addVirtualResAsRoot(args, *kwargs) Overloaded function.

1. addVirtualResAsRoot(pose : rosetta.core.pose.Pose) -> NoneType

Adds a VRT res to the end of the pose at the center of mass. Reroots the structure on this res.

1. addVirtualResAsRoot(xyz : rosetta.numeric.xyzVector_double_t, pose : rosetta.core.pose.Pose) -> NoneType

Adds a virtual residue to the end of the pose at the specified location. Roots the structure on this residue.

add_comment(pose : rosetta.core.pose.Pose, key : str, val : str) -> NoneType

Adds a key-value pair to the STRING_MAP in the Pose DataCache. If there is no STRING_MAP in the DataCache, one is created.

add_lower_terminus_type_to_pose_residue(pose : rosetta.core.pose.Pose, seqpos : int) -> NoneType

add_score_line_string(pose : rosetta.core.pose.Pose, key : str, val : str) -> NoneType

Sets a PDB-style REMARK entry in the Pose.

This is different from a comment in its interpretation by the silent-file output machinery. A REMARK is written on its own separate line in the output silent-file, while a comment is written as part of the Pose SCORE: lines.

add_upper_terminus_type_to_pose_residue(pose : rosetta.core.pose.Pose, seqpos : int) -> NoneType

add_variant_type_to_pose_residue(pose : rosetta.core.pose.Pose, variant_type : rosetta.core.chemical.VariantType, seqpos : int) -> NoneType

Construct a variant of an existing pose residue.

add_variant_type_to_residue(old_rsd : rosetta.core.conformation.Residue, variant_type : rosetta.core.chemical.VariantType, pose : rosetta.core.pose.Pose) -> rosetta.core.conformation.Residue

Construct a variant of an existing residue.

annotated_to_oneletter_sequence(annotated_seq : str) -> str

Returns the oneletter_sequence that corresponds to the given annotated sequence.

append_pose_to_pose(args, *kwargs) Overloaded function.

1. append_pose_to_pose(pose1 : rosetta.core.pose.Pose, pose2 : rosetta.core.pose.Pose) -> NoneType

Append residues of pose2 to pose1.

1. append_pose_to_pose(pose1 : rosetta.core.pose.Pose, pose2 : rosetta.core.pose.Pose, new_chain : bool) -> NoneType

Append residues of pose2 to pose1.

append_pose_with_glycan_residues(pose : rosetta.core.pose.Pose, residue_types : rosetta.utility.vector1_std_shared_ptr_const_core_chemical_ResidueType_t) -> NoneType

Append an empty or current Pose with saccharide residues, building branches as necessary.

append_subpose_to_pose(args, *kwargs) Overloaded function.

1. append_subpose_to_pose(pose1 : rosetta.core.pose.Pose, pose2 : rosetta.core.pose.Pose, start_res : int, end_res : int) -> NoneType

Append specified residues of pose2 to pose1.

1. append_subpose_to_pose(pose1 : rosetta.core.pose.Pose, pose2 : rosetta.core.pose.Pose, start_res : int, end_res : int, new_chain : bool) -> NoneType

Append specified residues of pose2 to pose1.

atom_id_to_named_atom_id(atom_id : rosetta.core.id.AtomID, pose : rosetta.core.pose.Pose) -> rosetta.core.id.NamedAtomID

canonical_atom_count(pose : rosetta.core.pose.Pose) -> int

count the number of canonical amino acid atoms in the pose

canonical_residue_count(pose : rosetta.core.pose.Pose) -> int

count the number of canonical residues in the pose

center_of_mass(args, *kwargs) Overloaded function.

1. center_of_mass(pose : rosetta.core.pose.Pose, residues : rosetta.utility.vector1_bool) -> rosetta.numeric.xyzVector_double_t

2. center_of_mass(pose : rosetta.core.pose.Pose, start : int, stop : int) -> rosetta.numeric.xyzVector_double_t

chain_end_res(args, *kwargs) Overloaded function.

1. chain_end_res(pose : rosetta.core.pose.Pose, chain : int) -> int

compute last residue number of a chain

1. chain_end_res(pose : rosetta.core.pose.Pose) -> rosetta.utility.vector1_unsigned_long

compute last residue numbers of all chains

clearPoseExtraScore(pose : rosetta.core.pose.Pose, name : str) -> NoneType

clearPoseExtraScores(pose : rosetta.core.pose.Pose) -> NoneType

compare_atom_coordinates(args, *kwargs) Overloaded function.

1. compare_atom_coordinates(lhs : rosetta.core.pose.Pose, rhs : rosetta.core.pose.Pose) -> bool

this function compares pose atom coordinates for equality; it is not the == operator because it does not compare all pose data.

Steven Lewis smlewi.com

one pose to compare

one pose to compare

number of decimal places to compare for the coordinates (remember == doesn't work for float); defaults to 3 which is PDB accuracy

1. compare_atom_coordinates(lhs : rosetta.core.pose.Pose, rhs : rosetta.core.pose.Pose, n_dec_places : int) -> bool

this function compares pose atom coordinates for equality; it is not the == operator because it does not compare all pose data.

Steven Lewis smlewi.com

one pose to compare

one pose to compare

number of decimal places to compare for the coordinates (remember == doesn't work for float); defaults to 3 which is PDB accuracy

compare_binary_protein_silent_struct(lhs : rosetta.core.pose.Pose, rhs : rosetta.core.pose.Pose) -> bool

this function compares poses for equality up to the information stored in the binary protein silent struct format.

compute_unique_chains(pose : rosetta.core.pose.Pose) -> rosetta.utility.vector1_bool

Compute uniq chains in a complex

Returns a vector of pose length with true/false of uniq chain true is unique, false is not

conf2pdb_chain(pose : rosetta.core.pose.Pose) -> rosetta.std.map_int_char

get Conformation chain -> PDBInfo chain mapping

Any chains whose PDBInfo chain records are marked entirely as PDBInfo::empty_record() will be mapped to that character. Note that Conformation -> PDBInfo is always unique, but the reverse may not be true.

the mapping if PDBInfo available and chains appear consistent, otherwise returns an empty mapping

convert_from_std_map(atom_map : rosetta.std.map_core_id_AtomID_core_id_AtomID, pose : rosetta.core.pose.Pose) -> rosetta.core.id.AtomID_Map_core_id_AtomID_t

correctly_add_cutpoint_variants(args, *kwargs) Overloaded function.

1. correctly_add_cutpoint_variants(pose : rosetta.core.pose.Pose) -> NoneType

Add cutpoint variants to all residues annotated as cutpoints in the pose.

1. correctly_add_cutpoint_variants(pose : rosetta.core.pose.Pose, cutpoint_res : int) -> NoneType

2. correctly_add_cutpoint_variants(pose : rosetta.core.pose.Pose, cutpoint_res : int, check_fold_tree : bool) -> NoneType

create_subpose(src : rosetta.core.pose.Pose, positions : rosetta.utility.vector1_unsigned_long, f : rosetta.core.kinematics.FoldTree, pose : rosetta.core.pose.Pose) -> NoneType

Create a subpose of the src pose. PDBInfo is set as NULL.

delete_comment(pose : rosetta.core.pose.Pose, key : str) -> NoneType

Deletes the entry in the STRING_MAP associated with the given key.

dump_comment_pdb(file_name : str, pose : rosetta.core.pose.Pose) -> NoneType

dumps pose+ comments to pdb file

energy_from_pose(args, *kwargs) Overloaded function.

1. energy_from_pose(pose : rosetta.core.pose.Pose, sc_type : rosetta.core.scoring.ScoreType) -> float

2. energy_from_pose(pose : rosetta.core.pose.Pose, sc_type : str) -> float

extract_tag_from_pose(pose : rosetta.core.pose.Pose) -> str

Returns a string giving the pose's tag if there is such a thing or "UnknownTag" otherwise.

getPoseExtraScore(args, *kwargs) Overloaded function.

1. getPoseExtraScore(pose : rosetta.core.pose.Pose, name : str, value : float) -> bool

getters/setters for things in the Pose DataCache

1. getPoseExtraScore(pose : rosetta.core.pose.Pose, name : str) -> float

2. getPoseExtraScore(pose : rosetta.core.pose.Pose, name : str, value : str) -> bool

get_all_comments(pose : rosetta.core.pose.Pose) -> rosetta.std.map_std_string_std_string

Gets a map< string, string > representing comments about the Pose in the form of key-value pairs.

get_all_score_line_strings(pose : rosetta.core.pose.Pose) -> rosetta.std.map_std_string_std_string

Gets a map< string, string > representing score_line_strings about the Pose in the form of key-value pairs.

get_bb_torsion(torsion_id : int, pose : rosetta.core.pose.Pose, sequence_position : int) -> float

Get a particular backbone torsion, phi, psi, omega (see core::types) Works with carbohydrates. Think about moving this to pose itself.

get_center_of_mass(pose : rosetta.core.pose.Pose) -> rosetta.numeric.xyzVector_double_t

Get center of mass of a pose.

get_chain_from_chain_id(chain_id : int, pose : rosetta.core.pose.Pose) -> str

get_chain_from_jump_id(jump_id : int, pose : rosetta.core.pose.Pose) -> str

get_chain_id_from_chain(args, *kwargs) Overloaded function.

1. get_chain_id_from_chain(chain : str, pose : rosetta.core.pose.Pose) -> int

2. get_chain_id_from_chain(chain : str, pose : rosetta.core.pose.Pose) -> int

get_chain_id_from_jump_id(jump_id : int, pose : rosetta.core.pose.Pose) -> int

get_chain_ids_from_chain(args, *kwargs) Overloaded function.

1. get_chain_ids_from_chain(chain : str, pose : rosetta.core.pose.Pose) -> rosetta.utility.vector1_unsigned_long

2. get_chain_ids_from_chain(chain : str, pose : rosetta.core.pose.Pose) -> rosetta.utility.vector1_unsigned_long

get_chain_ids_from_chains(chains : rosetta.utility.vector1_std_string, pose : rosetta.core.pose.Pose) -> rosetta.utility.vector1_unsigned_long

get_chain_residues(pose : rosetta.core.pose.Pose, chain_id : int) -> rosetta.utility.vector1_std_shared_ptr_const_core_conformation_Residue_t

get_chains(pose : rosetta.core.pose.Pose) -> rosetta.utility.vector1_int

Get all the chains from conformation

get_comment(pose : rosetta.core.pose.Pose, key : str, val : str) -> bool

Attempts to access the entry in the STRING_MAP associated with the given key. If an entry for the key exists, the value associated with the key is put into val, and this function returns true. Otherwise, this function returns false and val left unmodified.

get_constraints_from_link_records(pose : rosetta.core.pose.Pose, sfr : rosetta.core.io.StructFileRep) -> NoneType

get_hash_excluding_chain(chain : str, pose : rosetta.core.pose.Pose) -> int

get_hash_from_chain(chain : str, pose : rosetta.core.pose.Pose) -> int

get_jump_id_from_chain(args, *kwargs) Overloaded function.

1. get_jump_id_from_chain(chain : str, pose : rosetta.core.pose.Pose) -> int

2. get_jump_id_from_chain(chain : str, pose : rosetta.core.pose.Pose) -> int

get_jump_id_from_chain_id(chain_id : int, pose : rosetta.core.pose.Pose) -> int

get_jump_ids_from_chain(args, *kwargs) Overloaded function.

1. get_jump_ids_from_chain(chain : str, pose : rosetta.core.pose.Pose) -> rosetta.utility.vector1_unsigned_long

2. get_jump_ids_from_chain(chain : str, pose : rosetta.core.pose.Pose) -> rosetta.utility.vector1_unsigned_long

get_jump_ids_from_chain_ids(chain_ids : rosetta.std.set_unsigned_long_std_less_unsigned_long_std_allocator_unsigned_long_t, pose : rosetta.core.pose.Pose) -> rosetta.std.set_unsigned_long_std_less_unsigned_long_std_allocator_unsigned_long_t

get_resnum(args, *kwargs) Overloaded function.

1. get_resnum(tag_ptr : rosetta.utility.tag.Tag, pose : rosetta.core.pose.Pose) -> int

2. get_resnum(tag_ptr : rosetta.utility.tag.Tag, pose : rosetta.core.pose.Pose, prefix : str) -> int

get_resnum_list(args, *kwargs) Overloaded function.

1. get_resnum_list(tag_ptr : rosetta.utility.tag.Tag, tag : str, pose : rosetta.core.pose.Pose) -> rosetta.utility.vector1_unsigned_long

Extracts a list of residue numbers from a tag.

The tag should contain a comma-separated list of numbers, in either pdb or rosetta format (

parse_resnum for details)

1. get_resnum_list(str : str, pose : rosetta.core.pose.Pose) -> rosetta.std.set_unsigned_long_std_less_unsigned_long_std_allocator_unsigned_long_t

returns a resnum list directly from a string

get_resnum_list_ordered(str : str, pose : rosetta.core.pose.Pose) -> rosetta.utility.vector1_unsigned_long

returns a resnum list directly from a string, preserving order

get_resnumber_from_reference_pose(refpose_name : str, refpose_number : int, refpose_offset : int, pose : rosetta.core.pose.Pose) -> int

Given the name of a ReferencePose object in the pose, a residue number in that reference pose, and a residue offset, this function returns the Rosetta number of the corresponding residue in the pose. Should throw an error if the ReferencePose doesn't exist in the pose, or 0 if no corresponding residue exists in the pose.

Vikram K. Mulligan, Baker laboratory (vmullig.edu)

get_rsd_type_from_aa(residue_set : rosetta.core.chemical.ResidueTypeSet, my_aa : rosetta.core.chemical.AA, is_lower_terminus : bool, is_upper_terminus : bool) -> rosetta.core.chemical.ResidueType

use efficient residue type finder to find simplest residue type with this AA & requested termini.

get_score_line_string(pose : rosetta.core.pose.Pose, key : str, val : str) -> bool

get_sequence_len(sequence_in : str) -> int

Get the real length of a annotated sequence

get_sha1_hash_excluding_chain(chain : str, pose : rosetta.core.pose.Pose) -> str

hasPoseExtraScore(pose : rosetta.core.pose.Pose, name : str) -> bool

has_chain(args, *kwargs) Overloaded function.

1. has_chain(chain : str, pose : rosetta.core.pose.Pose) -> bool

2. has_chain(chain : str, pose : rosetta.core.pose.Pose) -> bool

3. has_chain(chain_id : int, pose : rosetta.core.pose.Pose) -> bool

initialize_atomid_map_AtomID(args, *kwargs) Overloaded function.

1. initialize_atomid_map_AtomID(atom_map : rosetta.core.id.AtomID_Map_core_id_AtomID_t, pose : rosetta.core.pose.Pose) -> NoneType

2. initialize_atomid_map_AtomID(atom_map : rosetta.core.id.AtomID_Map_core_id_AtomID_t, pose : rosetta.core.pose.Pose, value : rosetta.core.id.AtomID) -> NoneType

3. initialize_atomid_map_AtomID(atom_map : rosetta.core.id.AtomID_Map_core_id_AtomID_t, conformation : rosetta.core.conformation.Conformation) -> NoneType

4. initialize_atomid_map_AtomID(atom_map : rosetta.core.id.AtomID_Map_core_id_AtomID_t, conformation : rosetta.core.conformation.Conformation, value : rosetta.core.id.AtomID) -> NoneType

initialize_atomid_map_core_id_AtomID_t(args, *kwargs) Overloaded function.

1. initialize_atomid_map_core_id_AtomID_t(atom_map : rosetta.core.id.AtomID_Map_core_id_AtomID_t, pose : rosetta.core.pose.Pose) -> NoneType

2. initialize_atomid_map_core_id_AtomID_t(atom_map : rosetta.core.id.AtomID_Map_core_id_AtomID_t, pose : rosetta.core.pose.Pose, value : rosetta.core.id.AtomID) -> NoneType

3. initialize_atomid_map_core_id_AtomID_t(atom_map : rosetta.core.id.AtomID_Map_core_id_AtomID_t, conformation : rosetta.core.conformation.Conformation) -> NoneType

4. initialize_atomid_map_core_id_AtomID_t(atom_map : rosetta.core.id.AtomID_Map_core_id_AtomID_t, conformation : rosetta.core.conformation.Conformation, value : rosetta.core.id.AtomID) -> NoneType

initialize_disulfide_bonds(args, *kwargs) Overloaded function.

1. initialize_disulfide_bonds(pose : rosetta.core.pose.Pose) -> NoneType

detect and fix disulfide bonds

1. initialize_disulfide_bonds(pose : rosetta.core.pose.Pose, fd : rosetta.core.io.StructFileRep) -> NoneType

detect and fix disulfide bonds

is_atom_axial_or_equatorial_to_ring(pose : rosetta.core.pose.Pose, seqpos : int, query_atom : int, ring_atoms : rosetta.utility.vector1_unsigned_long) -> rosetta.core.chemical.rings.AxEqDesignation

Is the query atom in this pose residue axial or equatorial to the given ring or neither?

is_ideal_pose(pose : rosetta.core.pose.Pose) -> bool

Returns true if the geometry is ideal

The Pose to check.

true if all pose positions have ideal bond lengths and angles up to some very small epsilon

is_ideal_position(seqpos : int, pose : rosetta.core.pose.Pose) -> bool

Returns true if the geometry is ideal in position

The Pose to check.

true if position seqpos has ideal bond lengths and angles up to some very small epsilon

is_lower_terminus(pose : rosetta.core.pose.Pose, resid : int) -> bool

checks to see if this is a lower chain ending more intelligently than just checking residue variants

is_position_conserved_residue(pose : rosetta.core.pose.Pose, residue : int) -> bool

Returns true if is positionally conserved, false otherwise

is_referencepose_number(str : str, refpose_string : str, refpose_resnumber : int, refpose_offset : int) -> bool

Is a string of the format "refpose(,)" or "refpose(,)+/-"?

If this successfully determines that this is a string of this format, it populates the refpose_string, refpose_resnumber, and refpose_offset variables with the name of the ReferencePose, the number of the residue in the reference pose, and the +/- offset number parsed from this string.

Vikram K. Mulligan, Baker laboratory (vmullig.edu)

is_upper_terminus(pose : rosetta.core.pose.Pose, resid : int) -> bool

checks to see if this is a lower chain ending more intelligently than just checking residue variants

jumps_from_pose(pose : rosetta.core.pose.Pose, jumps : rosetta.std.set_int_std_less_int_std_allocator_int_t) -> NoneType

Retrieves jump information from , storing the result in . Jumps are keyed by their jump id.

make_atom_map(p : rosetta.core.pose.Pose, m : rosetta.core.pose.PoseCoordPickMode) -> rosetta.core.id.AtomID_Map_double_t

make_pose_from_saccharide_sequence(args, *kwargs) Overloaded function.

1. make_pose_from_saccharide_sequence(pose : rosetta.core.pose.Pose, sequence : str, residue_set : rosetta.core.chemical.ResidueTypeSet) -> NoneType

Create a Pose from an annotated, linear, IUPAC polysaccharide sequence with ResidueTypeSet and store it in .

1. make_pose_from_saccharide_sequence(pose : rosetta.core.pose.Pose, sequence : str, residue_set : rosetta.core.chemical.ResidueTypeSet, auto_termini : bool) -> NoneType

Create a Pose from an annotated, linear, IUPAC polysaccharide sequence with ResidueTypeSet and store it in .

1. make_pose_from_saccharide_sequence(pose : rosetta.core.pose.Pose, sequence : str, residue_set : rosetta.core.chemical.ResidueTypeSet, auto_termini : bool, idealize_linkages : bool) -> NoneType

Create a Pose from an annotated, linear, IUPAC polysaccharide sequence with ResidueTypeSet and store it in .

1. make_pose_from_saccharide_sequence(pose : rosetta.core.pose.Pose, sequence : str) -> NoneType

Create a Pose from an annotated, linear, IUPAC polysaccharide sequence with residue type set name and store it in .

1. make_pose_from_saccharide_sequence(pose : rosetta.core.pose.Pose, sequence : str, type_set_name : str) -> NoneType

Create a Pose from an annotated, linear, IUPAC polysaccharide sequence with residue type set name and store it in .

1. make_pose_from_saccharide_sequence(pose : rosetta.core.pose.Pose, sequence : str, type_set_name : str, auto_termini : bool) -> NoneType

Create a Pose from an annotated, linear, IUPAC polysaccharide sequence with residue type set name and store it in .

1. make_pose_from_saccharide_sequence(pose : rosetta.core.pose.Pose, sequence : str, type_set_name : str, auto_termini : bool, idealize_linkages : bool) -> NoneType

Create a Pose from an annotated, linear, IUPAC polysaccharide sequence with residue type set name and store it in .

make_pose_from_sequence(args, *kwargs) Overloaded function.

1. make_pose_from_sequence(pose : rosetta.core.pose.Pose, requested_types : rosetta.utility.vector1_std_shared_ptr_const_core_chemical_ResidueType_t) -> NoneType

Creates a Pose from the annotated protein sequence with ResidueTypeSet and stores it in

: any existing data in is cleared, auto_termini mark position 1, last_residue with lower, upper termini; default true

example(s): make_pose_from_sequence(pose,"THANKSEVAN",core::chemical::FA_STANDARD) See also: Pose PDBInfo pose_from_pdb pose_from_rcsb pose_from_sequence

1. make_pose_from_sequence(pose : rosetta.core.pose.Pose, requested_types : rosetta.utility.vector1_std_shared_ptr_const_core_chemical_ResidueType_t, auto_termini : bool) -> NoneType

Creates a Pose from the annotated protein sequence with ResidueTypeSet and stores it in

: any existing data in is cleared, auto_termini mark position 1, last_residue with lower, upper termini; default true

example(s): make_pose_from_sequence(pose,"THANKSEVAN",core::chemical::FA_STANDARD) See also: Pose PDBInfo pose_from_pdb pose_from_rcsb pose_from_sequence

1. make_pose_from_sequence(pose : rosetta.core.pose.Pose, sequence : str, residue_set : rosetta.core.chemical.ResidueTypeSet) -> NoneType

2. make_pose_from_sequence(pose : rosetta.core.pose.Pose, sequence : str, residue_set : rosetta.core.chemical.ResidueTypeSet, auto_termini : bool) -> NoneType

3. make_pose_from_sequence(pose : rosetta.core.pose.Pose, sequence : str, residue_set : rosetta.core.chemical.ResidueTypeSet) -> NoneType

4. make_pose_from_sequence(pose : rosetta.core.pose.Pose, sequence : str, residue_set : rosetta.core.chemical.ResidueTypeSet, auto_termini : bool) -> NoneType

5. make_pose_from_sequence(pose : rosetta.core.pose.Pose, sequence : str, type_set_name : str) -> NoneType

Creates a Pose from the annotated protein sequence with the desired and stores it in

: any existing data in is cleared, auto_termini mark position 1, last_residue with lower, upper termini; default true

1. make_pose_from_sequence(pose : rosetta.core.pose.Pose, sequence : str, type_set_name : str, auto_termini : bool) -> NoneType

Creates a Pose from the annotated protein sequence with the desired and stores it in

: any existing data in is cleared, auto_termini mark position 1, last_residue with lower, upper termini; default true

mass(begin : int, end : int, pose : rosetta.core.pose.Pose) -> float

named_atom_id_to_atom_id(args, *kwargs) Overloaded function.

1. named_atom_id_to_atom_id(named_atom_id : rosetta.core.id.NamedAtomID, pose : rosetta.core.pose.Pose) -> rosetta.core.id.AtomID

2. named_atom_id_to_atom_id(named_atom_id : rosetta.core.id.NamedAtomID, pose : rosetta.core.pose.Pose, raise_exception : bool) -> rosetta.core.id.AtomID

named_stub_id_to_stub_id(named_stub_id : rosetta.core.id.NamedStubID, pose : rosetta.core.pose.Pose) -> rosetta.core.id.StubID

noncanonical_atom_count(pose : rosetta.core.pose.Pose) -> int

count the number of non-canonical amino acids in thepose

noncanonical_chi_count(pose : rosetta.core.pose.Pose) -> int

count the number of non-canonical chi angles in the pose

noncanonical_residue_count(pose : rosetta.core.pose.Pose) -> int

count the number of non-canonical residues in the pose

nres_protein(pose : rosetta.core.pose.Pose) -> int

Number of protein residues in the pose

No virtuals, membrane residues or embedding residues counted

num_atoms(begin : int, end : int, pose : rosetta.core.pose.Pose) -> int

num_chi_angles(begin : int, end : int, pose : rosetta.core.pose.Pose) -> int

num_hbond_acceptors(begin : int, end : int, pose : rosetta.core.pose.Pose) -> int

num_hbond_donors(begin : int, end : int, pose : rosetta.core.pose.Pose) -> int

num_heavy_atoms(begin : int, end : int, pose : rosetta.core.pose.Pose) -> int

parse_PDBnum_icode(token : str, fname : str, lineno : int, PDBnum : int, icode : str) -> NoneType

Take the string "token" and try to interpret it as a PDB identifier in the form of an integer as well as an optional insertion code. For example the string "25A" would be interpretted as the residue 25 with the insertion code "A." Throws an exception if the input string is misformatted.

parse_resnum(args, *kwargs) Overloaded function.

1. parse_resnum(resnum : str, pose : rosetta.core.pose.Pose) -> int

Extracts a residue number from a string.

Recognizes three forms of numbering: - Rosetta residue numbers (numbered sequentially from 1 to the last residue in the pose). These have the form [0-9]+ - PDB numbers. These have the form [0-9]+[A-Z], where the trailing letter is the chain ID. - Reference pose numbers. These have the form refpose([refpose name], [refpose number]). In addition, relative numbers are permitted (of the form +[number] or -[number]) in conjunction with reference pose numbering. For example, one might say "refpose(state1,17)+3", which means three residues past the residue correpsonding to residue 17 in the reference pose called "state1".

the rosetta residue number for the string, or 0 upon an error

1. parse_resnum(resnum : str, pose : rosetta.core.pose.Pose, check_for_refpose : bool) -> int

Extracts a residue number from a string.

Recognizes three forms of numbering: - Rosetta residue numbers (numbered sequentially from 1 to the last residue in the pose). These have the form [0-9]+ - PDB numbers. These have the form [0-9]+[A-Z], where the trailing letter is the chain ID. - Reference pose numbers. These have the form refpose([refpose name], [refpose number]). In addition, relative numbers are permitted (of the form +[number] or -[number]) in conjunction with reference pose numbering. For example, one might say "refpose(state1,17)+3", which means three residues past the residue correpsonding to residue 17 in the reference pose called "state1".

the rosetta residue number for the string, or 0 upon an error

parse_sequence(sequence_in : str, fullname_list : rosetta.utility.vector1_std_string, oneletter_to_fullname_index : rosetta.std.vector_unsigned_long, one_letter_sequence : str) -> NoneType

Parse the input annotated sequence

partition_pose_by_jump(src : rosetta.core.pose.Pose, jump_number : int, partner1 : rosetta.core.pose.Pose, partner2 : rosetta.core.pose.Pose) -> NoneType

pdb_to_pose(args, *kwargs) Overloaded function.

1. pdb_to_pose(pose : rosetta.core.pose.Pose, pdb_res : rosetta.utility.vector1_int) -> rosetta.utility.vector1_unsigned_long

Convert PDB numbering to pose numbering. Must exist somewhere else, but I couldn't find it. -- rhiju

1. pdb_to_pose(pose : rosetta.core.pose.Pose, pdb_res : (rosetta.utility.vector1_int, rosetta.utility.vector1_char)) -> rosetta.utility.vector1_unsigned_long

Convert PDB numbering/chain to pose numbering. Must exist somewhere else, but I couldn't find it. -- rhiju

1. pdb_to_pose(pose : rosetta.core.pose.Pose, res_num : int) -> int

Convert PDB numbering to pose numbering. Must exist somewhere else, but I couldn't find it. -- rhiju

1. pdb_to_pose(pose : rosetta.core.pose.Pose, res_num : int, chain : str) -> int

Convert PDB numbering to pose numbering. Must exist somewhere else, but I couldn't find it. -- rhiju

pdbslice(args, *kwargs) Overloaded function.

1. pdbslice(new_pose : rosetta.core.pose.Pose, pose : rosetta.core.pose.Pose, slice_res : rosetta.utility.vector1_unsigned_long) -> NoneType

Create a subpose of the src pose -- figures out a reasonable fold tree.

1. pdbslice(pose : rosetta.core.pose.Pose, slice_res : rosetta.utility.vector1_unsigned_long) -> NoneType

Create a subpose of the src pose -- figures out a reasonable fold tree.

pose_from_saccharide_sequence(args, *kwargs) Overloaded function.

1. pose_from_saccharide_sequence(sequence : str) -> rosetta.core.pose.Pose

Return a Pose from an annotated, linear, IUPAC polysaccharide sequence with residue type set name .

1. pose_from_saccharide_sequence(sequence : str, type_set_name : str) -> rosetta.core.pose.Pose

Return a Pose from an annotated, linear, IUPAC polysaccharide sequence with residue type set name .

1. pose_from_saccharide_sequence(sequence : str, type_set_name : str, auto_termini : bool) -> rosetta.core.pose.Pose

Return a Pose from an annotated, linear, IUPAC polysaccharide sequence with residue type set name .

1. pose_from_saccharide_sequence(sequence : str, type_set_name : str, auto_termini : bool, idealize_linkages : bool) -> rosetta.core.pose.Pose

Return a Pose from an annotated, linear, IUPAC polysaccharide sequence with residue type set name .

pose_max_nbr_radius(pose : rosetta.core.pose.Pose) -> float

returns a Distance

pose_residue_is_terminal(pose : rosetta.core.pose.Pose, resid : int) -> bool

returns true if the given residue in the pose is a chain ending or has upper/lower terminal variants

pose_to_pdb(pose : rosetta.core.pose.Pose, pose_res : rosetta.utility.vector1_unsigned_long) -> rosetta.utility.vector1_unsigned_long

Convert pose numbering to pdb numbering. Must exist somewhere else, but I couldn't find it. -- rhiju

read_comment_pdb(file_name : str, pose : rosetta.core.pose.Pose) -> NoneType

Reads the comments from the pdb file and adds it into comments

read_psipred_ss2_file(pose : rosetta.core.pose.Pose) -> rosetta.utility.vector1_char

remove_ligand_canonical_residues(pose : rosetta.core.pose.Pose) -> NoneType

this function removes all residues with both UPPER and LOWER terminus types. This is intended for removing ligands that are canonical residues.

remove_lower_terminus_type_from_pose_residue(pose : rosetta.core.pose.Pose, seqpos : int) -> NoneType

remove_nonprotein_residues(pose : rosetta.core.pose.Pose) -> NoneType

this function removes all residues from the pose which are not protein residues. This removal includes, but is not limited to, metals, DNA, RNA, and ligands. It will NOT remove ligands which are canonical residues (for example, if a protein binds an alanine monomer, the monomer will be untouched).

remove_upper_terminus_type_from_pose_residue(pose : rosetta.core.pose.Pose, seqpos : int) -> NoneType

remove_variant_type_from_pose_residue(pose : rosetta.core.pose.Pose, variant_type : rosetta.core.chemical.VariantType, seqpos : int) -> NoneType

Construct a non-variant of an existing pose residue.

remove_variant_type_from_residue(old_rsd : rosetta.core.conformation.Residue, variant_type : rosetta.core.chemical.VariantType, pose : rosetta.core.pose.Pose) -> rosetta.core.conformation.Residue

Remove variant from an existing residue.

remove_virtual_residues(pose : rosetta.core.pose.Pose) -> NoneType

Removes all virtual residues from

renumber_pdbinfo_based_on_conf_chains(args, *kwargs) Overloaded function.

1. renumber_pdbinfo_based_on_conf_chains(pose : rosetta.core.pose.Pose) -> bool

renumber PDBInfo based on Conformation chains; each chain starts from 1

The Pose to modify.

If true, the procedure will attempt to fix any empty record characters it finds in the PDBInfo. (default true)

If true, will attempt to start each chain from the existing numbering in the PDBInfo. E.g. if the first residue of chain 2 in the Conformation is 27, then the renumbering of the chain in PDBInfo will start from 27. (default true)

If true, will maintain insertion codes and will not increment the pdb residue numbering for those residues. This means new numbering with insertion codes will only reflect properly if the old numbering included the base numbering of the insertion code residues, i.e. 100 100A 100B and not just 100A 100B (with 100 never appearing). (default false)

If true, allows support for more than 26 pdb chains by rotating [A,Z] continuously. WARNING: This will break the assumption made by the PDBPoseMap that each pdb chain id is unique, so make sure you are not using the PDBPoseMap feature downstream in your code path without corrections! (default false)

If fixing chains and there is only one chain and the PDBInfo exists but all records are marked as empty, will renumber and set the PDBInfo chain to 'A'.

true if renumbering successful, false otherwise

1. renumber_pdbinfo_based_on_conf_chains(pose : rosetta.core.pose.Pose, fix_chains : bool) -> bool

renumber PDBInfo based on Conformation chains; each chain starts from 1

The Pose to modify.

If true, the procedure will attempt to fix any empty record characters it finds in the PDBInfo. (default true)

If true, will attempt to start each chain from the existing numbering in the PDBInfo. E.g. if the first residue of chain 2 in the Conformation is 27, then the renumbering of the chain in PDBInfo will start from 27. (default true)

If true, will maintain insertion codes and will not increment the pdb residue numbering for those residues. This means new numbering with insertion codes will only reflect properly if the old numbering included the base numbering of the insertion code residues, i.e. 100 100A 100B and not just 100A 100B (with 100 never appearing). (default false)

If true, allows support for more than 26 pdb chains by rotating [A,Z] continuously. WARNING: This will break the assumption made by the PDBPoseMap that each pdb chain id is unique, so make sure you are not using the PDBPoseMap feature downstream in your code path without corrections! (default false)

If fixing chains and there is only one chain and the PDBInfo exists but all records are marked as empty, will renumber and set the PDBInfo chain to 'A'.

true if renumbering successful, false otherwise

1. renumber_pdbinfo_based_on_conf_chains(pose : rosetta.core.pose.Pose, fix_chains : bool, start_from_existing_numbering : bool) -> bool

renumber PDBInfo based on Conformation chains; each chain starts from 1

The Pose to modify.

If true, the procedure will attempt to fix any empty record characters it finds in the PDBInfo. (default true)

If true, will attempt to start each chain from the existing numbering in the PDBInfo. E.g. if the first residue of chain 2 in the Conformation is 27, then the renumbering of the chain in PDBInfo will start from 27. (default true)

If true, will maintain insertion codes and will not increment the pdb residue numbering for those residues. This means new numbering with insertion codes will only reflect properly if the old numbering included the base numbering of the insertion code residues, i.e. 100 100A 100B and not just 100A 100B (with 100 never appearing). (default false)

If true, allows support for more than 26 pdb chains by rotating [A,Z] continuously. WARNING: This will break the assumption made by the PDBPoseMap that each pdb chain id is unique, so make sure you are not using the PDBPoseMap feature downstream in your code path without corrections! (default false)

If fixing chains and there is only one chain and the PDBInfo exists but all records are marked as empty, will renumber and set the PDBInfo chain to 'A'.

true if renumbering successful, false otherwise

1. renumber_pdbinfo_based_on_conf_chains(pose : rosetta.core.pose.Pose, fix_chains : bool, start_from_existing_numbering : bool, keep_insertion_codes : bool) -> bool

renumber PDBInfo based on Conformation chains; each chain starts from 1

The Pose to modify.

If true, the procedure will attempt to fix any empty record characters it finds in the PDBInfo. (default true)

If true, will attempt to start each chain from the existing numbering in the PDBInfo. E.g. if the first residue of chain 2 in the Conformation is 27, then the renumbering of the chain in PDBInfo will start from 27. (default true)

If true, will maintain insertion codes and will not increment the pdb residue numbering for those residues. This means new numbering with insertion codes will only reflect properly if the old numbering included the base numbering of the insertion code residues, i.e. 100 100A 100B and not just 100A 100B (with 100 never appearing). (default false)

If true, allows support for more than 26 pdb chains by rotating [A,Z] continuously. WARNING: This will break the assumption made by the PDBPoseMap that each pdb chain id is unique, so make sure you are not using the PDBPoseMap feature downstream in your code path without corrections! (default false)

If fixing chains and there is only one chain and the PDBInfo exists but all records are marked as empty, will renumber and set the PDBInfo chain to 'A'.

true if renumbering successful, false otherwise

1. renumber_pdbinfo_based_on_conf_chains(pose : rosetta.core.pose.Pose, fix_chains : bool, start_from_existing_numbering : bool, keep_insertion_codes : bool, rotate_chain_ids : bool) -> bool

renumber PDBInfo based on Conformation chains; each chain starts from 1

The Pose to modify.

If true, the procedure will attempt to fix any empty record characters it finds in the PDBInfo. (default true)

If true, will attempt to start each chain from the existing numbering in the PDBInfo. E.g. if the first residue of chain 2 in the Conformation is 27, then the renumbering of the chain in PDBInfo will start from 27. (default true)

If true, will maintain insertion codes and will not increment the pdb residue numbering for those residues. This means new numbering with insertion codes will only reflect properly if the old numbering included the base numbering of the insertion code residues, i.e. 100 100A 100B and not just 100A 100B (with 100 never appearing). (default false)

If true, allows support for more than 26 pdb chains by rotating [A,Z] continuously. WARNING: This will break the assumption made by the PDBPoseMap that each pdb chain id is unique, so make sure you are not using the PDBPoseMap feature downstream in your code path without corrections! (default false)

If fixing chains and there is only one chain and the PDBInfo exists but all records are marked as empty, will renumber and set the PDBInfo chain to 'A'.

true if renumbering successful, false otherwise

reorder_saccharide_residue_types(residue_types : rosetta.utility.vector1_std_shared_ptr_const_core_chemical_ResidueType_t) -> NoneType

This is a subroutine/helper function to reorder saccharide ResidueTypes generated from an IUPAC sequence.

replace_pose_residue_copying_existing_coordinates(pose : rosetta.core.pose.Pose, seqpos : int, new_rsd_type : rosetta.core.chemical.ResidueType) -> NoneType

res_in_chain(pose : rosetta.core.pose.Pose, resnum : int, chain : str) -> bool

Is residue number in this chain?

residue_center_of_mass(args, *kwargs) Overloaded function.

1. residue_center_of_mass(pose : rosetta.core.pose.Pose, residues : rosetta.utility.vector1_bool) -> int

2. residue_center_of_mass(pose : rosetta.core.pose.Pose, start : int, stop : int) -> int

residue_types_from_saccharide_sequence(sequence : str, residue_set : rosetta.core.chemical.ResidueTypeSet) -> rosetta.utility.vector1_std_shared_ptr_const_core_chemical_ResidueType_t

Return a list of carbohydrate ResidueTypes corresponding to an annotated, linear, IUPAC polysaccharide sequence.

residue_types_from_sequence(args, *kwargs) Overloaded function.

1. residue_types_from_sequence(sequence_in : str, residue_set : rosetta.core.chemical.ResidueTypeSet) -> rosetta.utility.vector1_std_shared_ptr_const_core_chemical_ResidueType_t

return a list of ResidueTypes corresponding to an annotated protein sequence

an annotated sequence

the desired residue set

mark position 1, last_residue with lower, upper termini; default true

1. residue_types_from_sequence(sequence_in : str, residue_set : rosetta.core.chemical.ResidueTypeSet, auto_termini : bool) -> rosetta.utility.vector1_std_shared_ptr_const_core_chemical_ResidueType_t

return a list of ResidueTypes corresponding to an annotated protein sequence

an annotated sequence

the desired residue set

mark position 1, last_residue with lower, upper termini; default true

return_nearest_residue(args, *kwargs) Overloaded function.

1. return_nearest_residue(pose : rosetta.core.pose.Pose, residues : rosetta.utility.vector1_bool, center : rosetta.numeric.xyzVector_double_t) -> int

2. return_nearest_residue(pose : rosetta.core.pose.Pose, begin : int, end : int, center : rosetta.numeric.xyzVector_double_t) -> int

sequence_map_from_pdbinfo(first : rosetta.core.pose.Pose, second : rosetta.core.pose.Pose) -> rosetta.core.id.SequenceMapping

Create a sequence map of first pose onto the second, matching the PDBInfo If the PDBInfo of either Pose is missing or invalid, do a simple sequence alignment matching.

setPoseExtraScore(args, *kwargs) Overloaded function.

1. setPoseExtraScore(pose : rosetta.core.pose.Pose, name : str, value : float) -> NoneType

2. setPoseExtraScore(pose : rosetta.core.pose.Pose, name : str, value : str) -> NoneType

set_bb_torsion(torsion_id : int, pose : rosetta.core.pose.Pose, sequence_position : int, new_angle : float) -> NoneType

Set the BB torsion, phi, psi, omega (see core::types). Works with carbohydrates. Think about moving this to pose itself.

set_bfactors_from_atom_id_map(pose : rosetta.core.pose.Pose, bfactors : rosetta.core.id.AtomID_Map_double_t) -> NoneType

Set bfactors in a pose PDBInfo

set_reasonable_fold_tree(pose : rosetta.core.pose.Pose) -> NoneType

set_ss_from_phipsi(pose : rosetta.core.pose.Pose) -> NoneType

Analyzes residue phi/psi sets and guesses the secondary structure, ideally dssp should be used for that

setup_dof_mask_from_move_map(mm : core::kinematics::MoveMap, pose : rosetta.core.pose.Pose, dof_mask : rosetta.core.id.DOF_ID_Map_bool_t) -> NoneType

convert from allow-bb/allow-chi MoveMap to simple DOF_ID boolean mask needed by the minimizer

setup_dof_to_torsion_map(pose : rosetta.core.pose.Pose, dof_map : rosetta.core.id.DOF_ID_Map_core_id_TorsionID_t) -> NoneType

set up a map to look up TORSION_ID by DOF_ID (Map[DOF_ID] = TORISION_ID)

sort_pose_by_score(pose1 : rosetta.core.pose.Pose, pose2 : rosetta.core.pose.Pose) -> bool

stub_id_to_named_stub_id(stub_id : rosetta.core.id.StubID, pose : rosetta.core.pose.Pose) -> rosetta.core.id.NamedStubID

swap_transform(jump_num : int, xform : rosetta.core.kinematics.RT, pose : rosetta.core.pose.Pose) -> NoneType

Updates the rigid-body transform of the specified jump in

tag_from_pose(pose : rosetta.core.pose.Pose) -> str

////////////////////////////////////////////////////////////////

tag_into_pose(pose : rosetta.core.pose.Pose, tag : str) -> NoneType

total_energy_from_pose(pose : rosetta.core.pose.Pose) -> float

transfer_jumps(srcpose : rosetta.core.pose.Pose, tgtpose : rosetta.core.pose.Pose) -> NoneType

transfer_phi_psi(args, *kwargs) Overloaded function.

1. transfer_phi_psi(srcpose : rosetta.core.pose.Pose, tgtpose : rosetta.core.pose.Pose, ir : int, jr : int) -> NoneType

2. transfer_phi_psi(srcpose : rosetta.core.pose.Pose, tgtpose : rosetta.core.pose.Pose) -> NoneType

not quite (silent_structs don't necessarily have xyz). Kind of like a Conformation but without the overtree of an atom_tree.

Should save memory compared to keeping the full pose (which includes atom_tree, energies etc.) This is a bit like the SilentStruct -- although that class has gotten a bit complicated -- easier to start from scratch.

maintains pdb residue & atom information inside a Pose

Upon creation of new residue records, e.g. when calling the constructors without 'init' or appending/prepending residues, the chain id for the new records will be set to a character, currently '^', denoting "empty record". This character may be looked up by calling the static method PDBInfo::empty_record().

Class implementation is biased towards simplicity and fast lookup. Residue/atom information are kept in vectors. An internally maintained PDBPoseMap provides mapping from pdb -> pose residue numbering. This causes residue mutators to be a bit more expensive due to map updates, but this is ok because they are typically called sparingly. Accessors and mutators have overloaded method convention, while special mutators use .set_* convention.

PDBPoseMap can be queried with PDB information (chain, sequence position) and returns a pose's resid position. Useful for handing input/output in terms of PDB positions. Can be tucked into the pose for repeated access, or generated just-in-time for a single use. Basically a wrapper class for std::map.

The Pose class represents a molecular system (protein-dna-ligand...) as a container of Rosetta Residue objects together with a Conformation object that defines how internal coordinate changes propagate through the system and an Energies object that stores information from the last energy evaluation.

The main responsibilities of the pose are:

Kinematic: (a) to update the xyz coordinates in response to changes to internal degrees of freedom, and (b) to update internal coordinates when the user modifes the xyz (Cartesian) coords,

Scoring: (a) to keep track of what parts of the structure have changed since the last score evaluation, and (b) to cache residue and residue-pair energies for efficient re-use

As a container: The pose provides a single object for passing a molecular system and for copying of entire molecules or stretches of molecules from one Pose object into another.

Output Methods: Common Methods: Pose.assign Pose.atom_tree Pose.conformation Pose.dump_pdb Pose.dump_cif Pose.dump_file Pose.energies Pose.fold_tree Pose.pdb_info Pose.residue Pose.sequence Pose.total_residue

a class which can represent one of many ways in which to describe a particular residue in a pose, and can, when given a pose, find its index. The object should be constructed with all its needed parameters, but, one instance may be copied from another.

%ResidueIndexDescriptionFromFile differs from its parent only in its error reporting when a residue index resolution fails: it prints the file name and the line number that the residue index data came from.

info about an atom in a unrecognized res (not in pose, but we want to remember it)