: pyrosetta.rosetta.core.io.StructFileRepOptions) → bool¶: C++: core::io::StructFileRepOptions::remember_unrecognized_water() const –> bool

renumber_pdb(self: pyrosetta.rosetta.core.io.StructFileRepOptions) → bool¶: C++: core::io::StructFileRepOptions::renumber_pdb() const –> bool

residue_type_set_mode(self: pyrosetta.rosetta.core.import_pose.ImportPoseOptions) → pyrosetta.rosetta.core.chemical.TypeSetMode¶: C++: core::import_pose::ImportPoseOptions::residue_type_set_mode() const –> enum core::chemical::TypeSetMode

residues_for_atom_name_remapping(self: pyrosetta.rosetta.core.io.StructFileRepOptions) → pyrosetta.rosetta.utility.vector1_std_string¶: C++: core::io::StructFileRepOptions::residues_for_atom_name_remapping() const –> const class utility::vector1<std::string, class std::allocator<std::string > > &

set_auto_detect_glycan_connections(self: pyrosetta.rosetta.core.io.StructFileRepOptions, auto_detect_glycan_connections: bool) → None¶: C++: core::io::StructFileRepOptions::set_auto_detect_glycan_connections(const bool) –> void

set_centroid(self: pyrosetta.rosetta.core.import_pose.ImportPoseOptions, centroid: bool) → None¶: C++: core::import_pose::ImportPoseOptions::set_centroid(bool) –> void

set_chains_whose_residues_are_separate_chemical_entities(self: pyrosetta.rosetta.core.io.StructFileRepOptions, setting: str) → None¶: C++: core::io::StructFileRepOptions::set_chains_whose_residues_are_separate_chemical_entities(const std::string &) –> void

set_check_if_residues_are_Ctermini(self: pyrosetta.rosetta.core.io.StructFileRepOptions, check_if_residues_are_Ctermini: str) → None¶: C++: core::io::StructFileRepOptions::set_check_if_residues_are_Ctermini(const std::string &) –> void

set_check_if_residues_are_Ntermini(self: pyrosetta.rosetta.core.io.StructFileRepOptions, check_if_residues_are_Ntermini: str) → None¶: C++: core::io::StructFileRepOptions::set_check_if_residues_are_Ntermini(const std::string &) –> void

set_connect_info_cutoff(self: pyrosetta.rosetta.core.io.StructFileRepOptions, connect_info_cutoff: float) → None¶: C++: core::io::StructFileRepOptions::set_connect_info_cutoff(const double &) –> void

set_constraints_from_link_records(self: pyrosetta.rosetta.core.io.StructFileRepOptions, setting: bool) → None¶: C++: core::io::StructFileRepOptions::set_constraints_from_link_records(const bool) –> void

set_do_not_autoassign_SS(self: pyrosetta.rosetta.core.io.StructFileRepOptions, do_not_autoassign_SS: bool) → None¶: C++: core::io::StructFileRepOptions::set_do_not_autoassign_SS(const bool) –> void

set_exit_if_missing_heavy_atoms(self: pyrosetta.rosetta.core.io.StructFileRepOptions, exit_if_missing_heavy_atoms: bool) → None¶: C++: core::io::StructFileRepOptions::set_exit_if_missing_heavy_atoms(const bool) –> void

set_fast_restyping(self: pyrosetta.rosetta.core.io.StructFileRepOptions, fast_restyping: bool) → None¶: C++: core::io::StructFileRepOptions::set_fast_restyping(const bool) –> void

set_fold_tree_io(self: pyrosetta.rosetta.core.import_pose.ImportPoseOptions, fold_tree_io: bool) → None¶: C++: core::import_pose::ImportPoseOptions::set_fold_tree_io(bool) –> void

set_glycam_pdb_format(self: pyrosetta.rosetta.core.io.StructFileReaderOptions, setting: bool) → None¶: C++: core::io::StructFileReaderOptions::set_glycam_pdb_format(bool) –> void

set_guarantee_no_DNA(self: pyrosetta.rosetta.core.io.StructFileRepOptions, guarantee_no_DNA: bool) → None¶: C++: core::io::StructFileRepOptions::set_guarantee_no_DNA(const bool) –> void

set_ignore_sugars(self: pyrosetta.rosetta.core.io.StructFileRepOptions, setting: bool) → None¶: C++: core::io::StructFileRepOptions::set_ignore_sugars(const bool) –> void

set_ignore_unrecognized_res(self: pyrosetta.rosetta.core.io.StructFileRepOptions, ignore_unrecognized_res: bool) → None¶: C++: core::io::StructFileRepOptions::set_ignore_unrecognized_res(const bool) –> void

set_ignore_waters(self: pyrosetta.rosetta.core.io.StructFileRepOptions, ignore_waters: bool) → None¶: C++: core::io::StructFileRepOptions::set_ignore_waters(const bool) –> void

set_ignore_zero_occupancy(self: pyrosetta.rosetta.core.io.StructFileRepOptions, ignore_zero_occupancy: bool) → None¶: C++: core::io::StructFileRepOptions::set_ignore_zero_occupancy(const bool) –> void

set_integration_test_mode(self: pyrosetta.rosetta.core.io.StructFileRepOptions, setting: bool) → None¶: C++: core::io::StructFileRepOptions::set_integration_test_mode(const bool) –> void

set_keep_input_protonation_state(self: pyrosetta.rosetta.core.io.StructFileRepOptions, keep_input_protonation_state: bool) → None¶: C++: core::io::StructFileRepOptions::set_keep_input_protonation_state(const bool) –> void

set_maintain_links(self: pyrosetta.rosetta.core.io.StructFileRepOptions, maintain_links: bool) → None¶: C++: core::io::StructFileRepOptions::set_maintain_links(const bool) –> void

set_max_bond_length(self: pyrosetta.rosetta.core.io.StructFileRepOptions, max_bond_length: float) → None¶: C++: core::io::StructFileRepOptions::set_max_bond_length(const double) –> void

set_membrane(self: pyrosetta.rosetta.core.import_pose.ImportPoseOptions, membrane: bool) → None¶: C++: core::import_pose::ImportPoseOptions::set_membrane(bool) –> void

set_metal_bond_LJ_multiplier(self: pyrosetta.rosetta.core.import_pose.ImportPoseOptions, invalue: float) → None¶: C++: core::import_pose::ImportPoseOptions::set_metal_bond_LJ_multiplier(double) –> void

set_metal_bond_angle_constraint_multiplier(self: pyrosetta.rosetta.core.import_pose.ImportPoseOptions, invalue: float) → None¶: C++: core::import_pose::ImportPoseOptions::set_metal_bond_angle_constraint_multiplier(double) –> void

set_metal_bond_dist_constraint_multiplier(self: pyrosetta.rosetta.core.import_pose.ImportPoseOptions, invalue: float) → None¶: C++: core::import_pose::ImportPoseOptions::set_metal_bond_dist_constraint_multiplier(double) –> void

set_min_bond_length(self: pyrosetta.rosetta.core.io.StructFileRepOptions, min_bond_length: float) → None¶: C++: core::io::StructFileRepOptions::set_min_bond_length(const double) –> void

set_missing_dens_as_jump(self: pyrosetta.rosetta.core.io.StructFileRepOptions, missing_dens_as_jump: bool) → None¶: C++: core::io::StructFileRepOptions::set_missing_dens_as_jump(const bool) –> void

set_mmtf_extra_data_io(self: pyrosetta.rosetta.core.io.StructFileReaderOptions, setting: bool) → None¶: C++: core::io::StructFileReaderOptions::set_mmtf_extra_data_io(bool) –> void

set_new_chain_order(self: pyrosetta.rosetta.core.io.StructFileReaderOptions, setting: bool) → None¶: C++: core::io::StructFileReaderOptions::set_new_chain_order(bool) –> void

set_no_chainend_ter(self: pyrosetta.rosetta.core.io.StructFileRepOptions, no_chainend_ter: bool) → None¶: C++: core::io::StructFileRepOptions::set_no_chainend_ter(const bool) –> void

set_no_detect_pseudobonds(self: pyrosetta.rosetta.core.io.StructFileRepOptions, setting: bool) → None¶: C++: core::io::StructFileRepOptions::set_no_detect_pseudobonds(const bool) –> void

set_no_optH(self: pyrosetta.rosetta.core.import_pose.ImportPoseOptions, no_optH: bool) → None¶: C++: core::import_pose::ImportPoseOptions::set_no_optH(bool) –> void

set_no_output_cen(self: pyrosetta.rosetta.core.io.StructFileRepOptions, no_output_cen: bool) → None¶: C++: core::io::StructFileRepOptions::set_no_output_cen(const bool) –> void

set_normalize_to_thk(self: pyrosetta.rosetta.core.io.StructFileRepOptions, normalize_to_thk: bool) → None¶: C++: core::io::StructFileRepOptions::set_normalize_to_thk(const bool) –> void

set_obey_ENDMDL(self: pyrosetta.rosetta.core.io.StructFileReaderOptions, setting: bool) → None¶: C++: core::io::StructFileReaderOptions::set_obey_ENDMDL(bool) –> void

set_output_alternate_atomids(self: pyrosetta.rosetta.core.io.StructFileRepOptions, output_alternate_atomids: bool) → None¶: C++: core::io::StructFileRepOptions::set_output_alternate_atomids(const bool) –> void

set_output_ligands_as_separate_chains(self: pyrosetta.rosetta.core.io.StructFileRepOptions, output_ligands_as_separate_chains: bool) → None¶: C++: core::io::StructFileRepOptions::set_output_ligands_as_separate_chains(const bool) –> void

set_output_only_asymmetric_unit(self: pyrosetta.rosetta.core.io.StructFileRepOptions, output_only_asymmetric_unit: bool) → None¶: C++: core::io::StructFileRepOptions::set_output_only_asymmetric_unit(const bool) –> void

set_output_pose_cache_data(self: pyrosetta.rosetta.core.io.StructFileRepOptions, setting: bool) → None¶: C++: core::io::StructFileRepOptions::set_output_pose_cache_data(const bool) –> void

set_output_pose_energies_table(self: pyrosetta.rosetta.core.io.StructFileRepOptions, setting: bool) → None¶: C++: core::io::StructFileRepOptions::set_output_pose_energies_table(const bool) –> void

set_output_secondary_structure(self: pyrosetta.rosetta.core.io.StructFileRepOptions, output_secondary_structure: bool) → None¶: C++: core::io::StructFileRepOptions::set_output_secondary_structure(const bool) –> void

set_output_torsions(self: pyrosetta.rosetta.core.io.StructFileRepOptions, output_torsions: bool) → None¶: C++: core::io::StructFileRepOptions::set_output_torsions(const bool) –> void

set_output_virtual(self: pyrosetta.rosetta.core.io.StructFileRepOptions, output_virtual: bool) → None¶: C++: core::io::StructFileRepOptions::set_output_virtual(const bool) –> void

set_output_virtual_zero_occ(self: pyrosetta.rosetta.core.io.StructFileRepOptions, output_virtual_zero_occ: bool) → None¶: C++: core::io::StructFileRepOptions::set_output_virtual_zero_occ(const bool) –> void

set_pack_missing_sidechains(self: pyrosetta.rosetta.core.import_pose.ImportPoseOptions, pack_missing_sidechains: bool) → None¶: C++: core::import_pose::ImportPoseOptions::set_pack_missing_sidechains(bool) –> void

set_pdb_author(self: pyrosetta.rosetta.core.io.StructFileRepOptions, pdb_author: str) → None¶: C++: core::io::StructFileRepOptions::set_pdb_author(const std::string &) –> void

set_pdb_comments(self: pyrosetta.rosetta.core.io.StructFileRepOptions, pdb_comments: bool) → None¶: C++: core::io::StructFileRepOptions::set_pdb_comments(const bool) –> void

set_pdb_parents(self: pyrosetta.rosetta.core.io.StructFileRepOptions, pdb_parents: bool) → None¶: C++: core::io::StructFileRepOptions::set_pdb_parents(const bool) –> void

set_per_chain_renumbering(self: pyrosetta.rosetta.core.io.StructFileRepOptions, per_chain_renumbering: bool) → None¶: C++: core::io::StructFileRepOptions::set_per_chain_renumbering(const bool) –> void

set_preserve_crystinfo(self: pyrosetta.rosetta.core.io.StructFileRepOptions, preserve_crystinfo: bool) → None¶: C++: core::io::StructFileRepOptions::set_preserve_crystinfo(const bool) –> void

set_preserve_header(self: pyrosetta.rosetta.core.io.StructFileRepOptions, preserve_header: bool) → None¶: C++: core::io::StructFileRepOptions::set_preserve_header(const bool) –> void

set_randomize_missing_coords(self: pyrosetta.rosetta.core.io.StructFileRepOptions, randomize_missing_coords: bool) → None¶: C++: core::io::StructFileRepOptions::set_randomize_missing_coords(const bool) –> void

set_read_fold_tree(self: pyrosetta.rosetta.core.import_pose.ImportPoseOptions, read_fold_tree: bool) → None¶: C++: core::import_pose::ImportPoseOptions::set_read_fold_tree(bool) –> void

set_read_only_ATOM_entries(self: pyrosetta.rosetta.core.io.StructFileRepOptions, setting: bool) → None¶: C++: core::io::StructFileRepOptions::set_read_only_ATOM_entries(const bool) –> void

set_read_pdb_header(self: pyrosetta.rosetta.core.io.StructFileReaderOptions, setting: bool) → None¶: C++: core::io::StructFileReaderOptions::set_read_pdb_header(bool) –> void

set_remember_unrecognized_res(self: pyrosetta.rosetta.core.io.StructFileRepOptions, remember_unrecognized_res: bool) → None¶: C++: core::io::StructFileRepOptions::set_remember_unrecognized_res(const bool) –> void

set_remember_unrecognized_water(self: pyrosetta.rosetta.core.io.StructFileRepOptions, remember_unrecognized_water: bool) → None¶: C++: core::io::StructFileRepOptions::set_remember_unrecognized_water(const bool) –> void

set_renumber_pdb(self: pyrosetta.rosetta.core.io.StructFileRepOptions, setting: bool) → None¶: C++: core::io::StructFileRepOptions::set_renumber_pdb(const bool) –> void

set_residue_type_set_mode(self: pyrosetta.rosetta.core.import_pose.ImportPoseOptions, residue_type_set_mode: pyrosetta.rosetta.core.chemical.TypeSetMode) → None¶: C++: core::import_pose::ImportPoseOptions::set_residue_type_set_mode(enum core::chemical::TypeSetMode) –> void

set_residues_for_atom_name_remapping(self: pyrosetta.rosetta.core.io.StructFileRepOptions, setting: pyrosetta.rosetta.utility.vector1_std_string) → None¶: C++: core::io::StructFileRepOptions::set_residues_for_atom_name_remapping(const class utility::vector1<std::string, class std::allocator<std::string > > &) –> void

set_set_up_metal_bonds(self: pyrosetta.rosetta.core.import_pose.ImportPoseOptions, invalue: bool) → None¶: C++: core::import_pose::ImportPoseOptions::set_set_up_metal_bonds(bool) –> void

set_show_all_fixes(self: pyrosetta.rosetta.core.io.StructFileRepOptions, setting: bool) → None¶: C++: core::io::StructFileRepOptions::set_show_all_fixes(const bool) –> void

set_skip_connect_info(self: pyrosetta.rosetta.core.io.StructFileRepOptions, skip_connect_info: bool) → None¶: C++: core::io::StructFileRepOptions::set_skip_connect_info(const bool) –> void

set_skip_set_reasonable_fold_tree(self: pyrosetta.rosetta.core.import_pose.ImportPoseOptions, skip_set_reasonable_fold_tree: bool) → None¶: C++: core::import_pose::ImportPoseOptions::set_skip_set_reasonable_fold_tree(bool) –> void

set_suppress_zero_occ_pdb_output(self: pyrosetta.rosetta.core.io.StructFileRepOptions, setting: bool) → None¶: C++: core::io::StructFileRepOptions::set_suppress_zero_occ_pdb_output(const bool) –> void

set_up_metal_bonds(self: pyrosetta.rosetta.core.import_pose.ImportPoseOptions) → bool¶: C++: core::import_pose::ImportPoseOptions::set_up_metal_bonds() const –> bool

set_up_metal_constraints(self: pyrosetta.rosetta.core.import_pose.ImportPoseOptions) → bool¶: C++: core::import_pose::ImportPoseOptions::set_up_metal_constraints() const –> bool

set_use_pdb_format_HETNAM_records(self: pyrosetta.rosetta.core.io.StructFileRepOptions, setting: bool) → None¶: C++: core::io::StructFileRepOptions::set_use_pdb_format_HETNAM_records(const bool) –> void

set_write_all_connect_info(self: pyrosetta.rosetta.core.io.StructFileRepOptions, setting: bool) → None¶: C++: core::io::StructFileRepOptions::set_write_all_connect_info(const bool) –> void

set_write_glycan_pdb_codes(self: pyrosetta.rosetta.core.io.StructFileRepOptions, write_glycan_pdb_codes: bool) → None¶: C++: core::io::StructFileRepOptions::set_write_glycan_pdb_codes(const bool) –> void

set_write_pdb_link_records(self: pyrosetta.rosetta.core.io.StructFileRepOptions, setting: bool) → None¶: C++: core::io::StructFileRepOptions::set_write_pdb_link_records(const bool) –> void

set_write_pdb_parametric_info(self: pyrosetta.rosetta.core.io.StructFileRepOptions, setting: bool) → None¶: C++: core::io::StructFileRepOptions::set_write_pdb_parametric_info(const bool) –> void

set_write_pdb_title_section_records(self: pyrosetta.rosetta.core.io.StructFileRepOptions, setting: bool) → None¶: C++: core::io::StructFileRepOptions::set_write_pdb_title_section_records(const bool) –> void

set_write_seqres_records(self: pyrosetta.rosetta.core.io.StructFileRepOptions, setting: bool) → None¶: C++: core::io::StructFileRepOptions::set_write_seqres_records(const bool) –> void

show_all_fixes(self: pyrosetta.rosetta.core.io.StructFileRepOptions) → bool¶: C++: core::io::StructFileRepOptions::show_all_fixes() const –> bool

skip_connect_info(self: pyrosetta.rosetta.core.io.StructFileRepOptions) → bool¶: C++: core::io::StructFileRepOptions::skip_connect_info() const –> bool

skip_set_reasonable_fold_tree(self: pyrosetta.rosetta.core.import_pose.ImportPoseOptions) → bool¶: C++: core::import_pose::ImportPoseOptions::skip_set_reasonable_fold_tree() const –> bool

suppress_zero_occ_pdb_output(self: pyrosetta.rosetta.core.io.StructFileRepOptions) → bool¶: C++: core::io::StructFileRepOptions::suppress_zero_occ_pdb_output() const –> bool

type(self: pyrosetta.rosetta.core.import_pose.ImportPoseOptions) → str¶: C++: core::import_pose::ImportPoseOptions::type() const –> std::string

use_pdb_format_HETNAM_records(self: pyrosetta.rosetta.core.io.StructFileRepOptions) → bool¶: C++: core::io::StructFileRepOptions::use_pdb_format_HETNAM_records() const –> bool

write_all_connect_info(self: pyrosetta.rosetta.core.io.StructFileRepOptions) → bool¶: C++: core::io::StructFileRepOptions::write_all_connect_info() const –> bool

write_glycan_pdb_codes(self: pyrosetta.rosetta.core.io.StructFileRepOptions) → bool¶: C++: core::io::StructFileRepOptions::write_glycan_pdb_codes() const –> bool

write_pdb_link_records(self: pyrosetta.rosetta.core.io.StructFileRepOptions) → bool¶: C++: core::io::StructFileRepOptions::write_pdb_link_records() const –> bool

write_pdb_parametric_info(self: pyrosetta.rosetta.core.io.StructFileRepOptions) → bool¶: C++: core::io::StructFileRepOptions::write_pdb_parametric_info() const –> bool

write_pdb_title_section_records(self: pyrosetta.rosetta.core.io.StructFileRepOptions) → bool¶: C++: core::io::StructFileRepOptions::write_pdb_title_section_records() const –> bool

write_seqres_records(self: pyrosetta.rosetta.core.io.StructFileRepOptions) → bool¶: C++: core::io::StructFileRepOptions::write_seqres_records() const –> bool

class pyrosetta.rosetta.core.import_pose.PDBSilentStruct¶

Bases: SilentStruct

add_comment(self: pyrosetta.rosetta.core.io.silent.SilentStruct, name: str, value: str) → None¶

add a named comment to this SilentStruct object.: Similar to methods for playing with energies, but mapping is string => string rather than string => Real.

C++: core::io::silent::SilentStruct::add_comment(std::string, std::string) –> void

add_energy(*args, **kwargs)¶

Overloaded function.

add_energy(self: pyrosetta.rosetta.core.io.silent.SilentStruct, scorename: str, value: float) -> None
add_energy(self: pyrosetta.rosetta.core.io.silent.SilentStruct, scorename: str, value: float, weight: float) -> None

add a score of a given name and value to this SilentStruct.: Takes an optional weight that defaults to 1.0.

C++: core::io::silent::SilentStruct::add_energy(const std::string &, double, double) –> void

add_other_struct(self: pyrosetta.rosetta.core.io.silent.SilentStruct, silent_struct: pyrosetta.rosetta.core.io.silent.SilentStruct) → None¶: C++: core::io::silent::SilentStruct::add_other_struct(class std::shared_ptr<class core::io::silent::SilentStruct>) –> void

add_parent_remark(self: pyrosetta.rosetta.core.io.silent.SilentStruct, name: str, value: str) → None¶: C++: core::io::silent::SilentStruct::add_parent_remark(const std::string &, const std::string &) –> void

add_string_value(*args, **kwargs)¶

Overloaded function.

add_string_value(self: pyrosetta.rosetta.core.io.silent.SilentStruct, scorename: str, value: str) -> None
add_string_value(self: pyrosetta.rosetta.core.io.silent.SilentStruct, scorename: str, value: str, index: int) -> None

add a non-floating point score of a given name and value to this: SilentStruct.

C++: core::io::silent::SilentStruct::add_string_value(const std::string &, const std::string &, const int) –> void

add_submotif_info_from_line(self: pyrosetta.rosetta.core.io.silent.SilentStruct, line_stream: pyrosetta.rosetta.std.istream) → None¶: C++: core::io::silent::SilentStruct::add_submotif_info_from_line(std::istream &) –> void

assign(self: pyrosetta.rosetta.core.import_pose.PDBSilentStruct, src: pyrosetta.rosetta.core.import_pose.PDBSilentStruct) → pyrosetta.rosetta.core.import_pose.PDBSilentStruct¶

Test if this PDBSilentStruct is equal to the given PDBSilentStruct in terms of conformation.: Doesn’t check energies.

C++: core::import_pose::PDBSilentStruct::operator=(const class core::import_pose::PDBSilentStruct &) –> class core::import_pose::PDBSilentStruct &

clear_comments(self: pyrosetta.rosetta.core.io.silent.SilentStruct) → None¶: C++: core::io::silent::SilentStruct::clear_comments() –> void

clear_energies(self: pyrosetta.rosetta.core.io.silent.SilentStruct) → None¶

Clear all of the energies in the SilentStruct. Doesn’t just: zero the energies, it entirely removes all knowledge of all energies from this SilentStruct.

C++: core::io::silent::SilentStruct::clear_energies() –> void

clone(self: pyrosetta.rosetta.core.import_pose.PDBSilentStruct) → pyrosetta.rosetta.core.io.silent.SilentStruct¶: C++: core::import_pose::PDBSilentStruct::clone() const –> class std::shared_ptr<class core::io::silent::SilentStruct>

comment_from_line(*args, **kwargs)¶

Overloaded function.

comment_from_line(self: pyrosetta.rosetta.core.io.silent.SilentStruct, line: str) -> None

C++: core::io::silent::SilentStruct::comment_from_line(const std::string &) –> void

comment_from_line(self: pyrosetta.rosetta.core.io.silent.SilentStruct, line: str, include_silentfile_comments: bool) -> None

Creates and adds a comment from an input REMARK line

Input comment line, of the format “REMARK key value [value]*”

If true, ‘REMARK XXX SILENTFILE’ lines will be added to comments.

C++: core::io::silent::SilentStruct::comment_from_line(const std::string &, const bool) –> void

copy_scores(self: pyrosetta.rosetta.core.io.silent.SilentStruct, src_ss: pyrosetta.rosetta.core.io.silent.SilentStruct) → None¶

Copy the score information in the given SilentStruct into: this SilentStruct.

C++: core::io::silent::SilentStruct::copy_scores(const class core::io::silent::SilentStruct &) –> void

decoy_tag(*args, **kwargs)¶

Overloaded function.

decoy_tag(self: pyrosetta.rosetta.core.io.silent.SilentStruct) -> str

returns the tag associated with this SilentStruct.

C++: core::io::silent::SilentStruct::decoy_tag() const –> std::string

decoy_tag(self: pyrosetta.rosetta.core.io.silent.SilentStruct, tag: str) -> None

sets the tag associated with this SilentStruct.

C++: core::io::silent::SilentStruct::decoy_tag(const std::string &) –> void

energies(self: pyrosetta.rosetta.core.io.silent.SilentStruct) → pyrosetta.rosetta.utility.vector1_core_io_silent_SilentEnergy¶

Returns the vector of SilentEnergy objects associated with: this SilentStruct object.

C++: core::io::silent::SilentStruct::energies() const –> class utility::vector1<class core::io::silent::SilentEnergy, class std::allocator<class core::io::silent::SilentEnergy> >

energies_from_pose(self: pyrosetta.rosetta.core.io.silent.SilentStruct, pose: pyrosetta.rosetta.core.pose.Pose) → None¶

Initialize this SilentStruct’s energies from the given Pose.: This sets energies, energy weights, and the output widths for the energies.

C++: core::io::silent::SilentStruct::energies_from_pose(const class core::pose::Pose &) –> void

energies_into_pose(self: pyrosetta.rosetta.core.io.silent.SilentStruct, pose: pyrosetta.rosetta.core.pose.Pose) → None¶

Put the energy information from this SilentStruct into the: pose. Energies that correspond to a ScoreType are put into the pose.energies().total_energies() EnergyMap, all other energies are put into the ARBITRARY_FLOAT_DATA map in the pose DataCache. Also sets the scorefxn_weights in the Energies object using the information from this SilentStruct.

C++: core::io::silent::SilentStruct::energies_into_pose(class core::pose::Pose &) const –> void

energy_names(self: pyrosetta.rosetta.core.io.silent.SilentStruct) → core::io::silent::EnergyNames¶

Returns the EnergyNames that this SilentStruct contains.

C++: core::io::silent::SilentStruct::energy_names() const –> class core::io::silent::EnergyNames

erase_comment(self: pyrosetta.rosetta.core.io.silent.SilentStruct, name: str) → None¶: C++: core::io::silent::SilentStruct::erase_comment(const std::string &) –> void

figure_out_residue_numbers_from_line(self: pyrosetta.rosetta.core.io.silent.SilentStruct, line_stream: pyrosetta.rosetta.std.istream) → None¶: C++: core::io::silent::SilentStruct::figure_out_residue_numbers_from_line(std::istream &) –> void

figure_out_segment_ids_from_line(self: pyrosetta.rosetta.core.io.silent.SilentStruct, line_stream: pyrosetta.rosetta.std.istream) → None¶: C++: core::io::silent::SilentStruct::figure_out_segment_ids_from_line(std::istream &) –> void

fill_other_struct_list(self: pyrosetta.rosetta.core.io.silent.SilentStruct, pose: pyrosetta.rosetta.core.pose.Pose) → None¶: C++: core::io::silent::SilentStruct::fill_other_struct_list(const class core::pose::Pose &) –> void

fill_pose(*args, **kwargs)¶

Overloaded function.

fill_pose(self: pyrosetta.rosetta.core.import_pose.PDBSilentStruct, pose: pyrosetta.rosetta.core.pose.Pose) -> None
fill_pose(self: pyrosetta.rosetta.core.import_pose.PDBSilentStruct, pose: pyrosetta.rosetta.core.pose.Pose, metapatches: bool) -> None

Configure the conformation of the given Pose with the conformational data within this PDBSilentStruct.: Calls pose.clear() and rebuilds Pose from scratch using FA_STANDARD residue types.

C++: core::import_pose::PDBSilentStruct::fill_pose(class core::pose::Pose &, const bool) const –> void

fill_pose(self: pyrosetta.rosetta.core.import_pose.PDBSilentStruct, pose: pyrosetta.rosetta.core.pose.Pose, residue_set: pyrosetta.rosetta.core.chemical.ResidueTypeSet) -> None
fill_pose(self: pyrosetta.rosetta.core.import_pose.PDBSilentStruct, pose: pyrosetta.rosetta.core.pose.Pose, residue_set: pyrosetta.rosetta.core.chemical.ResidueTypeSet, metapatches: bool) -> None

Configure the conformation of the given Pose with the: conformational data within this PDBSilentStruct. Calls pose.clear() and rebuilds Pose from scratch using the / user-specified residue types.

C++: core::import_pose::PDBSilentStruct::fill_pose(class core::pose::Pose &, const class core::chemical::ResidueTypeSet &, const bool) const –> void

fill_struct(*args, **kwargs)¶

Overloaded function.

fill_struct(self: pyrosetta.rosetta.core.import_pose.PDBSilentStruct, pose: pyrosetta.rosetta.core.pose.Pose) -> None
fill_struct(self: pyrosetta.rosetta.core.import_pose.PDBSilentStruct, pose: pyrosetta.rosetta.core.pose.Pose, tag: str) -> None

opposite of fill_pose

C++: core::import_pose::PDBSilentStruct::fill_struct(const class core::pose::Pose &, const std::string &) –> void

fill_struct_with_residue_numbers(self: pyrosetta.rosetta.core.io.silent.SilentStruct, pose: pyrosetta.rosetta.core.pose.Pose) → None¶: C++: core::io::silent::SilentStruct::fill_struct_with_residue_numbers(const class core::pose::Pose &) –> void

fill_struct_with_submotif_info_list(self: pyrosetta.rosetta.core.io.silent.SilentStruct, pose: pyrosetta.rosetta.core.pose.Pose) → None¶: C++: core::io::silent::SilentStruct::fill_struct_with_submotif_info_list(const class core::pose::Pose &) –> void

finish_pose(self: pyrosetta.rosetta.core.io.silent.SilentStruct, pose: pyrosetta.rosetta.core.pose.Pose) → None¶

calls optH if command line requests optH.: must be called by derived classes.

C++: core::io::silent::SilentStruct::finish_pose(class core::pose::Pose &) const –> void

force_bitflip(self: pyrosetta.rosetta.core.io.silent.SilentStruct) → bool¶

Gets whether conversion from big-endian to little-endian (or the converse) should be forced: when a binary silent structure is initialized from lines.

C++: core::io::silent::SilentStruct::force_bitflip() const –> bool

full_model_info_into_pose(self: pyrosetta.rosetta.core.io.silent.SilentStruct, pose: pyrosetta.rosetta.core.pose.Pose) → None¶: C++: core::io::silent::SilentStruct::full_model_info_into_pose(class core::pose::Pose &) const –> void

full_model_parameters(self: pyrosetta.rosetta.core.io.silent.SilentStruct) → core::pose::full_model_info::FullModelParameters¶: C++: core::io::silent::SilentStruct::full_model_parameters() const –> class std::shared_ptr<const class core::pose::full_model_info::FullModelParameters>

get_CA_xyz(self: pyrosetta.rosetta.core.import_pose.PDBSilentStruct) → pyrosetta.rosetta.ObjexxFCL.FArray2D_double_t¶

returns the positions of the CA atoms in this PDBSilentStruct.: Useful for RMS calculations.

C++: core::import_pose::PDBSilentStruct::get_CA_xyz() const –> class ObjexxFCL::FArray2D<double>

get_all_comments(self: pyrosetta.rosetta.core.io.silent.SilentStruct) → pyrosetta.rosetta.std.map_std_string_std_string¶: C++: core::io::silent::SilentStruct::get_all_comments() const –> class std::map<std::string, std::string, struct std::less<std::string >, class std::allocator<struct std::pair<const std::string, std::string > > >

get_comment(self: pyrosetta.rosetta.core.io.silent.SilentStruct, name: str) → str¶: C++: core::io::silent::SilentStruct::get_comment(const std::string &) const –> std::string

get_debug_rmsd(self: pyrosetta.rosetta.core.import_pose.PDBSilentStruct) → float¶

calculates the RMSD between the C-alpha atoms of a Pose built from the torsions in this: PDBSilentStruct and the C-alpha atoms from this PDBSilentStruct.

C++: core::import_pose::PDBSilentStruct::get_debug_rmsd() –> double

get_energy(self: pyrosetta.rosetta.core.io.silent.SilentStruct, scorename: str) → float¶

Returns the energy associated with the given scorename if this: SilentStruct has an energy for that scorename. Otherwise returns 0.

C++: core::io::silent::SilentStruct::get_energy(const std::string &) const –> double

get_parent_remark(self: pyrosetta.rosetta.core.io.silent.SilentStruct, name: str) → str¶: C++: core::io::silent::SilentStruct::get_parent_remark(const std::string &) const –> std::string

get_parent_remark_from_line(self: pyrosetta.rosetta.core.io.silent.SilentStruct, line: str) → None¶: C++: core::io::silent::SilentStruct::get_parent_remark_from_line(const std::string &) –> void

get_pdb_lines(self: pyrosetta.rosetta.core.import_pose.PDBSilentStruct) → str¶: C++: core::import_pose::PDBSilentStruct::get_pdb_lines() const –> std::string

get_self_ptr(self: pyrosetta.rosetta.core.io.silent.SilentStruct) → pyrosetta.rosetta.core.io.silent.SilentStruct¶: C++: core::io::silent::SilentStruct::get_self_ptr() –> class std::shared_ptr<class core::io::silent::SilentStruct>

get_silent_energies(self: pyrosetta.rosetta.core.io.silent.SilentStruct) → pyrosetta.rosetta.utility.vector1_core_io_silent_SilentEnergy¶: C++: core::io::silent::SilentStruct::get_silent_energies() –> class utility::vector1<class core::io::silent::SilentEnergy, class std::allocator<class core::io::silent::SilentEnergy> >

get_silent_energy(self: pyrosetta.rosetta.core.io.silent.SilentStruct, scorename: str) → pyrosetta.rosetta.core.io.silent.SilentEnergy¶

Returns the SilentEnergy associated with this scorename.

C++: core::io::silent::SilentStruct::get_silent_energy(const std::string &) const –> const class core::io::silent::SilentEnergy &

get_string_value(self: pyrosetta.rosetta.core.io.silent.SilentStruct, scorename: str) → str¶

Returns the energy associated with the given scorename if this: SilentStruct has an energy for that scorename. Otherwise returns 0.

C++: core::io::silent::SilentStruct::get_string_value(const std::string &) const –> const std::string &

has_comment(self: pyrosetta.rosetta.core.io.silent.SilentStruct, name: str) → bool¶: C++: core::io::silent::SilentStruct::has_comment(const std::string &) const –> bool

has_energy(self: pyrosetta.rosetta.core.io.silent.SilentStruct, scorename: str) → bool¶

returns true if this SilentStruct has an energy for the given: scorename, returns false otherwise.

C++: core::io::silent::SilentStruct::has_energy(const std::string &) const –> bool

has_parent_remark(self: pyrosetta.rosetta.core.io.silent.SilentStruct, name: str) → bool¶: C++: core::io::silent::SilentStruct::has_parent_remark(const std::string &) const –> bool

init_from_lines(self: pyrosetta.rosetta.core.import_pose.PDBSilentStruct, lines: pyrosetta.rosetta.utility.vector1_std_string, container: core::io::silent::SilentFileData) → bool¶

Tells this PDBSilentStruct object to initialize itself from the given set of lines. Lines should: be of the format

C++: core::import_pose::PDBSilentStruct::init_from_lines(const class utility::vector1<std::string, class std::allocator<std::string > > &, class core::io::silent::SilentFileData &) –> bool

mem_footprint(self: pyrosetta.rosetta.core.io.silent.SilentStruct) → int¶: C++: core::io::silent::SilentStruct::mem_footprint() const –> unsigned long

nonconst_other_struct_list(self: pyrosetta.rosetta.core.io.silent.SilentStruct) → pyrosetta.rosetta.utility.vector1_std_shared_ptr_core_io_silent_SilentStruct_t¶: C++: core::io::silent::SilentStruct::nonconst_other_struct_list() –> class utility::vector1<class std::shared_ptr<class core::io::silent::SilentStruct>, class std::allocator<class std::shared_ptr<class core::io::silent::SilentStruct> > > &

nres(*args, **kwargs)¶

Overloaded function.

nres(self: pyrosetta.rosetta.core.io.silent.SilentStruct) -> int

returns the number of residues contained by this: SilentStruct.

C++: core::io::silent::SilentStruct::nres() const –> unsigned long

nres(self: pyrosetta.rosetta.core.io.silent.SilentStruct, nres: int) -> None

returns the number of residues in this SilentStruct.

C++: core::io::silent::SilentStruct::nres(unsigned long) –> void

one_letter_sequence(self: pyrosetta.rosetta.core.io.silent.SilentStruct) → str¶

strip […] comment from seqeunce_ and return pure: one-letter sequence

C++: core::io::silent::SilentStruct::one_letter_sequence() const –> std::string

options(self: pyrosetta.rosetta.core.io.silent.SilentStruct) → pyrosetta.rosetta.core.io.silent.SilentFileOptions¶: C++: core::io::silent::SilentStruct::options() const –> const class core::io::silent::SilentFileOptions &

other_struct_list(self: pyrosetta.rosetta.core.io.silent.SilentStruct) → pyrosetta.rosetta.utility.vector1_std_shared_ptr_core_io_silent_SilentStruct_t¶: C++: core::io::silent::SilentStruct::other_struct_list() const –> const class utility::vector1<class std::shared_ptr<class core::io::silent::SilentStruct>, class std::allocator<class std::shared_ptr<class core::io::silent::SilentStruct> > > &

parse_energies(self: pyrosetta.rosetta.core.io.silent.SilentStruct, input: pyrosetta.rosetta.std.istream, energy_names: pyrosetta.rosetta.utility.vector1_std_string) → None¶: C++: core::io::silent::SilentStruct::parse_energies(std::istream &, const class utility::vector1<std::string, class std::allocator<std::string > > &) –> void

precision(*args, **kwargs)¶

Overloaded function.

precision(self: pyrosetta.rosetta.core.io.silent.SilentStruct, precision: int) -> None

C++: core::io::silent::SilentStruct::precision(unsigned long) –> void

precision(self: pyrosetta.rosetta.core.io.silent.SilentStruct) -> int

C++: core::io::silent::SilentStruct::precision() const –> unsigned long

print_comments(self: pyrosetta.rosetta.core.io.silent.SilentStruct, out: pyrosetta.rosetta.std.ostream) → None¶

print the comments in this SilentStruct.

C++: core::io::silent::SilentStruct::print_comments(std::ostream &) const –> void

print_conformation(self: pyrosetta.rosetta.core.import_pose.PDBSilentStruct, output: pyrosetta.rosetta.std.ostream) → None¶

Prints the conformation information within this PDBSilentStruct: to the given std::ostream.

C++: core::import_pose::PDBSilentStruct::print_conformation(std::ostream &) const –> void

print_header(*args, **kwargs)¶

Overloaded function.

print_header(self: pyrosetta.rosetta.core.import_pose.PDBSilentStruct, out: pyrosetta.rosetta.std.ostream) -> None
print_header(self: pyrosetta.rosetta.core.import_pose.PDBSilentStruct, out: pyrosetta.rosetta.std.ostream) -> None

C++: core::import_pose::PDBSilentStruct::print_header(std::ostream &) –> void

print_parent_remarks(self: pyrosetta.rosetta.core.io.silent.SilentStruct, out: pyrosetta.rosetta.std.ostream) → None¶: C++: core::io::silent::SilentStruct::print_parent_remarks(std::ostream &) const –> void

print_residue_numbers(self: pyrosetta.rosetta.core.io.silent.SilentStruct, out: pyrosetta.rosetta.std.ostream) → None¶

print the resnum in this SilentStruct, if filled.

C++: core::io::silent::SilentStruct::print_residue_numbers(std::ostream &) const –> void

print_score_header(self: pyrosetta.rosetta.core.io.silent.SilentStruct, out: pyrosetta.rosetta.std.ostream) → None¶

only print SCORE: header line

C++: core::io::silent::SilentStruct::print_score_header(std::ostream &) const –> void

print_scores(self: pyrosetta.rosetta.core.io.silent.SilentStruct, out: pyrosetta.rosetta.std.ostream) → None¶

print out a SCORE line to the given ozstream.

C++: core::io::silent::SilentStruct::print_scores(std::ostream &) const –> void

print_submotif_info(self: pyrosetta.rosetta.core.io.silent.SilentStruct, out: pyrosetta.rosetta.std.ostream) → None¶

print the submotif_info in this SilentStruct, if filled.

C++: core::io::silent::SilentStruct::print_submotif_info(std::ostream &) const –> void

read_score_headers(self: pyrosetta.rosetta.core.io.silent.SilentStruct, line: str, enames: pyrosetta.rosetta.utility.vector1_std_string, container: core::io::silent::SilentFileData) → None¶: C++: core::io::silent::SilentStruct::read_score_headers(const std::string &, class utility::vector1<std::string, class std::allocator<std::string > > &, class core::io::silent::SilentFileData &) –> void

read_sequence(self: pyrosetta.rosetta.core.io.silent.SilentStruct, line: str) → bool¶: C++: core::io::silent::SilentStruct::read_sequence(const std::string &) –> bool

rename_energies(self: pyrosetta.rosetta.core.io.silent.SilentStruct) → None¶: C++: core::io::silent::SilentStruct::rename_energies() –> void

residue_numbers_into_pose(self: pyrosetta.rosetta.core.io.silent.SilentStruct, pose: pyrosetta.rosetta.core.pose.Pose) → None¶: C++: core::io::silent::SilentStruct::residue_numbers_into_pose(class core::pose::Pose &) const –> void

scoreline_prefix(*args, **kwargs)¶

Overloaded function.

scoreline_prefix(self: pyrosetta.rosetta.core.io.silent.SilentStruct, prefix: str) -> None

C++: core::io::silent::SilentStruct::scoreline_prefix(const std::string &) –> void

scoreline_prefix(self: pyrosetta.rosetta.core.io.silent.SilentStruct) -> str

C++: core::io::silent::SilentStruct::scoreline_prefix() const –> std::string

sequence(*args, **kwargs)¶

Overloaded function.

sequence(self: pyrosetta.rosetta.core.io.silent.SilentStruct) -> pyrosetta.rosetta.core.sequence.AnnotatedSequence

returns the sequence associated with this SilentStruct.

C++: core::io::silent::SilentStruct::sequence() const –> const class core::sequence::AnnotatedSequence &

sequence(self: pyrosetta.rosetta.core.io.silent.SilentStruct, sequence: pyrosetta.rosetta.core.sequence.AnnotatedSequence) -> None

sets the sequence for this SilentStruct.

C++: core::io::silent::SilentStruct::sequence(const class core::sequence::AnnotatedSequence &) –> void

set_chains(self: pyrosetta.rosetta.core.io.silent.SilentStruct, chains: pyrosetta.rosetta.utility.vector1_char) → None¶: C++: core::io::silent::SilentStruct::set_chains(const class utility::vector1<char, class std::allocator<char> > &) –> void

set_decoy_tag(self: pyrosetta.rosetta.core.io.silent.SilentStruct, tag: str) → None¶

set the tag associate with this SilentStruct

C++: core::io::silent::SilentStruct::set_decoy_tag(const std::string &) –> void

set_force_bitflip(self: pyrosetta.rosetta.core.io.silent.SilentStruct, setting: bool) → None¶

Sets whether conversion from big-endian to little-endian (or the converse) should be forced: when a binary silent structure is initialized from lines.

C++: core::io::silent::SilentStruct::set_force_bitflip(const bool) –> void

set_full_model_parameters(self: pyrosetta.rosetta.core.io.silent.SilentStruct, setting: core::pose::full_model_info::FullModelParameters) → None¶: C++: core::io::silent::SilentStruct::set_full_model_parameters(class std::shared_ptr<const class core::pose::full_model_info::FullModelParameters>) –> void

set_residue_numbers(self: pyrosetta.rosetta.core.io.silent.SilentStruct, residue_numbers: pyrosetta.rosetta.utility.vector1_int) → None¶: C++: core::io::silent::SilentStruct::set_residue_numbers(const class utility::vector1<int, class std::allocator<int> > &) –> void

set_segment_IDs(self: pyrosetta.rosetta.core.io.silent.SilentStruct, segids: pyrosetta.rosetta.utility.vector1_std_string) → None¶: C++: core::io::silent::SilentStruct::set_segment_IDs(const class utility::vector1<std::string, class std::allocator<std::string > > &) –> void

set_tag_from_pose(self: pyrosetta.rosetta.core.io.silent.SilentStruct, pose: pyrosetta.rosetta.core.pose.Pose) → None¶

Sets the tag from the Pose DataCache.

C++: core::io::silent::SilentStruct::set_tag_from_pose(const class core::pose::Pose &) –> void

set_valid_energies(self: pyrosetta.rosetta.core.io.silent.SilentStruct, valid: pyrosetta.rosetta.utility.vector1_std_string) → None¶: C++: core::io::silent::SilentStruct::set_valid_energies(class utility::vector1<std::string, class std::allocator<std::string > >) –> void

silent_energies(self: pyrosetta.rosetta.core.io.silent.SilentStruct, new_se: pyrosetta.rosetta.utility.vector1_core_io_silent_SilentEnergy) → None¶

sets the silent_energies for this SilentStruct.

C++: core::io::silent::SilentStruct::silent_energies(const class utility::vector1<class core::io::silent::SilentEnergy, class std::allocator<class core::io::silent::SilentEnergy> > &) –> void

sort_silent_scores(self: pyrosetta.rosetta.core.io.silent.SilentStruct) → None¶

sort all the silent energies by their name.

C++: core::io::silent::SilentStruct::sort_silent_scores() –> void

struct_file_rep(*args, **kwargs)¶

Overloaded function.

struct_file_rep(self: pyrosetta.rosetta.core.import_pose.PDBSilentStruct) -> pyrosetta.rosetta.core.io.StructFileRep

data getters/setters

C++: core::import_pose::PDBSilentStruct::struct_file_rep() const –> const class core::io::StructFileRep

struct_file_rep(self: pyrosetta.rosetta.core.import_pose.PDBSilentStruct, new_sfr: pyrosetta.rosetta.core.io.StructFileRep) -> None

C++: core::import_pose::PDBSilentStruct::struct_file_rep(class core::io::StructFileRep) –> void

class pyrosetta.rosetta.core.import_pose.PDBSilentStructCreator¶

Bases: SilentStructCreator

creator for the PDBSilentStruct class

assign(self: pyrosetta.rosetta.core.import_pose.PDBSilentStructCreator, : pyrosetta.rosetta.core.import_pose.PDBSilentStructCreator) → pyrosetta.rosetta.core.import_pose.PDBSilentStructCreator¶: C++: core::import_pose::PDBSilentStructCreator::operator=(const class core::import_pose::PDBSilentStructCreator &) –> class core::import_pose::PDBSilentStructCreator &

create_silent_struct(self: pyrosetta.rosetta.core.import_pose.PDBSilentStructCreator, opts: pyrosetta.rosetta.core.io.silent.SilentFileOptions) → pyrosetta.rosetta.core.io.silent.SilentStruct¶: C++: core::import_pose::PDBSilentStructCreator::create_silent_struct(const class core::io::silent::SilentFileOptions &) const –> class std::shared_ptr<class core::io::silent::SilentStruct>

keyname(self: pyrosetta.rosetta.core.import_pose.PDBSilentStructCreator) → str¶: C++: core::import_pose::PDBSilentStructCreator::keyname() const –> std::string

class pyrosetta.rosetta.core.import_pose.PoseResource¶

Bases: pybind11_object

assign(self: pyrosetta.rosetta.core.import_pose.PoseResource, : pyrosetta.rosetta.core.import_pose.PoseResource) → pyrosetta.rosetta.core.import_pose.PoseResource¶: C++: core::import_pose::PoseResource::operator=(const class core::import_pose::PoseResource &) –> class core::import_pose::PoseResource &

pose(self: pyrosetta.rosetta.core.import_pose.PoseResource, pose_to_hold: pyrosetta.rosetta.core.pose.Pose) → None¶: C++: core::import_pose::PoseResource::pose(class std::shared_ptr<const class core::pose::Pose>) –> void

pose_deep_copy(self: pyrosetta.rosetta.core.import_pose.PoseResource) → pyrosetta.rosetta.core.pose.Pose¶

The primary way of getting a Pose from a PoseResource:

to request a deep copy of the Pose that it is holding. This ensures that the Pose is safely copied to prevent thread-unsafe modification of its internal data.

Pose’s operator= is not threadsafe in that Poses maintain pointers to each other to silently communicate between themselves when one of them is modified, and these connections are established during an operator= call. The alternative is to call Pose::detached_copy( Pose const & source ) which this function does. No thread-unsafe connections are established between Poses copied with the detached_copy call.

Note that every call to this function creates a new Pose, and so there might end up with many copies of the Pose in memory. Use the protocols::moves::PoseFromPoseResourceMover to load a single Pose from the ResourceManager into the DataMap during its initialization. Then subsequent movers can read that Pose from the DataMap during their initialization.

C++: core::import_pose::PoseResource::pose_deep_copy() const –> class std::shared_ptr<class core::pose::Pose>

class pyrosetta.rosetta.core.import_pose.PoseResourceLoader¶

Bases: ResourceLoader

assign(self: pyrosetta.rosetta.core.import_pose.PoseResourceLoader, : pyrosetta.rosetta.core.import_pose.PoseResourceLoader) → pyrosetta.rosetta.core.import_pose.PoseResourceLoader¶: C++: core::import_pose::PoseResourceLoader::operator=(const class core::import_pose::PoseResourceLoader &) –> class core::import_pose::PoseResourceLoader &

static classname() → str¶: C++: core::import_pose::PoseResourceLoader::classname() –> std::string

static provide_xml_schema(xsd: utility::tag::XMLSchemaDefinition) → None¶: C++: core::import_pose::PoseResourceLoader::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) –> void

class pyrosetta.rosetta.core.import_pose.PoseResourceLoaderCreator¶

Bases: ResourceLoaderCreator

assign(self: pyrosetta.rosetta.core.import_pose.PoseResourceLoaderCreator, : pyrosetta.rosetta.core.import_pose.PoseResourceLoaderCreator) → pyrosetta.rosetta.core.import_pose.PoseResourceLoaderCreator¶: C++: core::import_pose::PoseResourceLoaderCreator::operator=(const class core::import_pose::PoseResourceLoaderCreator &) –> class core::import_pose::PoseResourceLoaderCreator &

create_resource_loader(self: pyrosetta.rosetta.core.import_pose.PoseResourceLoaderCreator) → pyrosetta.rosetta.basic.resource_manager.ResourceLoader¶: C++: core::import_pose::PoseResourceLoaderCreator::create_resource_loader() const –> class std::shared_ptr<class basic::resource_manager::ResourceLoader>

loader_type(self: pyrosetta.rosetta.core.import_pose.PoseResourceLoaderCreator) → str¶: C++: core::import_pose::PoseResourceLoaderCreator::loader_type() const –> std::string

provide_xml_schema(self: pyrosetta.rosetta.core.import_pose.PoseResourceLoaderCreator, xsd: utility::tag::XMLSchemaDefinition) → None¶: C++: core::import_pose::PoseResourceLoaderCreator::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) const –> void

class pyrosetta.rosetta.core.import_pose.RNA_BasePairHandler¶

Bases: pybind11_object

assign(self: pyrosetta.rosetta.core.import_pose.RNA_BasePairHandler, : pyrosetta.rosetta.core.import_pose.RNA_BasePairHandler) → pyrosetta.rosetta.core.import_pose.RNA_BasePairHandler¶: C++: core::import_pose::RNA_BasePairHandler::operator=(const class core::import_pose::RNA_BasePairHandler &) –> class core::import_pose::RNA_BasePairHandler &

chain_connections(self: pyrosetta.rosetta.core.import_pose.RNA_BasePairHandler) → pyrosetta.rosetta.utility.vector1_std_pair_utility_vector1_unsigned_long_std_allocator_unsigned_long_utility_vector1_unsigned_long_std_allocator_unsigned_long_t¶: C++: core::import_pose::RNA_BasePairHandler::chain_connections() const –> const class utility::vector1<struct std::pair<class utility::vector1<unsigned long, class std::allocator<unsigned long> >, class utility::vector1<unsigned long, class std::allocator<unsigned long> > >, class std::allocator<struct std::pair<class utility::vector1<unsigned long, class std::allocator<unsigned long> >, class utility::vector1<unsigned long, class std::allocator<unsigned long> > > > > &

check_base_pairs(self: pyrosetta.rosetta.core.import_pose.RNA_BasePairHandler, pose: pyrosetta.rosetta.core.pose.Pose, atom_level_domain_map: core::pose::toolbox::AtomLevelDomainMap) → bool¶: C++: core::import_pose::RNA_BasePairHandler::check_base_pairs(class core::pose::Pose &, class std::shared_ptr<const class core::pose::toolbox::AtomLevelDomainMap>) const –> bool

connections(self: pyrosetta.rosetta.core.import_pose.RNA_BasePairHandler) → pyrosetta.rosetta.std.map_unsigned_long_unsigned_long¶: C++: core::import_pose::RNA_BasePairHandler::connections() const –> class std::map<unsigned long, unsigned long, struct std::less<unsigned long>, class std::allocator<struct std::pair<const unsigned long, unsigned long> > >

get_stem_residues(self: pyrosetta.rosetta.core.import_pose.RNA_BasePairHandler, pose: pyrosetta.rosetta.core.pose.Pose) → pyrosetta.rosetta.utility.vector1_unsigned_long¶: C++: core::import_pose::RNA_BasePairHandler::get_stem_residues(const class core::pose::Pose &) const –> class utility::vector1<unsigned long, class std::allocator<unsigned long> >

rna_pairing_list(self: pyrosetta.rosetta.core.import_pose.RNA_BasePairHandler) → pyrosetta.rosetta.utility.vector1_core_pose_rna_BasePair¶: C++: core::import_pose::RNA_BasePairHandler::rna_pairing_list() const –> class utility::vector1<class core::pose::rna::BasePair, class std::allocator<class core::pose::rna::BasePair> >

setup_base_pair_constraints(*args, **kwargs)¶

Overloaded function.

setup_base_pair_constraints(self: pyrosetta.rosetta.core.import_pose.RNA_BasePairHandler, pose: pyrosetta.rosetta.core.pose.Pose, atom_level_domain_map: core::pose::toolbox::AtomLevelDomainMap) -> None
setup_base_pair_constraints(self: pyrosetta.rosetta.core.import_pose.RNA_BasePairHandler, pose: pyrosetta.rosetta.core.pose.Pose, atom_level_domain_map: core::pose::toolbox::AtomLevelDomainMap, suppress_bp_constraint: float) -> None

C++: core::import_pose::RNA_BasePairHandler::setup_base_pair_constraints(class core::pose::Pose &, class std::shared_ptr<const class core::pose::toolbox::AtomLevelDomainMap>, const double) const –> void

class pyrosetta.rosetta.core.import_pose.RNA_DeNovoParameters¶

Bases: pybind11_object

add_cutpoint_open(self: pyrosetta.rosetta.core.import_pose.RNA_DeNovoParameters, n: int) → None¶: C++: core::import_pose::RNA_DeNovoParameters::add_cutpoint_open(const unsigned long) –> void

add_obligate_pairing_set(self: pyrosetta.rosetta.core.import_pose.RNA_DeNovoParameters, set: pyrosetta.rosetta.utility.vector1_unsigned_long) → None¶: C++: core::import_pose::RNA_DeNovoParameters::add_obligate_pairing_set(const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &) –> void

add_rna_pairing(self: pyrosetta.rosetta.core.import_pose.RNA_DeNovoParameters, rna_pairing: pyrosetta.rosetta.core.pose.rna.BasePair) → None¶: C++: core::import_pose::RNA_DeNovoParameters::add_rna_pairing(const class core::pose::rna::BasePair &) –> void

allow_insert_res(self: pyrosetta.rosetta.core.import_pose.RNA_DeNovoParameters) → pyrosetta.rosetta.utility.vector1_unsigned_long¶: C++: core::import_pose::RNA_DeNovoParameters::allow_insert_res() const –> class utility::vector1<unsigned long, class std::allocator<unsigned long> >

block_stack_above_res(self: pyrosetta.rosetta.core.import_pose.RNA_DeNovoParameters) → pyrosetta.rosetta.utility.vector1_unsigned_long¶: C++: core::import_pose::RNA_DeNovoParameters::block_stack_above_res() const –> class utility::vector1<unsigned long, class std::allocator<unsigned long> >

block_stack_below_res(self: pyrosetta.rosetta.core.import_pose.RNA_DeNovoParameters) → pyrosetta.rosetta.utility.vector1_unsigned_long¶: C++: core::import_pose::RNA_DeNovoParameters::block_stack_below_res() const –> class utility::vector1<unsigned long, class std::allocator<unsigned long> >

chain_connections(self: pyrosetta.rosetta.core.import_pose.RNA_DeNovoParameters) → pyrosetta.rosetta.utility.vector1_std_pair_utility_vector1_unsigned_long_std_allocator_unsigned_long_utility_vector1_unsigned_long_std_allocator_unsigned_long_t¶: C++: core::import_pose::RNA_DeNovoParameters::chain_connections() const –> const class utility::vector1<struct std::pair<class utility::vector1<unsigned long, class std::allocator<unsigned long> >, class utility::vector1<unsigned long, class std::allocator<unsigned long> > >, class std::allocator<struct std::pair<class utility::vector1<unsigned long, class std::allocator<unsigned long> >, class utility::vector1<unsigned long, class std::allocator<unsigned long> > > > > &

check_in_pairing_sets(self: pyrosetta.rosetta.core.import_pose.RNA_DeNovoParameters, pairing_sets: pyrosetta.rosetta.utility.vector1_utility_vector1_unsigned_long_std_allocator_unsigned_long_t, rna_pairing_check: pyrosetta.rosetta.core.pose.rna.BasePair) → int¶: C++: core::import_pose::RNA_DeNovoParameters::check_in_pairing_sets(class utility::vector1<class utility::vector1<unsigned long, class std::allocator<unsigned long> >, class std::allocator<class utility::vector1<unsigned long, class std::allocator<unsigned long> > > >, const class core::pose::rna::BasePair &) const –> unsigned long

cutpoints_closed(self: pyrosetta.rosetta.core.import_pose.RNA_DeNovoParameters) → pyrosetta.rosetta.utility.vector1_unsigned_long¶: C++: core::import_pose::RNA_DeNovoParameters::cutpoints_closed() const –> class utility::vector1<unsigned long, class std::allocator<unsigned long> >

cutpoints_cyclize(self: pyrosetta.rosetta.core.import_pose.RNA_DeNovoParameters) → pyrosetta.rosetta.utility.vector1_unsigned_long¶: C++: core::import_pose::RNA_DeNovoParameters::cutpoints_cyclize() const –> class utility::vector1<unsigned long, class std::allocator<unsigned long> >

cutpoints_open(self: pyrosetta.rosetta.core.import_pose.RNA_DeNovoParameters) → pyrosetta.rosetta.utility.vector1_unsigned_long¶: C++: core::import_pose::RNA_DeNovoParameters::cutpoints_open() const –> class utility::vector1<unsigned long, class std::allocator<unsigned long> >

fiveprime_cap(self: pyrosetta.rosetta.core.import_pose.RNA_DeNovoParameters) → pyrosetta.rosetta.utility.vector1_unsigned_long¶: C++: core::import_pose::RNA_DeNovoParameters::fiveprime_cap() const –> class utility::vector1<unsigned long, class std::allocator<unsigned long> >

fold_tree_from_silent_file(self: pyrosetta.rosetta.core.import_pose.RNA_DeNovoParameters) → pyrosetta.rosetta.core.kinematics.FoldTree¶: C++: core::import_pose::RNA_DeNovoParameters::fold_tree_from_silent_file() const –> class core::kinematics::FoldTree

is_rna_and_protein(self: pyrosetta.rosetta.core.import_pose.RNA_DeNovoParameters) → bool¶: C++: core::import_pose::RNA_DeNovoParameters::is_rna_and_protein() const –> bool

obligate_pairing_sets(self: pyrosetta.rosetta.core.import_pose.RNA_DeNovoParameters) → pyrosetta.rosetta.utility.vector1_utility_vector1_unsigned_long_std_allocator_unsigned_long_t¶: C++: core::import_pose::RNA_DeNovoParameters::obligate_pairing_sets() const –> const class utility::vector1<class utility::vector1<unsigned long, class std::allocator<unsigned long> >, class std::allocator<class utility::vector1<unsigned long, class std::allocator<unsigned long> > > > &

rna_pairing_list(self: pyrosetta.rosetta.core.import_pose.RNA_DeNovoParameters) → pyrosetta.rosetta.utility.vector1_core_pose_rna_BasePair¶: C++: core::import_pose::RNA_DeNovoParameters::rna_pairing_list() const –> const class utility::vector1<class core::pose::rna::BasePair, class std::allocator<class core::pose::rna::BasePair> > &

rna_secstruct_legacy(self: pyrosetta.rosetta.core.import_pose.RNA_DeNovoParameters) → str¶: C++: core::import_pose::RNA_DeNovoParameters::rna_secstruct_legacy() const –> std::string

secstruct_defined(self: pyrosetta.rosetta.core.import_pose.RNA_DeNovoParameters) → bool¶: C++: core::import_pose::RNA_DeNovoParameters::secstruct_defined() const –> const bool &

set_allow_insert_res(self: pyrosetta.rosetta.core.import_pose.RNA_DeNovoParameters, setting: pyrosetta.rosetta.utility.vector1_unsigned_long) → None¶: C++: core::import_pose::RNA_DeNovoParameters::set_allow_insert_res(const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &) –> void

set_block_stack_above_res(self: pyrosetta.rosetta.core.import_pose.RNA_DeNovoParameters, setting: pyrosetta.rosetta.utility.vector1_unsigned_long) → None¶: C++: core::import_pose::RNA_DeNovoParameters::set_block_stack_above_res(const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &) –> void

set_block_stack_below_res(self: pyrosetta.rosetta.core.import_pose.RNA_DeNovoParameters, setting: pyrosetta.rosetta.utility.vector1_unsigned_long) → None¶: C++: core::import_pose::RNA_DeNovoParameters::set_block_stack_below_res(const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &) –> void

set_chain_connections(self: pyrosetta.rosetta.core.import_pose.RNA_DeNovoParameters, setting: pyrosetta.rosetta.utility.vector1_std_pair_utility_vector1_unsigned_long_std_allocator_unsigned_long_utility_vector1_unsigned_long_std_allocator_unsigned_long_t) → None¶: C++: core::import_pose::RNA_DeNovoParameters::set_chain_connections(const class utility::vector1<struct std::pair<class utility::vector1<unsigned long, class std::allocator<unsigned long> >, class utility::vector1<unsigned long, class std::allocator<unsigned long> > >, class std::allocator<struct std::pair<class utility::vector1<unsigned long, class std::allocator<unsigned long> >, class utility::vector1<unsigned long, class std::allocator<unsigned long> > > > > &) –> void

set_cutpoints_closed(self: pyrosetta.rosetta.core.import_pose.RNA_DeNovoParameters, setting: pyrosetta.rosetta.utility.vector1_unsigned_long) → None¶: C++: core::import_pose::RNA_DeNovoParameters::set_cutpoints_closed(const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &) –> void

set_cutpoints_cyclize(self: pyrosetta.rosetta.core.import_pose.RNA_DeNovoParameters, setting: pyrosetta.rosetta.utility.vector1_unsigned_long) → None¶: C++: core::import_pose::RNA_DeNovoParameters::set_cutpoints_cyclize(const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &) –> void

set_cutpoints_open(self: pyrosetta.rosetta.core.import_pose.RNA_DeNovoParameters, setting: pyrosetta.rosetta.utility.vector1_unsigned_long) → None¶: C++: core::import_pose::RNA_DeNovoParameters::set_cutpoints_open(const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &) –> void

set_fiveprime_cap(self: pyrosetta.rosetta.core.import_pose.RNA_DeNovoParameters, setting: pyrosetta.rosetta.utility.vector1_unsigned_long) → None¶: C++: core::import_pose::RNA_DeNovoParameters::set_fiveprime_cap(const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &) –> void

set_fold_tree_from_silent_file(self: pyrosetta.rosetta.core.import_pose.RNA_DeNovoParameters, fold_tree: pyrosetta.rosetta.core.kinematics.FoldTree) → None¶: C++: core::import_pose::RNA_DeNovoParameters::set_fold_tree_from_silent_file(const class core::kinematics::FoldTree &) –> void

set_obligate_pairing_sets(self: pyrosetta.rosetta.core.import_pose.RNA_DeNovoParameters, setting: pyrosetta.rosetta.utility.vector1_utility_vector1_unsigned_long_std_allocator_unsigned_long_t) → None¶: C++: core::import_pose::RNA_DeNovoParameters::set_obligate_pairing_sets(const class utility::vector1<class utility::vector1<unsigned long, class std::allocator<unsigned long> >, class std::allocator<class utility::vector1<unsigned long, class std::allocator<unsigned long> > > > &) –> void

set_rna_and_protein(self: pyrosetta.rosetta.core.import_pose.RNA_DeNovoParameters, setting: bool) → None¶: C++: core::import_pose::RNA_DeNovoParameters::set_rna_and_protein(const bool &) –> void

set_rna_pairing_list(self: pyrosetta.rosetta.core.import_pose.RNA_DeNovoParameters, setting: pyrosetta.rosetta.utility.vector1_core_pose_rna_BasePair) → None¶: C++: core::import_pose::RNA_DeNovoParameters::set_rna_pairing_list(const class utility::vector1<class core::pose::rna::BasePair, class std::allocator<class core::pose::rna::BasePair> > &) –> void

set_rna_secstruct_legacy(self: pyrosetta.rosetta.core.import_pose.RNA_DeNovoParameters, setting: str) → None¶: C++: core::import_pose::RNA_DeNovoParameters::set_rna_secstruct_legacy(const std::string &) –> void

set_stem_pairing_sets(self: pyrosetta.rosetta.core.import_pose.RNA_DeNovoParameters, setting: pyrosetta.rosetta.utility.vector1_utility_vector1_unsigned_long_std_allocator_unsigned_long_t) → None¶: C++: core::import_pose::RNA_DeNovoParameters::set_stem_pairing_sets(const class utility::vector1<class utility::vector1<unsigned long, class std::allocator<unsigned long> >, class std::allocator<class utility::vector1<unsigned long, class std::allocator<unsigned long> > > > &) –> void

set_twoprime(self: pyrosetta.rosetta.core.import_pose.RNA_DeNovoParameters, setting: pyrosetta.rosetta.utility.vector1_unsigned_long) → None¶: C++: core::import_pose::RNA_DeNovoParameters::set_twoprime(const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &) –> void

set_use_fold_tree_from_silent_file(self: pyrosetta.rosetta.core.import_pose.RNA_DeNovoParameters, setting: bool) → None¶: C++: core::import_pose::RNA_DeNovoParameters::set_use_fold_tree_from_silent_file(const bool &) –> void

set_virtual_anchor_attachment_points(self: pyrosetta.rosetta.core.import_pose.RNA_DeNovoParameters, setting: pyrosetta.rosetta.utility.vector1_unsigned_long) → None¶: C++: core::import_pose::RNA_DeNovoParameters::set_virtual_anchor_attachment_points(const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &) –> void

stem_pairing_sets(self: pyrosetta.rosetta.core.import_pose.RNA_DeNovoParameters) → pyrosetta.rosetta.utility.vector1_utility_vector1_unsigned_long_std_allocator_unsigned_long_t¶: C++: core::import_pose::RNA_DeNovoParameters::stem_pairing_sets() const –> const class utility::vector1<class utility::vector1<unsigned long, class std::allocator<unsigned long> >, class std::allocator<class utility::vector1<unsigned long, class std::allocator<unsigned long> > > > &

twoprime(self: pyrosetta.rosetta.core.import_pose.RNA_DeNovoParameters) → pyrosetta.rosetta.utility.vector1_unsigned_long¶: C++: core::import_pose::RNA_DeNovoParameters::twoprime() const –> class utility::vector1<unsigned long, class std::allocator<unsigned long> >

use_fold_tree_from_silent_file(self: pyrosetta.rosetta.core.import_pose.RNA_DeNovoParameters) → bool¶: C++: core::import_pose::RNA_DeNovoParameters::use_fold_tree_from_silent_file() const –> bool

virtual_anchor_attachment_points(self: pyrosetta.rosetta.core.import_pose.RNA_DeNovoParameters) → pyrosetta.rosetta.utility.vector1_unsigned_long¶: C++: core::import_pose::RNA_DeNovoParameters::virtual_anchor_attachment_points() const –> class utility::vector1<unsigned long, class std::allocator<unsigned long> >

class pyrosetta.rosetta.core.import_pose.RNA_DeNovoSetup¶

Bases: pybind11_object

assign(self: pyrosetta.rosetta.core.import_pose.RNA_DeNovoSetup, : pyrosetta.rosetta.core.import_pose.RNA_DeNovoSetup) → pyrosetta.rosetta.core.import_pose.RNA_DeNovoSetup¶: C++: core::import_pose::RNA_DeNovoSetup::operator=(const class core::import_pose::RNA_DeNovoSetup &) –> class core::import_pose::RNA_DeNovoSetup &

initialize_from_command_line(self: pyrosetta.rosetta.core.import_pose.RNA_DeNovoSetup) → None¶: C++: core::import_pose::RNA_DeNovoSetup::initialize_from_command_line() –> void

initialize_from_options(self: pyrosetta.rosetta.core.import_pose.RNA_DeNovoSetup, opts: pyrosetta.rosetta.utility.options.OptionCollection) → None¶: C++: core::import_pose::RNA_DeNovoSetup::initialize_from_options(const class utility::options::OptionCollection &) –> void

initialize_inputs_from_options(self: pyrosetta.rosetta.core.import_pose.RNA_DeNovoSetup, opts: pyrosetta.rosetta.utility.options.OptionCollection) → None¶

Initialize particular inputs first – like PDB files.

the idea is that these are most likely to be unspecified on the command line in a pyrosetta type of context, and this way we could re-spec them later.

C++: core::import_pose::RNA_DeNovoSetup::initialize_inputs_from_options(const class utility::options::OptionCollection &) –> void

static list_options_read(opts: pyrosetta.rosetta.std.list_utility_keys_VariantKey_utility_options_OptionKey_t) → None¶: C++: core::import_pose::RNA_DeNovoSetup::list_options_read(class std::list<class utility::keys::VariantKey<class utility::options::OptionKey>, class std::allocator<class utility::keys::VariantKey<class utility::options::OptionKey> > > &) –> void

native_pose(self: pyrosetta.rosetta.core.import_pose.RNA_DeNovoSetup) → pyrosetta.rosetta.core.pose.Pose¶: C++: core::import_pose::RNA_DeNovoSetup::native_pose() –> class std::shared_ptr<const class core::pose::Pose>

options(self: pyrosetta.rosetta.core.import_pose.RNA_DeNovoSetup) → core::import_pose::options::RNA_DeNovoProtocolOptions¶: C++: core::import_pose::RNA_DeNovoSetup::options() const –> class std::shared_ptr<const class core::import_pose::options::RNA_DeNovoProtocolOptions>

pose(self: pyrosetta.rosetta.core.import_pose.RNA_DeNovoSetup) → pyrosetta.rosetta.core.pose.Pose¶: C++: core::import_pose::RNA_DeNovoSetup::pose() –> class std::shared_ptr<class core::pose::Pose>

refine_pose_list(self: pyrosetta.rosetta.core.import_pose.RNA_DeNovoSetup) → pyrosetta.rosetta.utility.vector1_std_shared_ptr_core_pose_Pose_t¶: C++: core::import_pose::RNA_DeNovoSetup::refine_pose_list() const –> const class utility::vector1<class std::shared_ptr<class core::pose::Pose>, class std::allocator<class std::shared_ptr<class core::pose::Pose> > > &

rna_params(self: pyrosetta.rosetta.core.import_pose.RNA_DeNovoSetup) → pyrosetta.rosetta.core.import_pose.RNA_DeNovoParameters¶: C++: core::import_pose::RNA_DeNovoSetup::rna_params() const –> class std::shared_ptr<const class core::import_pose::RNA_DeNovoParameters>

set_align_pdb(self: pyrosetta.rosetta.core.import_pose.RNA_DeNovoSetup, align_pdb: str) → None¶: C++: core::import_pose::RNA_DeNovoSetup::set_align_pdb(const std::string &) –> void

set_fasta_files(self: pyrosetta.rosetta.core.import_pose.RNA_DeNovoSetup, fasta_files: pyrosetta.rosetta.utility.vector1_std_string) → None¶: C++: core::import_pose::RNA_DeNovoSetup::set_fasta_files(const class utility::vector1<std::string, class std::allocator<std::string > > &) –> void

set_input_pdbs(self: pyrosetta.rosetta.core.import_pose.RNA_DeNovoSetup, input_pdbs: pyrosetta.rosetta.utility.vector1_std_string) → None¶: C++: core::import_pose::RNA_DeNovoSetup::set_input_pdbs(const class utility::vector1<std::string, class std::allocator<std::string > > &) –> void

set_input_silent_files(self: pyrosetta.rosetta.core.import_pose.RNA_DeNovoSetup, input_silent_files: pyrosetta.rosetta.utility.vector1_std_string) → None¶: C++: core::import_pose::RNA_DeNovoSetup::set_input_silent_files(const class utility::vector1<std::string, class std::allocator<std::string > > &) –> void

set_minimize_rna(self: pyrosetta.rosetta.core.import_pose.RNA_DeNovoSetup, minimize_rna: bool) → None¶: C++: core::import_pose::RNA_DeNovoSetup::set_minimize_rna(const bool) –> void

set_native_pose(self: pyrosetta.rosetta.core.import_pose.RNA_DeNovoSetup, native_pose: pyrosetta.rosetta.core.pose.Pose) → None¶: C++: core::import_pose::RNA_DeNovoSetup::set_native_pose(class std::shared_ptr<class core::pose::Pose>) –> void

set_nstruct(self: pyrosetta.rosetta.core.import_pose.RNA_DeNovoSetup, nstruct: int) → None¶: C++: core::import_pose::RNA_DeNovoSetup::set_nstruct(const unsigned long) –> void

set_sequence_strings(self: pyrosetta.rosetta.core.import_pose.RNA_DeNovoSetup, sequence_strings: pyrosetta.rosetta.utility.vector1_std_string) → None¶: C++: core::import_pose::RNA_DeNovoSetup::set_sequence_strings(const class utility::vector1<std::string, class std::allocator<std::string > > &) –> void

set_silent_file(self: pyrosetta.rosetta.core.import_pose.RNA_DeNovoSetup, silent_file: str) → None¶: C++: core::import_pose::RNA_DeNovoSetup::set_silent_file(const std::string &) –> void

class pyrosetta.rosetta.core.import_pose.RNA_HelixAssembler¶

Bases: pybind11_object

The RNA de novo structure modeling protocol

apply(*args, **kwargs)¶

Overloaded function.

apply(self: pyrosetta.rosetta.core.import_pose.RNA_HelixAssembler, pose: pyrosetta.rosetta.core.pose.Pose) -> None

Apply the loop-rebuild protocol to the input pose

C++: core::import_pose::RNA_HelixAssembler::apply(class core::pose::Pose &) –> void

apply(self: pyrosetta.rosetta.core.import_pose.RNA_HelixAssembler, pose: pyrosetta.rosetta.core.pose.Pose, full_sequence_in: str) -> None

Apply the loop-rebuild protocol to the input pose

C++: core::import_pose::RNA_HelixAssembler::apply(class core::pose::Pose &, const std::string &) –> void

build_helix(self: pyrosetta.rosetta.core.import_pose.RNA_HelixAssembler, pose: pyrosetta.rosetta.core.pose.Pose) → None¶: C++: core::import_pose::RNA_HelixAssembler::build_helix(class core::pose::Pose &) –> void

build_init_pose(self: pyrosetta.rosetta.core.import_pose.RNA_HelixAssembler, seq1: str, seq2: str) → pyrosetta.rosetta.core.pose.Pose¶: C++: core::import_pose::RNA_HelixAssembler::build_init_pose(const std::string &, const std::string &) –> class std::shared_ptr<class core::pose::Pose>

get_name(self: pyrosetta.rosetta.core.import_pose.RNA_HelixAssembler) → str¶: C++: core::import_pose::RNA_HelixAssembler::get_name() const –> std::string

random_perturbation(self: pyrosetta.rosetta.core.import_pose.RNA_HelixAssembler, setting: bool) → None¶: C++: core::import_pose::RNA_HelixAssembler::random_perturbation(const bool &) –> void

set_dump(self: pyrosetta.rosetta.core.import_pose.RNA_HelixAssembler, setting: bool) → None¶: C++: core::import_pose::RNA_HelixAssembler::set_dump(const bool &) –> void

set_finish_scorefxn(self: pyrosetta.rosetta.core.import_pose.RNA_HelixAssembler, setting: pyrosetta.rosetta.core.scoring.ScoreFunction) → None¶: C++: core::import_pose::RNA_HelixAssembler::set_finish_scorefxn(class std::shared_ptr<class core::scoring::ScoreFunction>) –> void

set_minimize_all(self: pyrosetta.rosetta.core.import_pose.RNA_HelixAssembler, setting: bool) → None¶: C++: core::import_pose::RNA_HelixAssembler::set_minimize_all(const bool &) –> void

set_model_and_remove_capping_residues(self: pyrosetta.rosetta.core.import_pose.RNA_HelixAssembler, setting: bool) → None¶: C++: core::import_pose::RNA_HelixAssembler::set_model_and_remove_capping_residues(bool) –> void

set_scorefxn(self: pyrosetta.rosetta.core.import_pose.RNA_HelixAssembler, setting: pyrosetta.rosetta.core.scoring.ScoreFunction) → None¶: C++: core::import_pose::RNA_HelixAssembler::set_scorefxn(class std::shared_ptr<class core::scoring::ScoreFunction>) –> void

use_phenix_geo(self: pyrosetta.rosetta.core.import_pose.RNA_HelixAssembler, setting: bool) → None¶: C++: core::import_pose::RNA_HelixAssembler::use_phenix_geo(const bool) –> void

class pyrosetta.rosetta.core.import_pose.RNA_JumpMover¶

Bases: pybind11_object

add_new_RNA_jump(self: pyrosetta.rosetta.core.import_pose.RNA_JumpMover, pose: pyrosetta.rosetta.core.pose.Pose, which_jump: int, success: bool) → None¶: C++: core::import_pose::RNA_JumpMover::add_new_RNA_jump(class core::pose::Pose &, const unsigned long &, bool &) const –> void

assign(self: pyrosetta.rosetta.core.import_pose.RNA_JumpMover, : pyrosetta.rosetta.core.import_pose.RNA_JumpMover) → pyrosetta.rosetta.core.import_pose.RNA_JumpMover¶: C++: core::import_pose::RNA_JumpMover::operator=(const class core::import_pose::RNA_JumpMover &) –> class core::import_pose::RNA_JumpMover &

atom_level_domain_map(self: pyrosetta.rosetta.core.import_pose.RNA_JumpMover) → core::pose::toolbox::AtomLevelDomainMap¶: C++: core::import_pose::RNA_JumpMover::atom_level_domain_map() const –> class std::shared_ptr<const class core::pose::toolbox::AtomLevelDomainMap>

random_jump_change(self: pyrosetta.rosetta.core.import_pose.RNA_JumpMover, pose: pyrosetta.rosetta.core.pose.Pose) → bool¶: C++: core::import_pose::RNA_JumpMover::random_jump_change(class core::pose::Pose &) const –> bool

rna_pairing_list(self: pyrosetta.rosetta.core.import_pose.RNA_JumpMover) → pyrosetta.rosetta.utility.vector1_core_pose_rna_BasePair¶: C++: core::import_pose::RNA_JumpMover::rna_pairing_list() const –> class utility::vector1<class core::pose::rna::BasePair, class std::allocator<class core::pose::rna::BasePair> >

set_chain_connections(self: pyrosetta.rosetta.core.import_pose.RNA_JumpMover, setting: pyrosetta.rosetta.utility.vector1_std_pair_utility_vector1_unsigned_long_std_allocator_unsigned_long_utility_vector1_unsigned_long_std_allocator_unsigned_long_t) → None¶: C++: core::import_pose::RNA_JumpMover::set_chain_connections(const class utility::vector1<struct std::pair<class utility::vector1<unsigned long, class std::allocator<unsigned long> >, class utility::vector1<unsigned long, class std::allocator<unsigned long> > >, class std::allocator<struct std::pair<class utility::vector1<unsigned long, class std::allocator<unsigned long> >, class utility::vector1<unsigned long, class std::allocator<unsigned long> > > > > &) –> void

set_rna_pairing_list(self: pyrosetta.rosetta.core.import_pose.RNA_JumpMover, setting: pyrosetta.rosetta.utility.vector1_core_pose_rna_BasePair) → None¶: C++: core::import_pose::RNA_JumpMover::set_rna_pairing_list(const class utility::vector1<class core::pose::rna::BasePair, class std::allocator<class core::pose::rna::BasePair> > &) –> void

pyrosetta.rosetta.core.import_pose.add_cutpoint_closed(pose: pyrosetta.rosetta.core.pose.Pose, res_list: pyrosetta.rosetta.utility.vector1_unsigned_long, cutpoint_closed: pyrosetta.rosetta.utility.vector1_unsigned_long) → None¶: C++: core::import_pose::add_cutpoint_closed(class core::pose::Pose &, const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &, const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &) –> void

pyrosetta.rosetta.core.import_pose.add_virtual_sugar_res(pose: pyrosetta.rosetta.core.pose.Pose, res_list: pyrosetta.rosetta.utility.vector1_unsigned_long, virtual_sugar_res: pyrosetta.rosetta.utility.vector1_unsigned_long) → None¶: C++: core::import_pose::add_virtual_sugar_res(class core::pose::Pose &, const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &, const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &) –> void

pyrosetta.rosetta.core.import_pose.build_pose(*args, **kwargs)¶

Overloaded function.

build_pose(fd: pyrosetta.rosetta.core.io.StructFileRep, pose: pyrosetta.rosetta.core.pose.Pose, residue_set: pyrosetta.rosetta.core.chemical.ResidueTypeSet) -> None

Create pose object, using given StructFileRep object.: If PDB cleanin specified - it will be applied first. Constructs a ImportPoseOptions object from the command line

C++: core::import_pose::build_pose(class std::shared_ptr<class core::io::StructFileRep>, class core::pose::Pose &, const class core::chemical::ResidueTypeSet &) –> void

build_pose(fd: pyrosetta.rosetta.core.io.StructFileRep, pose: pyrosetta.rosetta.core.pose.Pose, residue_set: pyrosetta.rosetta.core.chemical.ResidueTypeSet, options: core::import_pose::ImportPoseOptions) -> None

Create pose object, using given StructFileRep object.: If PDB cleanin specified - it will be applied first

C++: core::import_pose::build_pose(class std::shared_ptr<class core::io::StructFileRep>, class core::pose::Pose &, const class core::chemical::ResidueTypeSet &, const class core::import_pose::ImportPoseOptions &) –> void

pyrosetta.rosetta.core.import_pose.build_pose_as_is(fd: pyrosetta.rosetta.core.io.StructFileRep, pose: pyrosetta.rosetta.core.pose.Pose, residue_set: pyrosetta.rosetta.core.chemical.ResidueTypeSet, options: core::import_pose::ImportPoseOptions) → None¶

Create pose object, using given StructFileRep object.: No PDB cleanin will be appliend.

C++: core::import_pose::build_pose_as_is(class std::shared_ptr<class core::io::StructFileRep>, class core::pose::Pose &, const class core::chemical::ResidueTypeSet &, const class core::import_pose::ImportPoseOptions &) –> void

pyrosetta.rosetta.core.import_pose.build_pose_as_is2(fd: pyrosetta.rosetta.core.io.StructFileRep, pose: pyrosetta.rosetta.core.pose.Pose, residue_set: pyrosetta.rosetta.core.chemical.ResidueTypeSet, missing: pyrosetta.rosetta.core.id.AtomID_Map_bool_t, options: core::import_pose::ImportPoseOptions) → None¶: C++: core::import_pose::build_pose_as_is2(class std::shared_ptr<const class core::io::StructFileRep>, class core::pose::Pose &, const class core::chemical::ResidueTypeSet &, class core::id::AtomID_Map<bool> &, const class core::import_pose::ImportPoseOptions &) –> void

pyrosetta.rosetta.core.import_pose.centroid_pose_from_pdb(*args, **kwargs)¶

Overloaded function.

centroid_pose_from_pdb(pose: pyrosetta.rosetta.core.pose.Pose, filename: str) -> None
centroid_pose_from_pdb(pose: pyrosetta.rosetta.core.pose.Pose, filename: str, read_fold_tree: bool) -> None

Reads in data from input PDB <filename> and stores it in the Pose: <pose> using the CENTROID ResidueTypeSet (centroid)

C++: core::import_pose::centroid_pose_from_pdb(class core::pose::Pose &, const std::string &, bool) –> void

pyrosetta.rosetta.core.import_pose.check_extra_minimize_res_are_input(extra_minimize_res: pyrosetta.rosetta.utility.vector1_unsigned_long, input_domain_map: pyrosetta.rosetta.utility.vector1_unsigned_long) → None¶: C++: core::import_pose::check_extra_minimize_res_are_input(const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &, const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &) –> void

pyrosetta.rosetta.core.import_pose.check_working_res(working_res: pyrosetta.rosetta.utility.vector1_unsigned_long, input_domain_map: pyrosetta.rosetta.utility.vector1_unsigned_long, sample_res: pyrosetta.rosetta.utility.vector1_unsigned_long) → None¶: C++: core::import_pose::check_working_res(const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &, const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &, const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &) –> void

pyrosetta.rosetta.core.import_pose.cleanup(*args, **kwargs)¶

Overloaded function.

cleanup(pose: pyrosetta.rosetta.core.pose.Pose) -> None
cleanup(pose: pyrosetta.rosetta.core.pose.Pose, force_cut_at_rna_chainbreak: bool) -> None

C++: core::import_pose::cleanup(class core::pose::Pose &, const bool) –> void

pyrosetta.rosetta.core.import_pose.compare_RNA_char(char1: str, char2: str) → bool¶: C++: core::import_pose::compare_RNA_char(const char, const char) –> bool

pyrosetta.rosetta.core.import_pose.compare_RNA_secstruct(char1: str, char2: str) → bool¶: C++: core::import_pose::compare_RNA_secstruct(const char, const char) –> bool

pyrosetta.rosetta.core.import_pose.convert_based_on_match_type(RNA_string: str, type: int) → str¶: C++: core::import_pose::convert_based_on_match_type(const std::string &, const unsigned long) –> const std::string

pyrosetta.rosetta.core.import_pose.define_chains(pose: pyrosetta.rosetta.core.pose.Pose, all_res_in_chain: pyrosetta.rosetta.utility.vector1_utility_vector1_unsigned_long_std_allocator_unsigned_long_t, all_fixed_res_in_chain: pyrosetta.rosetta.utility.vector1_utility_vector1_unsigned_long_std_allocator_unsigned_long_t, res_list: pyrosetta.rosetta.utility.vector1_unsigned_long, extra_min_res: pyrosetta.rosetta.utility.vector1_unsigned_long) → None¶: C++: core::import_pose::define_chains(const class core::pose::Pose &, class utility::vector1<class utility::vector1<unsigned long, class std::allocator<unsigned long> >, class std::allocator<class utility::vector1<unsigned long, class std::allocator<unsigned long> > > > &, class utility::vector1<class utility::vector1<unsigned long, class std::allocator<unsigned long> >, class std::allocator<class utility::vector1<unsigned long, class std::allocator<unsigned long> > > > &, const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &, const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &) –> void

pyrosetta.rosetta.core.import_pose.determine_file_type(contents_of_file: str) → pyrosetta.rosetta.core.import_pose.FileType¶

Determine what file type is passed to function: there should only be one function that calls this, pose_from_file and only calls it when the filetype is unknown

C++: core::import_pose::determine_file_type(const std::string &) –> enum core::import_pose::FileType

pyrosetta.rosetta.core.import_pose.extension_from_filetype(filetype: pyrosetta.rosetta.core.import_pose.FileType) → str¶

Given a filetype, return the string for the extension.

Extensions are in lowercase (e.g. “pdb”, “cif”, “mmtf”), etc.

Vikram K. Mulligan (vmulligan.org).

C++: core::import_pose::extension_from_filetype(const enum core::import_pose::FileType) –> std::string

pyrosetta.rosetta.core.import_pose.figure_out_dock_domain_map(cutpoint_open_in_full_model: pyrosetta.rosetta.utility.vector1_unsigned_long, pose_res_lists: pyrosetta.rosetta.utility.vector1_utility_vector1_unsigned_long_std_allocator_unsigned_long_t, working_res: pyrosetta.rosetta.utility.vector1_unsigned_long, sample_res: pyrosetta.rosetta.utility.vector1_unsigned_long, nres: int) → pyrosetta.rosetta.utility.vector1_unsigned_long¶: C++: core::import_pose::figure_out_dock_domain_map(class utility::vector1<unsigned long, class std::allocator<unsigned long> > &, const class utility::vector1<class utility::vector1<unsigned long, class std::allocator<unsigned long> >, class std::allocator<class utility::vector1<unsigned long, class std::allocator<unsigned long> > > > &, const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &, const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &, const unsigned long) –> class utility::vector1<unsigned long, class std::allocator<unsigned long> >

pyrosetta.rosetta.core.import_pose.figure_out_fixed_domain_map(input_domain_map: pyrosetta.rosetta.utility.vector1_unsigned_long, extra_minimize_res: pyrosetta.rosetta.utility.vector1_unsigned_long) → pyrosetta.rosetta.utility.vector1_unsigned_long¶: C++: core::import_pose::figure_out_fixed_domain_map(const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &, const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &) –> class utility::vector1<unsigned long, class std::allocator<unsigned long> >

pyrosetta.rosetta.core.import_pose.figure_out_motif_mode(extra_min_res: pyrosetta.rosetta.utility.vector1_unsigned_long, terminal_res: pyrosetta.rosetta.utility.vector1_unsigned_long, working_res: pyrosetta.rosetta.utility.vector1_unsigned_long, input_domain_map: pyrosetta.rosetta.utility.vector1_unsigned_long, cutpoint_open_in_full_model: pyrosetta.rosetta.utility.vector1_unsigned_long) → None¶: C++: core::import_pose::figure_out_motif_mode(class utility::vector1<unsigned long, class std::allocator<unsigned long> > &, class utility::vector1<unsigned long, class std::allocator<unsigned long> > &, const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &, const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &, const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &) –> void

pyrosetta.rosetta.core.import_pose.figure_out_sample_res(input_domain_map: pyrosetta.rosetta.utility.vector1_unsigned_long, working_res: pyrosetta.rosetta.utility.vector1_unsigned_long) → pyrosetta.rosetta.utility.vector1_unsigned_long¶: C++: core::import_pose::figure_out_sample_res(const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &, const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &) –> class utility::vector1<unsigned long, class std::allocator<unsigned long> >

pyrosetta.rosetta.core.import_pose.figure_out_working_res(input_domain_map: pyrosetta.rosetta.utility.vector1_unsigned_long, sample_res: pyrosetta.rosetta.utility.vector1_unsigned_long) → pyrosetta.rosetta.utility.vector1_unsigned_long¶: C++: core::import_pose::figure_out_working_res(const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &, const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &) –> class utility::vector1<unsigned long, class std::allocator<unsigned long> >

pyrosetta.rosetta.core.import_pose.get_anchor_rsd(pose: pyrosetta.rosetta.core.pose.Pose) → int¶: C++: core::import_pose::get_anchor_rsd(const class core::pose::Pose &) –> unsigned long

pyrosetta.rosetta.core.import_pose.get_chain(i: int, all_res_in_chain: pyrosetta.rosetta.utility.vector1_utility_vector1_unsigned_long_std_allocator_unsigned_long_t) → int¶: C++: core::import_pose::get_chain(const unsigned long, const class utility::vector1<class utility::vector1<unsigned long, class std::allocator<unsigned long> >, class std::allocator<class utility::vector1<unsigned long, class std::allocator<unsigned long> > > > &) –> unsigned long

pyrosetta.rosetta.core.import_pose.get_extra_cutpoints_from_names(nres: int, cutpoints: pyrosetta.rosetta.utility.vector1_unsigned_long, non_standard_residue_map: pyrosetta.rosetta.std.map_unsigned_long_std_string) → None¶: C++: core::import_pose::get_extra_cutpoints_from_names(const unsigned long, class utility::vector1<unsigned long, class std::allocator<unsigned long> > &, const class std::map<unsigned long, std::string, struct std::less<unsigned long>, class std::allocator<struct std::pair<const unsigned long, std::string > > > &) –> void

pyrosetta.rosetta.core.import_pose.get_other_poses(other_poses: pyrosetta.rosetta.utility.vector1_std_shared_ptr_core_pose_Pose_t, other_files: pyrosetta.rosetta.utility.vector1_std_string, rsd_set: pyrosetta.rosetta.core.chemical.ResidueTypeSet) → None¶: C++: core::import_pose::get_other_poses(class utility::vector1<class std::shared_ptr<class core::pose::Pose>, class std::allocator<class std::shared_ptr<class core::pose::Pose> > > &, const class utility::vector1<std::string, class std::allocator<std::string > > &, class std::shared_ptr<const class core::chemical::ResidueTypeSet>) –> void

pyrosetta.rosetta.core.import_pose.get_pdb_and_cleanup(*args, **kwargs)¶

Overloaded function.

get_pdb_and_cleanup(input_file: str) -> pyrosetta.rosetta.core.pose.Pose

C++: core::import_pose::get_pdb_and_cleanup(const std::string &) –> class std::shared_ptr<class core::pose::Pose>

get_pdb_and_cleanup(input_file: str, rsd_set: pyrosetta.rosetta.core.chemical.ResidueTypeSet) -> pyrosetta.rosetta.core.pose.Pose

C++: core::import_pose::get_pdb_and_cleanup(const std::string &, class std::shared_ptr<const class core::chemical::ResidueTypeSet>) –> class std::shared_ptr<class core::pose::Pose>

pyrosetta.rosetta.core.import_pose.get_pdb_with_full_model_info(input_file: str, rsd_set: pyrosetta.rosetta.core.chemical.ResidueTypeSet) → pyrosetta.rosetta.core.pose.Pose¶: C++: core::import_pose::get_pdb_with_full_model_info(const std::string &, class std::shared_ptr<const class core::chemical::ResidueTypeSet>) –> class std::shared_ptr<class core::pose::Pose>

pyrosetta.rosetta.core.import_pose.get_sequence_information(*args, **kwargs)¶

Overloaded function.

get_sequence_information(fasta_file: str, cutpoint_open_in_full_model: pyrosetta.rosetta.utility.vector1_unsigned_long) -> core::pose::full_model_info::FullModelParameters
get_sequence_information(fasta_file: str, cutpoint_open_in_full_model: pyrosetta.rosetta.utility.vector1_unsigned_long, add_virt: bool) -> core::pose::full_model_info::FullModelParameters

C++: core::import_pose::get_sequence_information(const std::string &, class utility::vector1<unsigned long, class std::allocator<unsigned long> > &, const bool) –> class std::shared_ptr<class core::pose::full_model_info::FullModelParameters>

pyrosetta.rosetta.core.import_pose.get_tree(*args, **kwargs)¶

Overloaded function.

get_tree(pose: pyrosetta.rosetta.core.pose.Pose, cuts: pyrosetta.rosetta.utility.vector1_unsigned_long, jump_partners1: pyrosetta.rosetta.utility.vector1_unsigned_long, jump_partners2: pyrosetta.rosetta.utility.vector1_unsigned_long) -> pyrosetta.rosetta.core.kinematics.FoldTree

C++: core::import_pose::get_tree(const class core::pose::Pose &, const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &, const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &, const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &) –> class core::kinematics::FoldTree

get_tree(nres: int, cuts: pyrosetta.rosetta.utility.vector1_unsigned_long, jump_partners1: pyrosetta.rosetta.utility.vector1_unsigned_long, jump_partners2: pyrosetta.rosetta.utility.vector1_unsigned_long, jump_atoms1: pyrosetta.rosetta.utility.vector1_std_string, jump_atoms2: pyrosetta.rosetta.utility.vector1_std_string) -> pyrosetta.rosetta.core.kinematics.FoldTree

C++: core::import_pose::get_tree(const unsigned long, const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &, const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &, const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &, const class utility::vector1<std::string, class std::allocator<std::string > > &, const class utility::vector1<std::string, class std::allocator<std::string > > &) –> class core::kinematics::FoldTree

pyrosetta.rosetta.core.import_pose.initialize_native_and_align_pose(native_pose: pyrosetta.rosetta.core.pose.Pose, align_pose: pyrosetta.rosetta.core.pose.Pose, rsd_set: pyrosetta.rosetta.core.chemical.ResidueTypeSet, start_pose: pyrosetta.rosetta.core.pose.Pose) → None¶: C++: core::import_pose::initialize_native_and_align_pose(class std::shared_ptr<class core::pose::Pose> &, class std::shared_ptr<class core::pose::Pose> &, class std::shared_ptr<const class core::chemical::ResidueTypeSet>, class std::shared_ptr<const class core::pose::Pose>) –> void

pyrosetta.rosetta.core.import_pose.initialize_pose_and_other_poses_from_command_line(rsd_set: pyrosetta.rosetta.core.chemical.ResidueTypeSet) → pyrosetta.rosetta.core.pose.Pose¶: C++: core::import_pose::initialize_pose_and_other_poses_from_command_line(class std::shared_ptr<const class core::chemical::ResidueTypeSet>) –> class std::shared_ptr<class core::pose::Pose>

pyrosetta.rosetta.core.import_pose.initialize_pose_and_other_poses_from_options(rsd_set: pyrosetta.rosetta.core.chemical.ResidueTypeSet, options: pyrosetta.rosetta.utility.options.OptionCollection) → pyrosetta.rosetta.core.pose.Pose¶: C++: core::import_pose::initialize_pose_and_other_poses_from_options(class std::shared_ptr<const class core::chemical::ResidueTypeSet>, const class utility::options::OptionCollection &) –> class std::shared_ptr<class core::pose::Pose>

pyrosetta.rosetta.core.import_pose.initialize_pose_and_other_poses_from_options_and_input_poses(rsd_set: pyrosetta.rosetta.core.chemical.ResidueTypeSet, options: pyrosetta.rosetta.utility.options.OptionCollection, input_poses: pyrosetta.rosetta.utility.vector1_std_shared_ptr_core_pose_Pose_t) → pyrosetta.rosetta.core.pose.Pose¶: C++: core::import_pose::initialize_pose_and_other_poses_from_options_and_input_poses(class std::shared_ptr<const class core::chemical::ResidueTypeSet>, const class utility::options::OptionCollection &, class utility::vector1<class std::shared_ptr<class core::pose::Pose>, class std::allocator<class std::shared_ptr<class core::pose::Pose> > > &) –> class std::shared_ptr<class core::pose::Pose>

pyrosetta.rosetta.core.import_pose.involved_in_phosphate_torsion(atomname: str) → bool¶: C++: core::import_pose::involved_in_phosphate_torsion(std::string) –> bool

pyrosetta.rosetta.core.import_pose.is_blank_seq(c: str) → bool¶: C++: core::import_pose::is_blank_seq(const char &) –> bool

pyrosetta.rosetta.core.import_pose.just_modeling_RNA(fasta_files: pyrosetta.rosetta.utility.vector1_std_string) → bool¶: C++: core::import_pose::just_modeling_RNA(const class utility::vector1<std::string, class std::allocator<std::string > > &) –> bool

pyrosetta.rosetta.core.import_pose.look_for_dna(fasta_sequences: pyrosetta.rosetta.utility.vector1_std_shared_ptr_core_sequence_Sequence_t) → None¶: C++: core::import_pose::look_for_dna(class utility::vector1<class std::shared_ptr<class core::sequence::Sequence>, class std::allocator<class std::shared_ptr<class core::sequence::Sequence> > > &) –> void

pyrosetta.rosetta.core.import_pose.make_coarse_pose(pose: pyrosetta.rosetta.core.pose.Pose, coarse_pose: pyrosetta.rosetta.core.pose.Pose) → None¶: C++: core::import_pose::make_coarse_pose(const class core::pose::Pose &, class core::pose::Pose &) –> void

pyrosetta.rosetta.core.import_pose.make_extended_coarse_pose(coarse_pose: pyrosetta.rosetta.core.pose.Pose, full_sequence: str) → None¶: C++: core::import_pose::make_extended_coarse_pose(class core::pose::Pose &, const std::string &) –> void

pyrosetta.rosetta.core.import_pose.poseOPs_from_files(*args, **kwargs)¶

Overloaded function.

poseOPs_from_files(filenames: pyrosetta.rosetta.utility.vector1_std_string) -> pyrosetta.rosetta.utility.vector1_std_shared_ptr_core_pose_Pose_t
poseOPs_from_files(filenames: pyrosetta.rosetta.utility.vector1_std_string, read_fold_tree: bool) -> pyrosetta.rosetta.utility.vector1_std_shared_ptr_core_pose_Pose_t
poseOPs_from_files(filenames: pyrosetta.rosetta.utility.vector1_std_string, read_fold_tree: bool, type: pyrosetta.rosetta.core.import_pose.FileType) -> pyrosetta.rosetta.utility.vector1_std_shared_ptr_core_pose_Pose_t

C++: core::import_pose::poseOPs_from_files(const class utility::vector1<std::string, class std::allocator<std::string > > &, bool, enum core::import_pose::FileType) –> class utility::vector1<class std::shared_ptr<class core::pose::Pose>, class std::allocator<class std::shared_ptr<class core::pose::Pose> > >

poseOPs_from_files(filenames: pyrosetta.rosetta.utility.vector1_std_string, options: core::import_pose::ImportPoseOptions) -> pyrosetta.rosetta.utility.vector1_std_shared_ptr_core_pose_Pose_t
poseOPs_from_files(filenames: pyrosetta.rosetta.utility.vector1_std_string, options: core::import_pose::ImportPoseOptions, read_fold_tree: bool) -> pyrosetta.rosetta.utility.vector1_std_shared_ptr_core_pose_Pose_t
poseOPs_from_files(filenames: pyrosetta.rosetta.utility.vector1_std_string, options: core::import_pose::ImportPoseOptions, read_fold_tree: bool, type: pyrosetta.rosetta.core.import_pose.FileType) -> pyrosetta.rosetta.utility.vector1_std_shared_ptr_core_pose_Pose_t

C++: core::import_pose::poseOPs_from_files(const class utility::vector1<std::string, class std::allocator<std::string > > &, const class core::import_pose::ImportPoseOptions &, bool, enum core::import_pose::FileType) –> class utility::vector1<class std::shared_ptr<class core::pose::Pose>, class std::allocator<class std::shared_ptr<class core::pose::Pose> > >

poseOPs_from_files(residue_set: pyrosetta.rosetta.core.chemical.ResidueTypeSet, filenames: pyrosetta.rosetta.utility.vector1_std_string, options: core::import_pose::ImportPoseOptions, read_fold_tree: bool) -> pyrosetta.rosetta.utility.vector1_std_shared_ptr_core_pose_Pose_t
poseOPs_from_files(residue_set: pyrosetta.rosetta.core.chemical.ResidueTypeSet, filenames: pyrosetta.rosetta.utility.vector1_std_string, options: core::import_pose::ImportPoseOptions, read_fold_tree: bool, type: pyrosetta.rosetta.core.import_pose.FileType) -> pyrosetta.rosetta.utility.vector1_std_shared_ptr_core_pose_Pose_t

C++: core::import_pose::poseOPs_from_files(const class core::chemical::ResidueTypeSet &, const class utility::vector1<std::string, class std::allocator<std::string > > &, const class core::import_pose::ImportPoseOptions &, bool, enum core::import_pose::FileType) –> class utility::vector1<class std::shared_ptr<class core::pose::Pose>, class std::allocator<class std::shared_ptr<class core::pose::Pose> > >

pyrosetta.rosetta.core.import_pose.pose_from_file(*args, **kwargs)¶

Overloaded function.

pose_from_file(filename: str) -> pyrosetta.rosetta.core.pose.Pose
pose_from_file(filename: str, read_fold_tree: bool) -> pyrosetta.rosetta.core.pose.Pose
pose_from_file(filename: str, read_fold_tree: bool, type: pyrosetta.rosetta.core.import_pose.FileType) -> pyrosetta.rosetta.core.pose.Pose

Returns a PoseOP object from the Pose created from input: PDB <filename>

: in PyRosetta, this will return a Pose object

example(s):
pose = pose_from_file(“YFP.pdb”)

See also:
Pose PDBInfo make_pose_from_sequence pose_from_rcsb pose_from_sequence

C++: core::import_pose::pose_from_file(const std::string &, bool, enum core::import_pose::FileType) –> class std::shared_ptr<class core::pose::Pose>

pose_from_file(filename: str, options: core::import_pose::ImportPoseOptions, read_fold_tree: bool, type: pyrosetta.rosetta.core.import_pose.FileType) -> pyrosetta.rosetta.core.pose.Pose

Returns a PoseOP object from the Pose created from input: PDB <filename>, taking a set of custom ImportPoseOptions parameters.

: in PyRosetta, this will return a Pose object

example(s):
pose = pose_from_file(“YFP.pdb”)

See also:
Pose PDBInfo make_pose_from_sequence pose_from_rcsb pose_from_sequence

C++: core::import_pose::pose_from_file(const std::string &, const class core::import_pose::ImportPoseOptions &, bool, enum core::import_pose::FileType) –> class std::shared_ptr<class core::pose::Pose>

pose_from_file(residue_set: pyrosetta.rosetta.core.chemical.ResidueTypeSet, filename: str) -> pyrosetta.rosetta.core.pose.Pose
pose_from_file(residue_set: pyrosetta.rosetta.core.chemical.ResidueTypeSet, filename: str, read_fold_tree: bool) -> pyrosetta.rosetta.core.pose.Pose
pose_from_file(residue_set: pyrosetta.rosetta.core.chemical.ResidueTypeSet, filename: str, read_fold_tree: bool, type: pyrosetta.rosetta.core.import_pose.FileType) -> pyrosetta.rosetta.core.pose.Pose

Returns a PoseOP object from the Pose created by reading the input: PDB <filename>, this constructor allows for a non-default ResidueTypeSet <residue_set>

C++: core::import_pose::pose_from_file(const class core::chemical::ResidueTypeSet &, const std::string &, bool, enum core::import_pose::FileType) –> class std::shared_ptr<class core::pose::Pose>

pose_from_file(pose: pyrosetta.rosetta.core.pose.Pose, residue_set: pyrosetta.rosetta.core.chemical.ResidueTypeSet, filename: str, options: core::import_pose::ImportPoseOptions) -> None
pose_from_file(pose: pyrosetta.rosetta.core.pose.Pose, residue_set: pyrosetta.rosetta.core.chemical.ResidueTypeSet, filename: str, options: core::import_pose::ImportPoseOptions, read_fold_tree: bool) -> None
pose_from_file(pose: pyrosetta.rosetta.core.pose.Pose, residue_set: pyrosetta.rosetta.core.chemical.ResidueTypeSet, filename: str, options: core::import_pose::ImportPoseOptions, read_fold_tree: bool, file_type: pyrosetta.rosetta.core.import_pose.FileType) -> None

C++: core::import_pose::pose_from_file(class core::pose::Pose &, const class core::chemical::ResidueTypeSet &, const std::string &, const class core::import_pose::ImportPoseOptions &, bool, enum core::import_pose::FileType) –> void

pose_from_file(pose: pyrosetta.rosetta.core.pose.Pose, residue_set: pyrosetta.rosetta.core.chemical.ResidueTypeSet, filename: str) -> None
pose_from_file(pose: pyrosetta.rosetta.core.pose.Pose, residue_set: pyrosetta.rosetta.core.chemical.ResidueTypeSet, filename: str, read_fold_tree: bool) -> None
pose_from_file(pose: pyrosetta.rosetta.core.pose.Pose, residue_set: pyrosetta.rosetta.core.chemical.ResidueTypeSet, filename: str, read_fold_tree: bool, type: pyrosetta.rosetta.core.import_pose.FileType) -> None

Reads in data from input PDB <filename> and stores it in the Pose: <pose>, this constructor allows for a non-default ResidueTypeSet <residue_set>

C++: core::import_pose::pose_from_file(class core::pose::Pose &, const class core::chemical::ResidueTypeSet &, const std::string &, bool, enum core::import_pose::FileType) –> void

pose_from_file(pose: pyrosetta.rosetta.core.pose.Pose, filename: str) -> None
pose_from_file(pose: pyrosetta.rosetta.core.pose.Pose, filename: str, read_fold_tree: bool) -> None
pose_from_file(pose: pyrosetta.rosetta.core.pose.Pose, filename: str, read_fold_tree: bool, type: pyrosetta.rosetta.core.import_pose.FileType) -> None

Reads in data from input PDB <filename> and stores it in the Pose: <pose>, uses the FA_STANDARD ResidueTypeSet (fullatom) by default

: will use centroid if in::file::centroid_input is true

example(s):
pose_from_file(pose,”YFP.pdb”)

See also:
Pose PDBInfo

C++: core::import_pose::pose_from_file(class core::pose::Pose &, const std::string &, bool, enum core::import_pose::FileType) –> void

pose_from_file(pose: pyrosetta.rosetta.core.pose.Pose, filename: str, options: core::import_pose::ImportPoseOptions) -> None
pose_from_file(pose: pyrosetta.rosetta.core.pose.Pose, filename: str, options: core::import_pose::ImportPoseOptions, read_fold_tree: bool) -> None
pose_from_file(pose: pyrosetta.rosetta.core.pose.Pose, filename: str, options: core::import_pose::ImportPoseOptions, read_fold_tree: bool, type: pyrosetta.rosetta.core.import_pose.FileType) -> None

C++: core::import_pose::pose_from_file(class core::pose::Pose &, const std::string &, const class core::import_pose::ImportPoseOptions &, bool, enum core::import_pose::FileType) –> void

pose_from_file(poses: pyrosetta.rosetta.utility.vector1_core_pose_Pose, residue_set: pyrosetta.rosetta.core.chemical.ResidueTypeSet, filename: str) -> None
pose_from_file(poses: pyrosetta.rosetta.utility.vector1_core_pose_Pose, residue_set: pyrosetta.rosetta.core.chemical.ResidueTypeSet, filename: str, read_fold_tree: bool) -> None
pose_from_file(poses: pyrosetta.rosetta.utility.vector1_core_pose_Pose, residue_set: pyrosetta.rosetta.core.chemical.ResidueTypeSet, filename: str, read_fold_tree: bool, type: pyrosetta.rosetta.core.import_pose.FileType) -> None

Reads data from an input PDB containing multiple models named: <filename> and stores it in a vector of Pose objects named <poses> using ResidueTypeSet <residue_set>

C++: core::import_pose::pose_from_file(class utility::vector1<class core::pose::Pose, class std::allocator<class core::pose::Pose> > &, const class core::chemical::ResidueTypeSet &, const std::string &, bool, enum core::import_pose::FileType) –> void

pose_from_file(poses: pyrosetta.rosetta.utility.vector1_core_pose_Pose, residue_set: pyrosetta.rosetta.core.chemical.ResidueTypeSet, filename: str, options: core::import_pose::ImportPoseOptions) -> None
pose_from_file(poses: pyrosetta.rosetta.utility.vector1_core_pose_Pose, residue_set: pyrosetta.rosetta.core.chemical.ResidueTypeSet, filename: str, options: core::import_pose::ImportPoseOptions, read_fold_tree: bool) -> None
pose_from_file(poses: pyrosetta.rosetta.utility.vector1_core_pose_Pose, residue_set: pyrosetta.rosetta.core.chemical.ResidueTypeSet, filename: str, options: core::import_pose::ImportPoseOptions, read_fold_tree: bool, type: pyrosetta.rosetta.core.import_pose.FileType) -> None

C++: core::import_pose::pose_from_file(class utility::vector1<class core::pose::Pose, class std::allocator<class core::pose::Pose> > &, const class core::chemical::ResidueTypeSet &, const std::string &, const class core::import_pose::ImportPoseOptions &, bool, enum core::import_pose::FileType) –> void

pose_from_file(poses: pyrosetta.rosetta.utility.vector1_core_pose_Pose, filename: str) -> None
pose_from_file(poses: pyrosetta.rosetta.utility.vector1_core_pose_Pose, filename: str, read_fold_tree: bool) -> None
pose_from_file(poses: pyrosetta.rosetta.utility.vector1_core_pose_Pose, filename: str, read_fold_tree: bool, type: pyrosetta.rosetta.core.import_pose.FileType) -> None

Reads data from an input PDB containing multiple models named: <filename> and stores it in a vector of Pose objects named <poses> using the FA_STANDARD ResidueTypeSet (fullatom)

C++: core::import_pose::pose_from_file(class utility::vector1<class core::pose::Pose, class std::allocator<class core::pose::Pose> > &, const std::string &, bool, enum core::import_pose::FileType) –> void

pyrosetta.rosetta.core.import_pose.pose_from_pdb_stream(pose: pyrosetta.rosetta.core.pose.Pose, pdb_stream: pyrosetta.rosetta.std.istream, filename: str, options: core::import_pose::ImportPoseOptions) → None¶: C++: core::import_pose::pose_from_pdb_stream(class core::pose::Pose &, std::istream &, const std::string &, const class core::import_pose::ImportPoseOptions &) –> void

pyrosetta.rosetta.core.import_pose.pose_from_pdbstring(*args, **kwargs)¶

Overloaded function.

pose_from_pdbstring(pose: pyrosetta.rosetta.core.pose.Pose, pdbcontents: str) -> None
pose_from_pdbstring(pose: pyrosetta.rosetta.core.pose.Pose, pdbcontents: str, filename: str) -> None

C++: core::import_pose::pose_from_pdbstring(class core::pose::Pose &, const std::string &, const std::string &) –> void

pose_from_pdbstring(pose: pyrosetta.rosetta.core.pose.Pose, pdbcontents: str, options: core::import_pose::ImportPoseOptions) -> None
pose_from_pdbstring(pose: pyrosetta.rosetta.core.pose.Pose, pdbcontents: str, options: core::import_pose::ImportPoseOptions, filename: str) -> None

C++: core::import_pose::pose_from_pdbstring(class core::pose::Pose &, const std::string &, const class core::import_pose::ImportPoseOptions &, const std::string &) –> void

pose_from_pdbstring(pose: pyrosetta.rosetta.core.pose.Pose, pdbcontents: str, residue_set: pyrosetta.rosetta.core.chemical.ResidueTypeSet, filename: str) -> None

C++: core::import_pose::pose_from_pdbstring(class core::pose::Pose &, const std::string &, const class core::chemical::ResidueTypeSet &, const std::string &) –> void

pose_from_pdbstring(pose: pyrosetta.rosetta.core.pose.Pose, pdbcontents: str, residue_set: pyrosetta.rosetta.core.chemical.ResidueTypeSet, options: core::import_pose::ImportPoseOptions, filename: str) -> None

C++: core::import_pose::pose_from_pdbstring(class core::pose::Pose &, const std::string &, const class core::chemical::ResidueTypeSet &, const class core::import_pose::ImportPoseOptions &, const std::string &) –> void

pyrosetta.rosetta.core.import_pose.poses_from_files(*args, **kwargs)¶

Overloaded function.

poses_from_files(filenames: pyrosetta.rosetta.utility.vector1_std_string) -> pyrosetta.rosetta.utility.vector1_core_pose_Pose
poses_from_files(filenames: pyrosetta.rosetta.utility.vector1_std_string, read_fold_tree: bool) -> pyrosetta.rosetta.utility.vector1_core_pose_Pose
poses_from_files(filenames: pyrosetta.rosetta.utility.vector1_std_string, read_fold_tree: bool, type: pyrosetta.rosetta.core.import_pose.FileType) -> pyrosetta.rosetta.utility.vector1_core_pose_Pose

C++: core::import_pose::poses_from_files(const class utility::vector1<std::string, class std::allocator<std::string > > &, bool, enum core::import_pose::FileType) –> class utility::vector1<class core::pose::Pose, class std::allocator<class core::pose::Pose> >

poses_from_files(residue_set: pyrosetta.rosetta.core.chemical.ResidueTypeSet, filenames: pyrosetta.rosetta.utility.vector1_std_string, read_fold_tree: bool) -> pyrosetta.rosetta.utility.vector1_core_pose_Pose
poses_from_files(residue_set: pyrosetta.rosetta.core.chemical.ResidueTypeSet, filenames: pyrosetta.rosetta.utility.vector1_std_string, read_fold_tree: bool, type: pyrosetta.rosetta.core.import_pose.FileType) -> pyrosetta.rosetta.utility.vector1_core_pose_Pose

C++: core::import_pose::poses_from_files(const class core::chemical::ResidueTypeSet &, const class utility::vector1<std::string, class std::allocator<std::string > > &, bool, enum core::import_pose::FileType) –> class utility::vector1<class core::pose::Pose, class std::allocator<class core::pose::Pose> >

pyrosetta.rosetta.core.import_pose.process_input_file(*args, **kwargs)¶

Overloaded function.

process_input_file(silent_file: str, pose_list: pyrosetta.rosetta.utility.vector1_std_shared_ptr_core_pose_Pose_t) -> None
process_input_file(silent_file: str, pose_list: pyrosetta.rosetta.utility.vector1_std_shared_ptr_core_pose_Pose_t, is_pdb: bool) -> None
process_input_file(silent_file: str, pose_list: pyrosetta.rosetta.utility.vector1_std_shared_ptr_core_pose_Pose_t, is_pdb: bool, coarse_rna: bool) -> None

C++: core::import_pose::process_input_file(const std::string &, class utility::vector1<class std::shared_ptr<class core::pose::Pose>, class std::allocator<class std::shared_ptr<class core::pose::Pose> > > &, bool, bool) –> void

pyrosetta.rosetta.core.import_pose.put_in_cutpoint(pose: pyrosetta.rosetta.core.pose.Pose, i: int) → None¶: C++: core::import_pose::put_in_cutpoint(class core::pose::Pose &, const unsigned long) –> void

pyrosetta.rosetta.core.import_pose.read_additional_pdb_data(*args, **kwargs)¶

Overloaded function.

read_additional_pdb_data(file: str, pose: pyrosetta.rosetta.core.pose.Pose, fd: pyrosetta.rosetta.core.io.StructFileRep) -> None
read_additional_pdb_data(file: str, pose: pyrosetta.rosetta.core.pose.Pose, fd: pyrosetta.rosetta.core.io.StructFileRep, read_fold_tree: bool) -> None

C++: core::import_pose::read_additional_pdb_data(const std::string &, class core::pose::Pose &, class std::shared_ptr<const class core::io::StructFileRep>, bool) –> void

read_additional_pdb_data(file: str, pose: pyrosetta.rosetta.core.pose.Pose, options: core::import_pose::ImportPoseOptions) -> None
read_additional_pdb_data(file: str, pose: pyrosetta.rosetta.core.pose.Pose, options: core::import_pose::ImportPoseOptions, read_fold_tree: bool) -> None

C++: core::import_pose::read_additional_pdb_data(const std::string &, class core::pose::Pose &, const class core::import_pose::ImportPoseOptions &, bool) –> void

pyrosetta.rosetta.core.import_pose.read_all_poses(filenames: pyrosetta.rosetta.utility.vector1_std_string, poses: pyrosetta.rosetta.utility.vector1_std_shared_ptr_core_pose_Pose_t) → None¶: C++: core::import_pose::read_all_poses(const class utility::vector1<std::string, class std::allocator<std::string > > &, class utility::vector1<class std::shared_ptr<class core::pose::Pose>, class std::allocator<class std::shared_ptr<class core::pose::Pose> > > &) –> void

pyrosetta.rosetta.core.import_pose.remove_cutpoint_closed(pose: pyrosetta.rosetta.core.pose.Pose, i: int) → None¶: C++: core::import_pose::remove_cutpoint_closed(class core::pose::Pose &, const unsigned long) –> void

pyrosetta.rosetta.core.import_pose.remove_cutpoints_closed(pose: pyrosetta.rosetta.core.pose.Pose) → None¶: C++: core::import_pose::remove_cutpoints_closed(class core::pose::Pose &) –> void

pyrosetta.rosetta.core.import_pose.reorder_pose(pose: pyrosetta.rosetta.core.pose.Pose, res_list: pyrosetta.rosetta.utility.vector1_unsigned_long) → None¶: C++: core::import_pose::reorder_pose(class core::pose::Pose &, class utility::vector1<unsigned long, class std::allocator<unsigned long> > &) –> void

pyrosetta.rosetta.core.import_pose.setup_for_density_scoring(pose: pyrosetta.rosetta.core.pose.Pose) → None¶: C++: core::import_pose::setup_for_density_scoring(class core::pose::Pose &) –> void

pyrosetta.rosetta.core.import_pose.setup_jumps(pose: pyrosetta.rosetta.core.pose.Pose, jump_partners1: pyrosetta.rosetta.utility.vector1_unsigned_long, jump_partners2: pyrosetta.rosetta.utility.vector1_unsigned_long, chain_connections: pyrosetta.rosetta.utility.vector1_std_pair_unsigned_long_unsigned_long_t, all_res_in_chain: pyrosetta.rosetta.utility.vector1_utility_vector1_unsigned_long_std_allocator_unsigned_long_t, resnum_and_chain_and_segid_in_pose: Tuple[pyrosetta.rosetta.utility.vector1_int, pyrosetta.rosetta.utility.vector1_char, pyrosetta.rosetta.utility.vector1_std_string]) → None¶: C++: core::import_pose::setup_jumps(const class core::pose::Pose &, class utility::vector1<unsigned long, class std::allocator<unsigned long> > &, class utility::vector1<unsigned long, class std::allocator<unsigned long> > &, class utility::vector1<struct std::pair<unsigned long, unsigned long>, class std::allocator<struct std::pair<unsigned long, unsigned long> > > &, const class utility::vector1<class utility::vector1<unsigned long, class std::allocator<unsigned long> >, class std::allocator<class utility::vector1<unsigned long, class std::allocator<unsigned long> > > > &, const class std::tuple<class utility::vector1<int, class std::allocator<int> >, class utility::vector1<char, class std::allocator<char> >, class utility::vector1<std::string, class std::allocator<std::string > > > &) –> void

pyrosetta.rosetta.core.import_pose.setup_user_defined_jumps(jump_res: pyrosetta.rosetta.utility.vector1_unsigned_long, jump_partners1: pyrosetta.rosetta.utility.vector1_unsigned_long, jump_partners2: pyrosetta.rosetta.utility.vector1_unsigned_long, chain_connections: pyrosetta.rosetta.utility.vector1_std_pair_unsigned_long_unsigned_long_t, res_list: pyrosetta.rosetta.utility.vector1_unsigned_long, all_res_in_chain: pyrosetta.rosetta.utility.vector1_utility_vector1_unsigned_long_std_allocator_unsigned_long_t) → None¶: C++: core::import_pose::setup_user_defined_jumps(const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &, class utility::vector1<unsigned long, class std::allocator<unsigned long> > &, class utility::vector1<unsigned long, class std::allocator<unsigned long> > &, class utility::vector1<struct std::pair<unsigned long, unsigned long>, class std::allocator<struct std::pair<unsigned long, unsigned long> > > &, const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &, const class utility::vector1<class utility::vector1<unsigned long, class std::allocator<unsigned long> >, class std::allocator<class utility::vector1<unsigned long, class std::allocator<unsigned long> > > > &) –> void

pyrosetta.rosetta.core.import_pose.setup_water_bank_for_magnesiums(non_standard_residue_map: pyrosetta.rosetta.std.map_unsigned_long_std_string, fasta_sequences: pyrosetta.rosetta.utility.vector1_std_shared_ptr_core_sequence_Sequence_t) → None¶: C++: core::import_pose::setup_water_bank_for_magnesiums(class std::map<unsigned long, std::string, struct std::less<unsigned long>, class std::allocator<struct std::pair<const unsigned long, std::string > > > &, class utility::vector1<class std::shared_ptr<class core::sequence::Sequence>, class std::allocator<class std::shared_ptr<class core::sequence::Sequence> > > &) –> void

pyrosetta.rosetta.core.import_pose.update_fixed_domain_from_extra_minimize_jump_res(fixed_domain: pyrosetta.rosetta.utility.vector1_unsigned_long, pose: pyrosetta.rosetta.core.pose.Pose, res_list: pyrosetta.rosetta.utility.vector1_unsigned_long, extra_minimize_jump_res: pyrosetta.rosetta.utility.vector1_unsigned_long) → None¶: C++: core::import_pose::update_fixed_domain_from_extra_minimize_jump_res(class utility::vector1<unsigned long, class std::allocator<unsigned long> > &, const class core::pose::Pose &, const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &, const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &) –> void

pyrosetta.rosetta.core.import_pose.update_jump_res(jump_res: pyrosetta.rosetta.utility.vector1_unsigned_long, extra_minimize_jump_res: pyrosetta.rosetta.utility.vector1_unsigned_long) → None¶: C++: core::import_pose::update_jump_res(class utility::vector1<unsigned long, class std::allocator<unsigned long> > &, const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &) –> void

pyrosetta.rosetta.core.import_pose.update_pose_fold_tree(pose: pyrosetta.rosetta.core.pose.Pose, res_list: pyrosetta.rosetta.utility.vector1_unsigned_long, extra_min_res: pyrosetta.rosetta.utility.vector1_unsigned_long, sample_res: pyrosetta.rosetta.utility.vector1_unsigned_long, jump_res: pyrosetta.rosetta.utility.vector1_unsigned_long, full_model_parameters: core::pose::full_model_info::FullModelParameters) → None¶: C++: core::import_pose::update_pose_fold_tree(class core::pose::Pose &, const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &, const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &, const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &, const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &, const class core::pose::full_model_info::FullModelParameters &) –> void