import_pose

Bindings for core::import_pose namespace

class pyrosetta.rosetta.core.import_pose.FileType

Bases: pybind11_builtins.pybind11_object

Members:

PDB_file

CIF_file

Unknown_file

class pyrosetta.rosetta.core.import_pose.ImportPoseOptions

Bases: pyrosetta.rosetta.core.io.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!

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

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

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

keep_input_protonation_state(self: pyrosetta.rosetta.core.io.StructFileRepOptions) → bool

C++: core::io::StructFileRepOptions::keep_input_protonation_state() const –> 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

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_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: pyrosetta.rosetta.utility.tag.Tag) → None

C++: core::import_pose::ImportPoseOptions::parse_my_tag(class std::shared_ptr<const class utility::tag::Tag>) –> void

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 class std::basic_string<char> &) –> 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 class std::basic_string<char> &) –> 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 class std::basic_string<char> &) –> 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

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_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_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

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_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_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_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<class std::basic_string<char>, class std::allocator<class std::basic_string<char> > > &) –> 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

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

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

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

class pyrosetta.rosetta.core.import_pose.PDBSilentStructCreator

Bases: pyrosetta.rosetta.core.io.silent.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.RNA_HelixAssembler

Bases: pybind11_builtins.pybind11_object

The RNA de novo structure modeling protocol

apply(*args, **kwargs)

Overloaded function.

  1. 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

  1. 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 class std::basic_string<char> &) –> 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 class std::basic_string<char> &, const class std::basic_string<char> &) –> 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

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.

  1. 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

  1. 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.

  1. centroid_pose_from_pdb(pose: pyrosetta.rosetta.core.pose.Pose, filename: str) -> None
  2. 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 class std::basic_string<char> &, 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.

  1. cleanup(pose: pyrosetta.rosetta.core.pose.Pose) -> None
  2. 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 class std::basic_string<char> &, 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 class std::basic_string<char> &) –> enum core::import_pose::FileType

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, class std::basic_string<char>, struct std::less<unsigned long>, class std::allocator<struct std::pair<const unsigned long, class std::basic_string<char> > > > &) –> 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<class std::basic_string<char>, class std::allocator<class std::basic_string<char> > > &, class std::shared_ptr<const class core::chemical::ResidueTypeSet>) –> void

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

Overloaded function.

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

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

  1. 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 class std::basic_string<char> &, 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 class std::basic_string<char> &, 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.

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

C++: core::import_pose::get_sequence_information(const class std::basic_string<char> &, 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.

  1. 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

  1. 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<class std::basic_string<char>, class std::allocator<class std::basic_string<char> > > &, const class utility::vector1<class std::basic_string<char>, class std::allocator<class std::basic_string<char> > > &) –> 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(class std::basic_string<char>) –> 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<class std::basic_string<char>, class std::allocator<class std::basic_string<char> > > &) –> 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 class std::basic_string<char> &) –> void

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

Overloaded function.

  1. poseOPs_from_files(filenames: pyrosetta.rosetta.utility.vector1_std_string) -> pyrosetta.rosetta.utility.vector1_std_shared_ptr_core_pose_Pose_t
  2. 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
  3. 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<class std::basic_string<char>, class std::allocator<class std::basic_string<char> > > &, 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> > >

  1. 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
  2. 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
  3. 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<class std::basic_string<char>, class std::allocator<class std::basic_string<char> > > &, 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> > >

  1. 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
  2. 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<class std::basic_string<char>, class std::allocator<class std::basic_string<char> > > &, 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.

  1. pose_from_file(filename: str) -> pyrosetta.rosetta.core.pose.Pose
  2. pose_from_file(filename: str, read_fold_tree: bool) -> pyrosetta.rosetta.core.pose.Pose
  3. 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 class std::basic_string<char> &, bool, enum core::import_pose::FileType) –> class std::shared_ptr<class core::pose::Pose>

  1. 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 class std::basic_string<char> &, const class core::import_pose::ImportPoseOptions &, bool, enum core::import_pose::FileType) –> class std::shared_ptr<class core::pose::Pose>

  1. pose_from_file(residue_set: pyrosetta.rosetta.core.chemical.ResidueTypeSet, filename: str) -> pyrosetta.rosetta.core.pose.Pose
  2. pose_from_file(residue_set: pyrosetta.rosetta.core.chemical.ResidueTypeSet, filename: str, read_fold_tree: bool) -> pyrosetta.rosetta.core.pose.Pose
  3. 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 class std::basic_string<char> &, bool, enum core::import_pose::FileType) –> class std::shared_ptr<class core::pose::Pose>

  1. pose_from_file(pose: pyrosetta.rosetta.core.pose.Pose, residue_set: pyrosetta.rosetta.core.chemical.ResidueTypeSet, filename: str, options: core::import_pose::ImportPoseOptions) -> None
  2. 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
  3. 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 class std::basic_string<char> &, const class core::import_pose::ImportPoseOptions &, bool, enum core::import_pose::FileType) –> void

  1. pose_from_file(pose: pyrosetta.rosetta.core.pose.Pose, residue_set: pyrosetta.rosetta.core.chemical.ResidueTypeSet, filename: str) -> None
  2. pose_from_file(pose: pyrosetta.rosetta.core.pose.Pose, residue_set: pyrosetta.rosetta.core.chemical.ResidueTypeSet, filename: str, read_fold_tree: bool) -> None
  3. 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 class std::basic_string<char> &, bool, enum core::import_pose::FileType) –> void

  1. pose_from_file(pose: pyrosetta.rosetta.core.pose.Pose, filename: str) -> None
  2. pose_from_file(pose: pyrosetta.rosetta.core.pose.Pose, filename: str, read_fold_tree: bool) -> None
  3. 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 class std::basic_string<char> &, bool, enum core::import_pose::FileType) –> void

  1. pose_from_file(pose: pyrosetta.rosetta.core.pose.Pose, filename: str, options: core::import_pose::ImportPoseOptions) -> None
  2. pose_from_file(pose: pyrosetta.rosetta.core.pose.Pose, filename: str, options: core::import_pose::ImportPoseOptions, read_fold_tree: bool) -> None
  3. 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 class std::basic_string<char> &, const class core::import_pose::ImportPoseOptions &, bool, enum core::import_pose::FileType) –> void

  1. pose_from_file(poses: pyrosetta.rosetta.utility.vector1_core_pose_Pose, residue_set: pyrosetta.rosetta.core.chemical.ResidueTypeSet, filename: str) -> None
  2. 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
  3. 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 class std::basic_string<char> &, bool, enum core::import_pose::FileType) –> void

  1. 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
  2. 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
  3. 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 class std::basic_string<char> &, const class core::import_pose::ImportPoseOptions &, bool, enum core::import_pose::FileType) –> void

  1. pose_from_file(poses: pyrosetta.rosetta.utility.vector1_core_pose_Pose, filename: str) -> None
  2. pose_from_file(poses: pyrosetta.rosetta.utility.vector1_core_pose_Pose, filename: str, read_fold_tree: bool) -> None
  3. 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 class std::basic_string<char> &, 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 &, class std::basic_istream<char> &, const class std::basic_string<char> &, const class core::import_pose::ImportPoseOptions &) –> void

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

Overloaded function.

  1. pose_from_pdbstring(pose: pyrosetta.rosetta.core.pose.Pose, pdbcontents: str) -> None
  2. 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 class std::basic_string<char> &, const class std::basic_string<char> &) –> void

  1. pose_from_pdbstring(pose: pyrosetta.rosetta.core.pose.Pose, pdbcontents: str, options: core::import_pose::ImportPoseOptions) -> None
  2. 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 class std::basic_string<char> &, const class core::import_pose::ImportPoseOptions &, const class std::basic_string<char> &) –> void

  1. 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 class std::basic_string<char> &, const class core::chemical::ResidueTypeSet &, const class std::basic_string<char> &) –> void

  1. 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 class std::basic_string<char> &, const class core::chemical::ResidueTypeSet &, const class core::import_pose::ImportPoseOptions &, const class std::basic_string<char> &) –> void

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

Overloaded function.

  1. poses_from_files(filenames: pyrosetta.rosetta.utility.vector1_std_string) -> pyrosetta.rosetta.utility.vector1_core_pose_Pose
  2. poses_from_files(filenames: pyrosetta.rosetta.utility.vector1_std_string, read_fold_tree: bool) -> pyrosetta.rosetta.utility.vector1_core_pose_Pose
  3. 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<class std::basic_string<char>, class std::allocator<class std::basic_string<char> > > &, bool, enum core::import_pose::FileType) –> class utility::vector1<class core::pose::Pose, class std::allocator<class core::pose::Pose> >

  1. 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
  2. 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<class std::basic_string<char>, class std::allocator<class std::basic_string<char> > > &, 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.

  1. process_input_file(silent_file: str, pose_list: pyrosetta.rosetta.utility.vector1_std_shared_ptr_core_pose_Pose_t) -> None
  2. process_input_file(silent_file: str, pose_list: pyrosetta.rosetta.utility.vector1_std_shared_ptr_core_pose_Pose_t, is_pdb: bool) -> None
  3. 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 class std::basic_string<char> &, 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.

  1. read_additional_pdb_data(file: str, pose: pyrosetta.rosetta.core.pose.Pose, fd: pyrosetta.rosetta.core.io.StructFileRep) -> None
  2. 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 class std::basic_string<char> &, class core::pose::Pose &, class std::shared_ptr<const class core::io::StructFileRep>, bool) –> void

  1. read_additional_pdb_data(file: str, pose: pyrosetta.rosetta.core.pose.Pose, options: core::import_pose::ImportPoseOptions) -> None
  2. 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 class std::basic_string<char> &, 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<class std::basic_string<char>, class std::allocator<class std::basic_string<char> > > &, 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<class std::basic_string<char>, class std::allocator<class std::basic_string<char> > > > &) –> 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, class std::basic_string<char>, struct std::less<unsigned long>, class std::allocator<struct std::pair<const unsigned long, class std::basic_string<char> > > > &, 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: pyrosetta.rosetta.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