Welcome to PyRosetta’s documentation!

Contents:

Bindings for core::pose namespace

class rosetta.core.pose.MiniPose

Bases: object

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.

assign(self : rosetta.core.pose.MiniPose, : rosetta.core.pose.MiniPose) → rosetta.core.pose.MiniPose

atom_name(self : rosetta.core.pose.MiniPose, atom_id : rosetta.core.id.AtomID) → str

atom_names_list(rosetta.core.pose.MiniPose) → rosetta.utility.vector1_utility_vector1_std_string_std_allocator_std_string_t

coords(rosetta.core.pose.MiniPose) → rosetta.utility.vector1_utility_vector1_numeric_xyzVector_double_std_allocator_numeric_xyzVector_double_t

fold_tree(rosetta.core.pose.MiniPose) → rosetta.core.kinematics.FoldTree

sequence(rosetta.core.pose.MiniPose) → str

size(rosetta.core.pose.MiniPose) → int

total_residue(rosetta.core.pose.MiniPose) → int

variant_types(self : rosetta.core.pose.MiniPose, seq_num : int) → rosetta.utility.vector1_std_string

variant_types_list(rosetta.core.pose.MiniPose) → rosetta.utility.vector1_utility_vector1_std_string_std_allocator_std_string_t

xyz(self : rosetta.core.pose.MiniPose, atom_id : rosetta.core.id.AtomID) → rosetta.numeric.xyzVector_double_t

class rosetta.core.pose.PDBInfo

Bases: object

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.

add_reslabel(self : rosetta.core.pose.PDBInfo, res : int, label : str) → NoneType

adds a label associated to a pose resid.

residue in pose numbering

string that is the “label”

add_unrecognized_atoms(self : rosetta.core.pose.PDBInfo, UAs : rosetta.utility.vector1_core_pose_UnrecognizedAtomRecord) → NoneType

remembers info about atoms not read into the pose

alt_loc(*args, **kwargs)

Overloaded function.

1. alt_loc(self : rosetta.core.pose.PDBInfo, res : int, atom_index : int) -> str

Returns the alternate location for the <atom_index> atom of pose

residue <res>

example(s):

pose.pdb_info().alt_loc(1,1)

See also:

Pose PDBInfo PDBInfo.pdb2pose PDBInfo.pose2pdb

2. alt_loc(self : rosetta.core.pose.PDBInfo, res : int, atom_index : int, loc : str) -> NoneType

Sets the alternate location of the <atom_index> atom of pose

residue <res> to <loc>

: <loc> is an alternate location character

append_res(*args, **kwargs)

Overloaded function.

1. append_res(self : rosetta.core.pose.PDBInfo, res : int, natoms : int) -> NoneType

Appends residue records given a pose residue number <res>

residue to append after (in internal/pose numbering)

number of atoms in type of appended residue

number of residue records to append

2. append_res(self : rosetta.core.pose.PDBInfo, res : int, natoms : int, n : int) -> NoneType

Appends residue records given a pose residue number <res>

residue to append after (in internal/pose numbering)

number of atoms in type of appended residue

number of residue records to append

assign(self : rosetta.core.pose.PDBInfo, info : rosetta.core.pose.PDBInfo) → rosetta.core.pose.PDBInfo

copy assignment

attach_to(self : rosetta.core.pose.PDBInfo, conf : rosetta.core.conformation.Conformation) → NoneType

Attaches the Conformation <conf> and begins observation

example(s):

See also:

Pose PDBInfo

bfactor(*args, **kwargs)

Overloaded function.

1. bfactor(self : rosetta.core.pose.PDBInfo, res : int, atom_index : int) -> float

Returns the temperature for the <atom_index> atom of pose residue <res>

example(s):

pose.pdb_info().temperature(1,1)

See also:

Pose PDBInfo PDBInfo.pdb2pose PDBInfo.pose2pdb

2. bfactor(self : rosetta.core.pose.PDBInfo, res : int, atom_index : int, t : float) -> NoneType

Sets the temperature of the <atom_index> atom of pose residue

<res> to <t>

chain(*args, **kwargs)

Overloaded function.

1. chain(self : rosetta.core.pose.PDBInfo, res : int) -> str

Returns the chain id for pose residue <res>

example(s):

pose.pdb_info().chain(3)

See also:

Pose PDBInfo PDBInfo.pdb2pose PDBInfo.pose2pdb

2. chain(self : rosetta.core.pose.PDBInfo, res : int, chain_id : str) -> NoneType

Sets the chain id of pose residue <res> to <chain_id>

chain id should not be the empty record character, currently ‘^’

Returns the pdb insertion code of residue <res>

example(s):

pose.pdb_info().chain(3,”R”)

See also:

Pose PDBInfo PDBInfo.pdb2pose PDBInfo.pose2pdb

clear_reslabel(self : rosetta.core.pose.PDBInfo, res : int) → NoneType

clean all the label(s) associated to a pose resid.

residue in pose numbering

copy(self : rosetta.core.pose.PDBInfo, input_info : rosetta.core.pose.PDBInfo, copy_from : int, copy_to : int, start_from : int) → NoneType

Copyies a section from PDBInfo <input_info>

the PDBInfo to copy from

the first residue position in input_info to copy

the final residue position in input_info to copy

the first residue position in this PDBInfo to

copy into

crystinfo(rosetta.core.pose.PDBInfo) → rosetta.core.io.CrystInfo

Returns the pdb crystinfo

delete_res(*args, **kwargs)

Overloaded function.

1. delete_res(self : rosetta.core.pose.PDBInfo, res : int) -> NoneType

Deletes <n> residue records starting from pose residue <res>

residue to start deleting from (in internal/pose numbering)

number of residue records to delete

2. delete_res(self : rosetta.core.pose.PDBInfo, res : int, n : int) -> NoneType

Deletes <n> residue records starting from pose residue <res>

residue to start deleting from (in internal/pose numbering)

number of residue records to delete

detach_from(rosetta.core.pose.PDBInfo) → NoneType

Detaches the Conformation and stops observation

takes no arguments because PDBInfo can only observe one Conformation at a time

example(s):

pose.pdb_info().detach_from()

See also:

Pose PDBInfo

empty_record() → str

Returns the chain id character specifying “empty record”,

currently ‘^’

get_num_unrecognized_atoms(rosetta.core.pose.PDBInfo) → int

get_num_unrecognized_res(rosetta.core.pose.PDBInfo) → int

get_reslabels(self : rosetta.core.pose.PDBInfo, res : int) → rosetta.utility.vector1_std_string

returns the pose(number) labels associated to the residue

residue in pose numbering

get_unrecognized_atoms(rosetta.core.pose.PDBInfo) → rosetta.utility.vector1_core_pose_UnrecognizedAtomRecord

remembers info about atoms not read into the pose

get_unrecognized_res_name(self : rosetta.core.pose.PDBInfo, i : int) → str

get_unrecognized_res_size(self : rosetta.core.pose.PDBInfo, i : int) → int

header_information(*args, **kwargs)

Overloaded function.

1. header_information(self : rosetta.core.pose.PDBInfo, header_information : rosetta.core.io.HeaderInformation) -> NoneType

Note: The header information is only initialized if it is needed.

Generally this requires using the -run:preserve_header options flag.

2. header_information(rosetta.core.pose.PDBInfo) -> rosetta.core.io.HeaderInformation
3. header_information(rosetta.core.pose.PDBInfo) -> rosetta.core.io.HeaderInformation

icode(*args, **kwargs)

Overloaded function.

1. icode(self : rosetta.core.pose.PDBInfo, res : int) -> str

Returns the pdb insertion code of residue <res>

example(s):

pose.pdb_info().icode(3)

See also:

Pose PDBInfo PDBInfo.pdb2pose PDBInfo.pose2pdb

2. icode(self : rosetta.core.pose.PDBInfo, res : int, ins_code : str) -> NoneType

Sets the insertion code of pose residue <res> to _code>

Returns the pdb insertion code of residue <res>

example(s):

See also:

Pose PDBInfo PDBInfo.pdb2pose PDBInfo.pose2pdb

is_het(*args, **kwargs)

Overloaded function.

1. is_het(self : rosetta.core.pose.PDBInfo, res : int, atom_index : int) -> bool

Returns true if the <atom_index> atom of pose residue <res>

is a heteratom

: atom index within instance of core::conformation::Residue,

currently Rosetta’s pdb file output treats the value of .is_het() as an override – if this is set to true, the record will be hetatm, otherwise it will decide by Residue type (the usual default)

2. is_het(self : rosetta.core.pose.PDBInfo, res : int, atom_index : int, flag : bool) -> NoneType

Sets the heteroatom flag of the <atom_index> atom of pose

residue <res> to <flag>

currently Rosetta’s pdb file output treats the value of .is_het() as an override – if this is set to true, the record will be hetatm, otherwise it will decide by Residue type (the usual default)

is_observing(rosetta.core.pose.PDBInfo) → rosetta.std.weak_ptr_const_core_conformation_Conformation_t

Returns the Conformation if this PDBInfo is currently observing

a conformation, otherwise return NULL

example(s):

pose.pdb_info().is_observing()

See also:

Pose PDBInfo

modeltag(*args, **kwargs)

Overloaded function.

1. modeltag(rosetta.core.pose.PDBInfo) -> str

Returns the model tag for a multi-model pdb

example(s):

pose.pdb_info().modeltag()

See also:

Pose PDBInfo

2. modeltag(self : rosetta.core.pose.PDBInfo, tag : str) -> NoneType

Sets the model tag for a multi-model pdb to <tag>

example(s):

pose.pdb_info().modeltag(‘Number1’)

See also:

Pose PDBInfo

name(*args, **kwargs)

Overloaded function.

1. name(rosetta.core.pose.PDBInfo) -> str

Returns the pdb name

example(s):

pose.pdb_info().name()

See also:

Pose PDBInfo

2. name(self : rosetta.core.pose.PDBInfo, s : str) -> NoneType

Sets the pdb name

example(s):

pose.pdb_info().name(‘MyPDB’)

See also:

Pose PDBInfo

natoms(self : rosetta.core.pose.PDBInfo, res : int) → int

Returns the number of atoms represented for the residue <res>

: residue <res> must be in pose numbering

example(s):

pose.pdb_info().natoms(3)

See also:

Pose PDBInfo

nres(rosetta.core.pose.PDBInfo) → int

Returns the number of residues represented in PDBInfo

example(s):

pose.pdb_info().nres()

See also:

Pose PDBInfo

number(*args, **kwargs)

Overloaded function.

1. number(self : rosetta.core.pose.PDBInfo, res : int) -> int

Returns the pdb sequence number of pose residue <res>

example(s):

pose.pdb_info().number(3)

See also:

Pose PDBInfo PDBInfo.pdb2pose PDBInfo.pose2pdb

2. number(self : rosetta.core.pose.PDBInfo, res : int, pdb_res : int) -> NoneType

Sets the pdb sequence residue number of pose residue <res> to <pdb_res>

Returns the pdb insertion code of residue <res>

example(s):

pose.pdb_info().number(3,81)

See also:

Pose PDBInfo PDBInfo.pdb2pose PDBInfo.pose2pdb

obsolete(*args, **kwargs)

Overloaded function.

1. obsolete(rosetta.core.pose.PDBInfo) -> bool

Returns true if PDBInfo is obsolete and needs updating

This flag is currently not used within the class and is provided for user convenience. Setting this will forcibly turn off pdb numbering when dumping pdbs.

example(s):

pose.pdb_info().obsolete()

See also:

Pose PDBInfo

2. obsolete(self : rosetta.core.pose.PDBInfo, flag : bool) -> NoneType

Sets the obsolete state to <flag>

this flag is currently not used within the class and is provided for user convenience. Setting this will forcibly turn off pdb numbering when dumping pdbs.

occupancy(*args, **kwargs)

Overloaded function.

1. occupancy(self : rosetta.core.pose.PDBInfo, res : int, atom_index : int) -> float

Returns the occupancy for the <atom_index> atom of pose residue <res>

example(s):

pose.pdb_info().occupancy(1,1)

See also:

Pose PDBInfo PDBInfo.pdb2pose PDBInfo.pose2pdb

2. occupancy(self : rosetta.core.pose.PDBInfo, res : int, atom_index : int, occ : float) -> NoneType

Sets the occupancy of the <atom_index> atom of pose residue

<res> to <occ>

on_connection_change(self : rosetta.core.pose.PDBInfo, event : rosetta.core.conformation.signals.ConnectionEvent) → NoneType

Updates when connection to Conformation is changed

on_identity_change(self : rosetta.core.pose.PDBInfo, event : rosetta.core.conformation.signals.IdentityEvent) → NoneType

Updates atom records when residue identity changes in Conformation

on_length_change(self : rosetta.core.pose.PDBInfo, event : rosetta.core.conformation.signals.LengthEvent) → NoneType

Updates residue and atom records when length changes in Conformation,

obsoletes PDBInfo

pdb2pose(*args, **kwargs)

Overloaded function.

1. pdb2pose(self : rosetta.core.pose.PDBInfo, chain : str, res : int) -> int

Returns the pose numbering of the pdb residue with chain <chain>,

pdb residue <res>, and insertion code <icode>

: <icode> is not required, returns 0 if not found,

pose numbering is sequential ie. starts at 1 and goes up pdb numbering can be anything

example(s):

pose.pdb_info().pdb2pose(“B”,5)

See also:

Pose PDBInfo PDBInfo.pose2pdb

2. pdb2pose(self : rosetta.core.pose.PDBInfo, chain : str, res : int, icode : str) -> int

Returns the pose numbering of the pdb residue with chain <chain>,

pdb residue <res>, and insertion code <icode>

: <icode> is not required, returns 0 if not found,

pose numbering is sequential ie. starts at 1 and goes up pdb numbering can be anything

example(s):

pose.pdb_info().pdb2pose(“B”,5)

See also:

Pose PDBInfo PDBInfo.pose2pdb

3. pdb2pose(rosetta.core.pose.PDBInfo) -> rosetta.core.pose.PDBPoseMap

Returns the internally maintained PDBPoseMap

example(s):

See also:

Pose PDBInfo PDBInfo.pdb2pose PDBInfo.pose2pdb

pose2pdb(self : rosetta.core.pose.PDBInfo, res : int) → str

Returns the pdb numbering string of pose residue <res>

: pdb string contains the chainID and number

pose numbering is sequential ie. starts at 1 and goes up pdb numbering can be anything

example(s):

pose.pdb_info().pose2pdb(25)

See also:

Pose PDBInfo PDBInfo.pdb2pose

prepend_res(*args, **kwargs)

Overloaded function.

1. prepend_res(self : rosetta.core.pose.PDBInfo, res : int, natoms : int) -> NoneType

Prepends residue records before given pose residue number <res>

residue to prepend before (in internal/pose numbering)

number of atoms in type of appended residue

number of residue records to prepend

2. prepend_res(self : rosetta.core.pose.PDBInfo, res : int, natoms : int, n : int) -> NoneType

Prepends residue records before given pose residue number <res>

residue to prepend before (in internal/pose numbering)

number of atoms in type of appended residue

number of residue records to prepend

rebuild_pdb2pose(rosetta.core.pose.PDBInfo) → NoneType

rebuilds PDBPoseMap from scratch

remarks(*args, **kwargs)

Overloaded function.

1. remarks(rosetta.core.pose.PDBInfo) -> rosetta.core.io.Remarks

Returns the pdb remarks (const)

example(s):

pose.pdb_info().remarks()

See also:

Pose PDBInfo

2. remarks(rosetta.core.pose.PDBInfo) -> rosetta.core.io.Remarks

Returns the pdb remarks (mutable)

we allow direct access to the remarks vector because its state is independent of the rest of PDBInfo and it’s much more convenient for the user

example(s):

pose.pdb_info().remarks()

See also:

Pose PDBInfo

3. remarks(self : rosetta.core.pose.PDBInfo, in : rosetta.core.io.Remarks) -> NoneType

Sets the pdb remarks to <in>

example(s):

See also:

Pose PDBInfo

replace_res(self : rosetta.core.pose.PDBInfo, res : int, natoms : int) → NoneType

“Replaces” residue record for pose residue <res>

Leaves information in residue record untouched, but resizes and zeroes atom records for the residue.

residue to replace

number of atoms in type of residue

replace_res_remap_bfactors(self : rosetta.core.pose.PDBInfo, res : int, tgt : rosetta.core.conformation.Residue) → NoneType

same as replace_res BUT remaps B factors from src to tgt

res_haslabel(self : rosetta.core.pose.PDBInfo, res : int, target_label : str) → bool

uses std iterators to check if a residue has a label associated to it

residue in pose numbering

string to look for inside the labes associated to the residue

resize_atom_records(*args, **kwargs)

Overloaded function.

1. resize_atom_records(self : rosetta.core.pose.PDBInfo, res : int, n : int) -> NoneType

Ensures <n> atom records for residue <res> are available

: if <zero> is true, zero the atom records for this residue

2. resize_atom_records(self : rosetta.core.pose.PDBInfo, res : int, n : int, zero : bool) -> NoneType

Ensures <n> atom records for residue <res> are available

: if <zero> is true, zero the atom records for this residue

3. resize_atom_records(self : rosetta.core.pose.PDBInfo, n : int) -> NoneType

Ensures <n> atom records for residue <res> are available

: if <zero> is true, zero the atom records for this residue

4. resize_atom_records(self : rosetta.core.pose.PDBInfo, n : int, zero : bool) -> NoneType

Ensures <n> atom records for residue <res> are available

: if <zero> is true, zero the atom records for this residue

5. resize_atom_records(self : rosetta.core.pose.PDBInfo, pose : rosetta.core.pose.Pose) -> NoneType

Updates the number of atom records with respect to atoms in <pose>

Number of internally available atom records will be adjusted to match number of atoms within each residue in Pose. Only newly created records will be zeroed, any existing records are untouched.

resize_residue_records(self : rosetta.core.pose.PDBInfo, n : int) → NoneType

Resizes for <n> residue records

Leaves atom record state inconsistent. Atom records for remaining residues are untouched while new residues have no atom records, so make sure and call one of resize_atom_records() afterwards if necessary.

Do not use this method for ins/del of residues, as it leaves the data state inconsistent. See append_res/prepend_res/delete_res for that type of functionality.

segmentID(*args, **kwargs)

Overloaded function.

1. segmentID(self : rosetta.core.pose.PDBInfo, res : int) -> str
2. segmentID(self : rosetta.core.pose.PDBInfo, res : int, segmentID : str) -> NoneType

Sets the insertion code of pose residue <res> to _code>

Returns the pdb insertion code of residue <res>

example(s):

See also:

Pose PDBInfo PDBInfo.pdb2pose PDBInfo.pose2pdb

set_chains(self : rosetta.core.pose.PDBInfo, id : str) → NoneType

Sets all residue chain ids to the character <id>

set_crystinfo(self : rosetta.core.pose.PDBInfo, crystinfoin : rosetta.core.io.CrystInfo) → NoneType

Sets the pdb crystinfo

set_resinfo(*args, **kwargs)

Overloaded function.

1. set_resinfo(self : rosetta.core.pose.PDBInfo, res : int, chain_id : str, pdb_res : int) -> NoneType

Sets the chain id, pdb sequence residue numbering, and insertion

code for pose residue <res> to <chain_id> , <pdb_res> , and _code> respectfully

: convenience method; more efficient than doing each individually

due to map updates

Returns the pdb insertion code of residue <res>

example(s):

pose.pdb_info().icode(3)

See also:

Pose PDBInfo PDBInfo.chain PDBInfo.icode PDBInfo.number PDBInfo.pdb2pose PDBInfo.pose2pdb

2. set_resinfo(self : rosetta.core.pose.PDBInfo, res : int, chain_id : str, pdb_res : int, ins_code : str) -> NoneType

Sets the chain id, pdb sequence residue numbering, and insertion

code for pose residue <res> to <chain_id> , <pdb_res> , and _code> respectfully

: convenience method; more efficient than doing each individually

due to map updates

Returns the pdb insertion code of residue <res>

example(s):

pose.pdb_info().icode(3)

See also:

Pose PDBInfo PDBInfo.chain PDBInfo.icode PDBInfo.number PDBInfo.pdb2pose PDBInfo.pose2pdb

temperature(*args, **kwargs)

Overloaded function.

1. temperature(self : rosetta.core.pose.PDBInfo, res : int, atom_index : int) -> float

Returns the temperature for the <atom_index> atom of pose residue <res>

example(s):

pose.pdb_info().temperature(1,1)

See also:

Pose PDBInfo PDBInfo.pdb2pose PDBInfo.pose2pdb

2. temperature(self : rosetta.core.pose.PDBInfo, res : int, atom_index : int, t : float) -> NoneType

Sets the temperature of the <atom_index> atom of pose residue

<res> to <t>

tighten_memory(rosetta.core.pose.PDBInfo) → NoneType

Tightens memory usage

class rosetta.core.pose.PDBPoseMap

Bases: object

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.

assign(self : rosetta.core.pose.PDBPoseMap, m : rosetta.core.pose.PDBPoseMap) → rosetta.core.pose.PDBPoseMap

copy assignment

clear(rosetta.core.pose.PDBPoseMap) → NoneType

clear the current mapping data

conditional_erase(self : rosetta.core.pose.PDBPoseMap, chain : str, pdb_res : int, ins_code : str, pose_res : int) → bool

remove mapping for pdb residue key only if Pose residue matches

chain id

pdb residue numbering

insertion code, use ‘ ‘ if no insertion code

the mapped Pose residue

true if key-value pair erase, false otherwise

erase(self : rosetta.core.pose.PDBPoseMap, chain : str, pdb_res : int, ins_code : str) → NoneType

forcibly remove mapping for pdb residue key

chain id

pdb residue numbering

insertion code, use ‘ ‘ if no insertion code

fill(self : rosetta.core.pose.PDBPoseMap, info : core::pose::PDBInfo) → NoneType

fill with corresponding pdb -> pose residue mapping

does not clear any currently existing mapping data

find(*args, **kwargs)

Overloaded function.

1. find(self : rosetta.core.pose.PDBPoseMap, chain : str, pdb_res : int) -> int

lookup pose numbering

chain id

pdb residue numbering

insertion code

pose numbering for residue, returns 0 if not found

2. find(self : rosetta.core.pose.PDBPoseMap, chain : str, pdb_res : int, ins_code : str) -> int

lookup pose numbering

chain id

pdb residue numbering

insertion code

pose numbering for residue, returns 0 if not found

insert(self : rosetta.core.pose.PDBPoseMap, chain : str, pdb_res : int, ins_code : str, pose_res : int) → NoneType

insert pdb -> pose number mapping

chain id

pdb residue numbering

insertion code, use ‘ ‘ if no insertion code

pose numbering for residue

if the chain is equal to the PDBInfo’s empty record character,

the insertion will be skipped

size(rosetta.core.pose.PDBPoseMap) → int

number of mappings

class rosetta.core.pose.Pose

Bases: object

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

aa(self : rosetta.core.pose.Pose, seqpos : int) → rosetta.core.chemical.AA

Returns the chemical::AA of the residue at <seqpos>

example(s):

pose.aa(17)

See also:

Pose

Pose.Residue

Pose.sequence Residue

add_constraint(self : rosetta.core.pose.Pose, cst : core::scoring::constraints::Constraint) → core::scoring::constraints::Constraint

adding a constraint is done by cloning the input constraint. A const copy is then returned

add_constraints(self : rosetta.core.pose.Pose, csts : rosetta.utility.vector1_std_shared_ptr_const_core_scoring_constraints_Constraint_t) → rosetta.utility.vector1_std_shared_ptr_const_core_scoring_constraints_Constraint_t

alpha(self : rosetta.core.pose.Pose, pos : int) → float

Returns the alpha torsion angle of residue <seqpos>

assumes the residue is an nucleic acid

example(s):

pose.alpha(1)

See also:

Pose Pose.residue Pose.set_alpha Residue

annotated_sequence(*args, **kwargs)

Overloaded function.

1. annotated_sequence(rosetta.core.pose.Pose) -> str

Returns the variant-tagged string representing the

residue types that make up a conformation; e.g. M[MET:N-Terminus-Variant]CDH[HIS_D]LLR[ARG:C-Terminus-Variant]

example(s):

pose.annotated_sequence()

See also:

Pose Pose.sequence Pose.total_residue

Residue

2. annotated_sequence(self : rosetta.core.pose.Pose, show_all_variants : bool) -> str

Returns the variant-tagged string representing the

residue types that make up a conformation; e.g. M[MET:N-Terminus-Variant]CDH[HIS_D]LLR[ARG:C-Terminus-Variant]

example(s):

pose.annotated_sequence()

See also:

Pose Pose.sequence Pose.total_residue

Residue

append_polymer_residue_after_seqpos(self : rosetta.core.pose.Pose, new_rsd : rosetta.core.conformation.Residue, seqpos : int, build_ideal_geometry : bool) → NoneType

glues to seqpos and perhaps also seqpos+1

append_pose_by_jump(*args, **kwargs)

Overloaded function.

1. append_pose_by_jump(self : rosetta.core.pose.Pose, src : rosetta.core.pose.Pose, jump_anchor_residue : int) -> NoneType

Appends source pose conformation to pose by a new jump

2. append_pose_by_jump(self : rosetta.core.pose.Pose, src : rosetta.core.pose.Pose, jump_anchor_residue : int, jump_anchor_atom : str) -> NoneType

Appends source pose conformation to pose by a new jump

3. append_pose_by_jump(self : rosetta.core.pose.Pose, src : rosetta.core.pose.Pose, jump_anchor_residue : int, jump_anchor_atom : str, jump_root_atom : str) -> NoneType

Appends source pose conformation to pose by a new jump

append_residue_by_atoms(*args, **kwargs)

Overloaded function.

1. append_residue_by_atoms(self : rosetta.core.pose.Pose, new_rsd : rosetta.core.conformation.Residue, build_ideal_geometry : bool, connect_atom : str, anchor_rsd_seqpos : int, anchor_connect_atom : str) -> NoneType

Appends <new_rsd> (a residue) to pose by a new bond to a given atom

This function effectively wraps append_residue_by_bond for an easier syntax. Instead of having to know what the connection, anchor residue, and anchor connection are, we give the atoms and query the ResidueType for the remaining information.

If build_ideal_bond is TRUE it will transform the coordinates of the new residue so that the bond geometry of the new bond is ideal according to the icoor_internal data in the residues.

Otherwise the incoming coordinates of new_rsd are preserved.

2. append_residue_by_atoms(self : rosetta.core.pose.Pose, new_rsd : rosetta.core.conformation.Residue, build_ideal_geometry : bool, connect_atom : str, anchor_rsd_seqpos : int, anchor_connect_atom : str, start_new_chain : bool) -> NoneType

Appends <new_rsd> (a residue) to pose by a new bond to a given atom

This function effectively wraps append_residue_by_bond for an easier syntax. Instead of having to know what the connection, anchor residue, and anchor connection are, we give the atoms and query the ResidueType for the remaining information.

If build_ideal_bond is TRUE it will transform the coordinates of the new residue so that the bond geometry of the new bond is ideal according to the icoor_internal data in the residues.

Otherwise the incoming coordinates of new_rsd are preserved.

3. append_residue_by_atoms(self : rosetta.core.pose.Pose, new_rsd : rosetta.core.conformation.Residue, build_ideal_geometry : bool, connect_atom : str, anchor_rsd_seqpos : int, anchor_connect_atom : str, start_new_chain : bool, lookup_bond_length : bool) -> NoneType

Appends <new_rsd> (a residue) to pose by a new bond to a given atom

This function effectively wraps append_residue_by_bond for an easier syntax. Instead of having to know what the connection, anchor residue, and anchor connection are, we give the atoms and query the ResidueType for the remaining information.

If build_ideal_bond is TRUE it will transform the coordinates of the new residue so that the bond geometry of the new bond is ideal according to the icoor_internal data in the residues.

Otherwise the incoming coordinates of new_rsd are preserved.

append_residue_by_bond(*args, **kwargs)

Overloaded function.

1. append_residue_by_bond(self : rosetta.core.pose.Pose, new_rsd : rosetta.core.conformation.Residue) -> NoneType

Appends <new_rsd> (a residue) to pose by a new bond

The default behavior is to append by a polymeric connection to the preceding residue If we want to connect via a non-polymer connection, we give the connection number, anchor residue and the connection number for the anchor residue. These connection numbers are wrt the connections_ arrays in Residue and ResidueType

If build_ideal_bond is TRUE it will transform the coordinates of the new residue so that the bond geometry of the new bond is ideal according to the icoor_internal data in the residues.

Otherwise the incoming coordinates of new_rsd are preserved.

2. append_residue_by_bond(self : rosetta.core.pose.Pose, new_rsd : rosetta.core.conformation.Residue, build_ideal_geometry : bool) -> NoneType

Appends <new_rsd> (a residue) to pose by a new bond

The default behavior is to append by a polymeric connection to the preceding residue If we want to connect via a non-polymer connection, we give the connection number, anchor residue and the connection number for the anchor residue. These connection numbers are wrt the connections_ arrays in Residue and ResidueType

If build_ideal_bond is TRUE it will transform the coordinates of the new residue so that the bond geometry of the new bond is ideal according to the icoor_internal data in the residues.

Otherwise the incoming coordinates of new_rsd are preserved.

3. append_residue_by_bond(self : rosetta.core.pose.Pose, new_rsd : rosetta.core.conformation.Residue, build_ideal_geometry : bool, connection : int) -> NoneType

Appends <new_rsd> (a residue) to pose by a new bond

The default behavior is to append by a polymeric connection to the preceding residue If we want to connect via a non-polymer connection, we give the connection number, anchor residue and the connection number for the anchor residue. These connection numbers are wrt the connections_ arrays in Residue and ResidueType

If build_ideal_bond is TRUE it will transform the coordinates of the new residue so that the bond geometry of the new bond is ideal according to the icoor_internal data in the residues.

Otherwise the incoming coordinates of new_rsd are preserved.

4. append_residue_by_bond(self : rosetta.core.pose.Pose, new_rsd : rosetta.core.conformation.Residue, build_ideal_geometry : bool, connection : int, anchor_residue : int) -> NoneType

Appends <new_rsd> (a residue) to pose by a new bond

The default behavior is to append by a polymeric connection to the preceding residue If we want to connect via a non-polymer connection, we give the connection number, anchor residue and the connection number for the anchor residue. These connection numbers are wrt the connections_ arrays in Residue and ResidueType

If build_ideal_bond is TRUE it will transform the coordinates of the new residue so that the bond geometry of the new bond is ideal according to the icoor_internal data in the residues.

Otherwise the incoming coordinates of new_rsd are preserved.

5. append_residue_by_bond(self : rosetta.core.pose.Pose, new_rsd : rosetta.core.conformation.Residue, build_ideal_geometry : bool, connection : int, anchor_residue : int, anchor_connection : int) -> NoneType

Appends <new_rsd> (a residue) to pose by a new bond

The default behavior is to append by a polymeric connection to the preceding residue If we want to connect via a non-polymer connection, we give the connection number, anchor residue and the connection number for the anchor residue. These connection numbers are wrt the connections_ arrays in Residue and ResidueType

If build_ideal_bond is TRUE it will transform the coordinates of the new residue so that the bond geometry of the new bond is ideal according to the icoor_internal data in the residues.

Otherwise the incoming coordinates of new_rsd are preserved.

6. append_residue_by_bond(self : rosetta.core.pose.Pose, new_rsd : rosetta.core.conformation.Residue, build_ideal_geometry : bool, connection : int, anchor_residue : int, anchor_connection : int, start_new_chain : bool) -> NoneType

Appends <new_rsd> (a residue) to pose by a new bond

The default behavior is to append by a polymeric connection to the preceding residue If we want to connect via a non-polymer connection, we give the connection number, anchor residue and the connection number for the anchor residue. These connection numbers are wrt the connections_ arrays in Residue and ResidueType

If build_ideal_bond is TRUE it will transform the coordinates of the new residue so that the bond geometry of the new bond is ideal according to the icoor_internal data in the residues.

Otherwise the incoming coordinates of new_rsd are preserved.

7. append_residue_by_bond(self : rosetta.core.pose.Pose, new_rsd : rosetta.core.conformation.Residue, build_ideal_geometry : bool, connection : int, anchor_residue : int, anchor_connection : int, start_new_chain : bool, lookup_bond_length : bool) -> NoneType

Appends <new_rsd> (a residue) to pose by a new bond

The default behavior is to append by a polymeric connection to the preceding residue If we want to connect via a non-polymer connection, we give the connection number, anchor residue and the connection number for the anchor residue. These connection numbers are wrt the connections_ arrays in Residue and ResidueType

If build_ideal_bond is TRUE it will transform the coordinates of the new residue so that the bond geometry of the new bond is ideal according to the icoor_internal data in the residues.

Otherwise the incoming coordinates of new_rsd are preserved.

append_residue_by_jump(*args, **kwargs)

Overloaded function.

1. append_residue_by_jump(self : rosetta.core.pose.Pose, new_rsd : rosetta.core.conformation.Residue, jump_anchor_residue : int) -> NoneType

Appends <new_rsd> (a residue) to pose by a new jump

2. append_residue_by_jump(self : rosetta.core.pose.Pose, new_rsd : rosetta.core.conformation.Residue, jump_anchor_residue : int, jump_anchor_atom : str) -> NoneType

Appends <new_rsd> (a residue) to pose by a new jump

3. append_residue_by_jump(self : rosetta.core.pose.Pose, new_rsd : rosetta.core.conformation.Residue, jump_anchor_residue : int, jump_anchor_atom : str, jump_root_atom : str) -> NoneType

Appends <new_rsd> (a residue) to pose by a new jump

4. append_residue_by_jump(self : rosetta.core.pose.Pose, new_rsd : rosetta.core.conformation.Residue, jump_anchor_residue : int, jump_anchor_atom : str, jump_root_atom : str, start_new_chain : bool) -> NoneType

Appends <new_rsd> (a residue) to pose by a new jump

apply_transform_Rx_plus_v(self : rosetta.core.pose.Pose, R : rosetta.numeric.xyzMatrix_double_t, v : rosetta.numeric.xyzVector_double_t) → NoneType

Apply a transform of the Rx + v form, where R is a

rotation matrix and v is a translation vector.

assign(self : rosetta.core.pose.Pose, src : rosetta.core.pose.Pose) → rosetta.core.pose.Pose

Copies <src> into the pose where it remains possible that two

Poses may point to each other in non-const ways or share non-bitwise constant data between them (E.g. the AtomTree observer system).

example(s):

test_pose.assign(pose)

See also:

Pose

atom_tree(rosetta.core.pose.Pose) → core::kinematics::AtomTree

Returns the pose AtomTree

batch_get_xyz(self : rosetta.core.pose.Pose, ids : rosetta.utility.vector1_core_id_AtomID, points : rosetta.utility.vector1_numeric_xyzVector_double_t) → NoneType

Gets the locations (xyz) of pose AtomIDs in <ids>

batch_set_xyz(self : rosetta.core.pose.Pose, ids : rosetta.utility.vector1_core_id_AtomID, points : rosetta.utility.vector1_numeric_xyzVector_double_t) → NoneType

Sets the locations (xyz) of pose AtomIDs in <ids>

to mathcing PointPositions in <points>

beta(self : rosetta.core.pose.Pose, seqpos : int) → float

Returns the beta torsion angle of residue <seqpos>

assumes the residue is an nucleic acid

example(s):

pose.beta(2)

See also:

Pose Pose.residue Pose.set_beta Residue

center(rosetta.core.pose.Pose) → NoneType

Sets pose coordinates such that the pose center is at the Euclidean origin

chain(self : rosetta.core.pose.Pose, seqpos : int) → int

Returns the chain number of residue <seqpos>

example(s):

pose.chain(3)

See also:

Pose Pose.annotated_sequence

Pose.chain_sequence

Pose.fold_tree Pose.sequence FoldTree

chain_sequence(self : rosetta.core.pose.Pose, chain_in : int) → str

Returns the sequence for the chain <chain_in>

Example(s):

pose.chain_sequence(1)

See also:

Pose Pose.chain Pose.residue Pose.sequence

chi(*args, **kwargs)

Overloaded function.

1. chi(self : rosetta.core.pose.Pose, chino : int, seqpos : int) -> float

Returns the <chino> chi torsion angle of residue <seqpos>

assumes the residue is an amino acid or monosaccharide

example(s):

pose.chi(1,7)

See also:

Pose Pose.set_chi Pose.residue Residue

2. chi(self : rosetta.core.pose.Pose, seqpos : int) -> float

Returns the chi torsion angle of residue <seqpos>

assumes the residue is an nucleic acid

example(s):

pose.chi(7)

See also:

Pose Pose.residue Pose.set_chi Residue

clear(rosetta.core.pose.Pose) → NoneType

Empty the pose contents

example(s):

pose.clear()

See also:

Pose Pose.assign Pose.empty

clear_sequence_constraints(rosetta.core.pose.Pose) → NoneType

Remove all sequence constraints from this pose.

clone(rosetta.core.pose.Pose) → rosetta.core.pose.Pose

clone the conformation

conformation(*args, **kwargs)

Overloaded function.

1. conformation(rosetta.core.pose.Pose) -> rosetta.core.conformation.Conformation

Returns the pose Conformation (const-access)

example(s):

pose.Conformation()

See also:

Pose Conformation

2. conformation(rosetta.core.pose.Pose) -> rosetta.core.conformation.Conformation

Returns the pose Conformation (non-const access)

conformation_ptr(*args, **kwargs)

Overloaded function.

1. conformation_ptr(rosetta.core.pose.Pose) -> rosetta.core.conformation.Conformation

Returns the pose Conformation pointer (const access)

2. conformation_ptr(rosetta.core.pose.Pose) -> rosetta.core.conformation.Conformation

Returns the pose Conformation pointer (const access)

WHOA: This is not cool. The Pose cannot hand out access to the OP directly. Do not use.

const_data_cache(rosetta.core.pose.Pose) → rosetta.basic.datacache.ConstDataMap

Read access to the const data cache

constraint_set(*args, **kwargs)

Overloaded function.

1. constraint_set(rosetta.core.pose.Pose) -> core::scoring::constraints::ConstraintSet
2. constraint_set(self : rosetta.core.pose.Pose, : core::scoring::constraints::ConstraintSet) -> NoneType

copy_segment(self : rosetta.core.pose.Pose, size : int, src : rosetta.core.pose.Pose, begin : int, src_begin : int) → NoneType

Copy a stretch of coordinates/torsions from <src>

to pose

corresponding_residue_in_current(self : rosetta.core.pose.Pose, ref_residue_index : int, ref_pose_name : str) → int

Returns the index of a residue in this pose corresponding to a residue in a reference pose.

Throws an error if the reference pose with the given name doesn’t exist, or the residue number doesn’t exist in that reference pose. Returns zero if no corresponding residue exists in this pose (e.g. if the residue in question has been deleted.

data(*args, **kwargs)

Overloaded function.

1. data(rosetta.core.pose.Pose) -> rosetta.basic.datacache.BasicDataCache

BasicDataCache indexed by enum in core/pose/datacache/CacheableDataType.hh

2. data(rosetta.core.pose.Pose) -> rosetta.basic.datacache.BasicDataCache

BasicDataCache indexed by enum in core/pose/datacache/CacheableDataType.hh

decrement_reference_pose_mapping_after_seqpos(self : rosetta.core.pose.Pose, seqpos : int) → NoneType

Find all mappings in the new pose after seqpos in all ReferencePose objects, and decrement them by 1.

If there is no ReferencePose object, do nothing.

delete_polymer_residue(self : rosetta.core.pose.Pose, seqpos : int) → NoneType

Delete a residue in the pose.

Update Observers. Update any Reference Poses

delete_residue_range_slow(self : rosetta.core.pose.Pose, start : int, end : int) → NoneType

Delete a range of residues in the pose.

Calls confromation::delete_residue_range_slow().

Update Observers. Update any Reference Poses

delete_residue_slow(self : rosetta.core.pose.Pose, seqpos : int) → NoneType

Slow method that relies on FoldTree::delete_seqpos, rebuilds atomtree, can handle jumps/root residue.

Update Observers. Update any Reference Poses

delta(self : rosetta.core.pose.Pose, pos : int) → float

Returns the delta torsion angle of residue <seqpos>

assumes the residue is an nucleic acid

example(s):

pose.delta(4)

See also:

Pose Pose.residue Pose.set_delta Residue

detached_copy(self : rosetta.core.pose.Pose, src : rosetta.core.pose.Pose) → NoneType

Performs a deep copy of the src Pose into this Pose in a way

that guarantees that no non-bitwise-constant data is shared between them (such as the AtomTree’s observer system) – this Pose will be effectively detached from any data that lives in other objects.

dof(self : rosetta.core.pose.Pose, id : rosetta.core.id.DOF_ID) → float

Returns the value of the AtomTree DOF <id>

See also:

Pose DOF_ID

dump_cif(self : rosetta.core.pose.Pose, file_name : str) → NoneType

Export pose data to the mmCIF file <file_name>

example(s):

pose.dump_cif(‘new_01.cif’)

See also:

Pose pose_from_cif dump_file

dump_file(self : rosetta.core.pose.Pose, file_name : str) → NoneType

Export pose data to a file, <file_name>, determining which type of file format to write based on the file extension

example(s):

pose.dump_file(‘new_01.pdb’) pose.dump_file(‘new_01.cif’)

See also:

Pose dump_cif dump_file

dump_pdb(*args, **kwargs)

Overloaded function.

1. dump_pdb(self : rosetta.core.pose.Pose, file_name : str) -> bool

Export pose data to the PDB file <file_name>

example(s):

pose.dump_pdb(‘new_01.pdb’)

See also:

Pose pose_from_pdb dump_cif dump_file

2. dump_pdb(self : rosetta.core.pose.Pose, file_name : str, tag : str) -> bool

Export pose data to the PDB file <file_name>

example(s):

pose.dump_pdb(‘new_01.pdb’)

See also:

Pose pose_from_pdb dump_cif dump_file

dump_scored_pdb(*args, **kwargs)

Overloaded function.

1. dump_scored_pdb(self : rosetta.core.pose.Pose, file_name : str, scorefxn : core::scoring::ScoreFunction) -> NoneType

Export pose data to the PDB file <file_name>,

add some score output

2. dump_scored_pdb(self : rosetta.core.pose.Pose, file_name : str, scorefxn : core::scoring::ScoreFunction, tag : str) -> NoneType

Export pose data to the PDB file <file_name>,

add some score output

empty(rosetta.core.pose.Pose) → bool

Returns true if there are no residues in the conformation

example(s):

pose.empty()

See also:

Pose Pose.clear

Pose.sequence

Pose.total_residue

energies(*args, **kwargs)

Overloaded function.

1. energies(rosetta.core.pose.Pose) -> core::scoring::Energies

Returns the pose Energies (const-access)

example(s):

pose.energies()

See also:

Pose Energies PDBInfo ScoreFunction create_score_function

2. energies(rosetta.core.pose.Pose) -> core::scoring::Energies

Returns the pose Energies (non-const access)

epsilon(self : rosetta.core.pose.Pose, seqpos : int) → float

Returns the epsilon torsion angle of residue <seqpos>

assumes the residue is an nucleic acid

example(s):

pose.epsilon(5)

See also:

Pose Pose.residue Pose.set_epsilon Residue

fold_tree(*args, **kwargs)

Overloaded function.

1. fold_tree(rosetta.core.pose.Pose) -> rosetta.core.kinematics.FoldTree

Returns the pose FoldTree

example(s):

pose.fold_tree()

See also:

Pose FoldTree

2. fold_tree(self : rosetta.core.pose.Pose, fold_tree_in : rosetta.core.kinematics.FoldTree) -> NoneType

Sets the pose FoldTree to <fold_tree_in>

example(s):

pose.fold_tree( foldtree )

See also:

Pose pose.fold_tree FoldTree

gamma(self : rosetta.core.pose.Pose, seqpos : int) → float

Returns the gamma torsion angle of residue <seqpos>

assumes the residue is an nucleic acid

example(s):

pose.gamma(3)

See also:

Pose Pose.residue Pose.set_gamma Residue

get_self_ptr(*args, **kwargs)

Overloaded function.

1. get_self_ptr(rosetta.core.pose.Pose) -> rosetta.core.pose.Pose

self pointers

2. get_self_ptr(rosetta.core.pose.Pose) -> rosetta.core.pose.Pose

get_self_weak_ptr(*args, **kwargs)

Overloaded function.

1. get_self_weak_ptr(rosetta.core.pose.Pose) -> rosetta.std.weak_ptr_const_core_pose_Pose_t
2. get_self_weak_ptr(rosetta.core.pose.Pose) -> rosetta.std.weak_ptr_core_pose_Pose_t

has_dof(self : rosetta.core.pose.Pose, id : rosetta.core.id.DOF_ID) → bool

Returns true if pose has DOF <id>

See also:

Pose DOF_ID

has_reference_pose(rosetta.core.pose.Pose) → bool

Returns true if a pose has at least one reference pose, false otherwise.

increment_reference_pose_mapping_after_seqpos(self : rosetta.core.pose.Pose, seqpos : int) → NoneType

Find all mappings in the new pose after seqpos in all ReferencePose objects, and increment them by 1.

If there is no ReferencePose object, do nothing.

insert_residue_by_bond(*args, **kwargs)

Overloaded function.

1. insert_residue_by_bond(self : rosetta.core.pose.Pose, new_rsd_in : rosetta.core.conformation.Residue, seqpos : int, anchor_pos : int) -> NoneType

This code sorely belongs in Pose.cc

Adds <new_rsd_in> to pose at <seqpos>

2. insert_residue_by_bond(self : rosetta.core.pose.Pose, new_rsd_in : rosetta.core.conformation.Residue, seqpos : int, anchor_pos : int, build_ideal_geometry : bool) -> NoneType

This code sorely belongs in Pose.cc

Adds <new_rsd_in> to pose at <seqpos>

3. insert_residue_by_bond(self : rosetta.core.pose.Pose, new_rsd_in : rosetta.core.conformation.Residue, seqpos : int, anchor_pos : int, build_ideal_geometry : bool, anchor_atom : str) -> NoneType

This code sorely belongs in Pose.cc

Adds <new_rsd_in> to pose at <seqpos>

4. insert_residue_by_bond(self : rosetta.core.pose.Pose, new_rsd_in : rosetta.core.conformation.Residue, seqpos : int, anchor_pos : int, build_ideal_geometry : bool, anchor_atom : str, root_atom : str) -> NoneType

This code sorely belongs in Pose.cc

Adds <new_rsd_in> to pose at <seqpos>

5. insert_residue_by_bond(self : rosetta.core.pose.Pose, new_rsd_in : rosetta.core.conformation.Residue, seqpos : int, anchor_pos : int, build_ideal_geometry : bool, anchor_atom : str, root_atom : str, new_chain : bool) -> NoneType

This code sorely belongs in Pose.cc

Adds <new_rsd_in> to pose at <seqpos>

6. insert_residue_by_bond(self : rosetta.core.pose.Pose, new_rsd_in : rosetta.core.conformation.Residue, seqpos : int, anchor_pos : int, build_ideal_geometry : bool, anchor_atom : str, root_atom : str, new_chain : bool, lookup_bond_length : bool) -> NoneType

This code sorely belongs in Pose.cc

Adds <new_rsd_in> to pose at <seqpos>

insert_residue_by_jump(*args, **kwargs)

Overloaded function.

1. insert_residue_by_jump(self : rosetta.core.pose.Pose, new_rsd_in : rosetta.core.conformation.Residue, seqpos : int, anchor_pos : int) -> NoneType

This code sorely belongs in Pose.cc

Adds <new_rsd_in> to pose at <seqpos>

2. insert_residue_by_jump(self : rosetta.core.pose.Pose, new_rsd_in : rosetta.core.conformation.Residue, seqpos : int, anchor_pos : int, anchor_atomno : str) -> NoneType

This code sorely belongs in Pose.cc

Adds <new_rsd_in> to pose at <seqpos>

3. insert_residue_by_jump(self : rosetta.core.pose.Pose, new_rsd_in : rosetta.core.conformation.Residue, seqpos : int, anchor_pos : int, anchor_atomno : str, root_atomno : str) -> NoneType

This code sorely belongs in Pose.cc

Adds <new_rsd_in> to pose at <seqpos>

is_centroid(rosetta.core.pose.Pose) → bool

Returns true if pose is ResidueType centroid

convenience test for residue_type_set ( based on two middle residue – to avoid hitting on ligands or pseudos )

example(s):

pose.is_centroid()

See also:

Pose Pose.is_fullatom Residue ResidueType

this is nt a good test –Doug

is_fullatom(rosetta.core.pose.Pose) → bool

Returns true if pose is ResidueType fullatom

convenience test for residue_type_set ( based on two middle residue – to avoid hitting on ligands or pseudos )

example(s):

pose.is_fullatom()

See also:

Pose Pose.is_centroid Residue ResidueType

this is nt a good test –Doug

jump(*args, **kwargs)

Overloaded function.

1. jump(self : rosetta.core.pose.Pose, jump_number : int) -> rosetta.core.kinematics.Jump

Returns the pose FoldTree Jump <jump_number>

example(s):

pose.jump(1)

See also:

Pose Pose.fold_tree Pose.set_jump FoldTree FoldTree.jump_edge Jump

2. jump(self : rosetta.core.pose.Pose, id : rosetta.core.id.AtomID) -> rosetta.core.kinematics.Jump

Returns the pose FoldTree Jump <id>

example(s):

pose.set_jump(R5N)

See also:

Pose Pose.fold_tree Pose.set_jump FoldTree FoldTree.jump_edge AtomID

metric(self : rosetta.core.pose.Pose, calculator_name : str, key : str, val : rosetta.basic.MetricValueBase) → NoneType

n_residue(rosetta.core.pose.Pose) → int

Returns the number of residues in the pose conformation

example(s):

pose.n_residue()

See also:

Pose Pose.sequence Pose.total_residue

num_jump(rosetta.core.pose.Pose) → int

Returns the number of jumps in the pose FoldTree

example(s):

pose.num_jump()

See also:

Pose Pose.jump Pose.set_jump FoldTree Jump

observer_cache(*args, **kwargs)

Overloaded function.

1. observer_cache(rosetta.core.pose.Pose) -> core::pose::datacache::ObserverCache

ObserverCache indexed by enum in core/pose/datacache/CacheableObserverType.hh

2. observer_cache(rosetta.core.pose.Pose) -> core::pose::datacache::ObserverCache

ObserverCache indexed by enum in core/pose/datacache/CacheableObserverType.hh

omega(self : rosetta.core.pose.Pose, seqpos : int) → float

Returns the omega torsion angle of residue <seqpos>

assumes the residue is an amino acid or monosaccharide

example(s):

pose.omega(3)

See also:

Pose Pose.residue Pose.set_omega Residue

pdb_info(*args, **kwargs)

Overloaded function.

1. pdb_info(rosetta.core.pose.Pose) -> core::pose::PDBInfo

Returns the pose PDBInfo (const)

example(s):

pose.pdb_info()

See also:

Pose Energies PDBInfo

ScoreFunction pose_from_pdb

NULL if no PDBInfo instance exists, the pdb info instance otherwise

2. pdb_info(rosetta.core.pose.Pose) -> core::pose::PDBInfo

Returns the pose PDBInfo

NULL if no PDBInfo instance exists, the PDBInfo instance otherwise

3. pdb_info(self : rosetta.core.pose.Pose, new_info : core::pose::PDBInfo) -> core::pose::PDBInfo

Sets pose PDBInfo to <new_info>

the new PDBInfo to copy, pass NULL

if you want to zero the existence of PDBInfo inside this Pose

the prior PDBInfo instance

phi(self : rosetta.core.pose.Pose, seqpos : int) → float

Returns the phi torsion angle of residue <seqpos>

assumes the residue is an amino acid or monosaccharide

example(s):

pose.phi(1)

See also:

Pose Pose.residue Pose.set_phi Residue

prepend_polymer_residue_before_seqpos(self : rosetta.core.pose.Pose, new_rsd : rosetta.core.conformation.Residue, seqpos : int, build_ideal_geometry : bool) → NoneType

glues to seqpos and perhaps also seqpos-1

print_metric(self : rosetta.core.pose.Pose, calculator_name : str, key : str) → str

psi(self : rosetta.core.pose.Pose, seqpos : int) → float

Returns the psi torsion angle of residue <seqpos>

Note: assumes the residue is an amino acid or monosaccharide

example(s):

pose.psi(2)

See also:

Pose Pose.residue Pose.set_psi Residue

reference_pose_from_current(*args, **kwargs)

Overloaded function.

1. reference_pose_from_current(self : rosetta.core.pose.Pose, ref_pose_name : str) -> NoneType

Create a new reference pose from the current state of the pose.

If a ReferencePoseSet object does not exist, this function will create it.

If override_current is set to true, will override any currently set reference pose with the ref_pose_name.

2. reference_pose_from_current(self : rosetta.core.pose.Pose, ref_pose_name : str, override_current : bool) -> NoneType

Create a new reference pose from the current state of the pose.

If a ReferencePoseSet object does not exist, this function will create it.

If override_current is set to true, will override any currently set reference pose with the ref_pose_name.

reference_pose_set(rosetta.core.pose.Pose) → core::pose::reference_pose::ReferencePoseSet

Access the ReferencePoseSet object (non-const).

If a ReferencePoseSet object does not exist, this function will create it.

reference_pose_set_cop(rosetta.core.pose.Pose) → core::pose::reference_pose::ReferencePoseSet

Const-access the ReferencePoseSet object.

If a ReferencePoseSet object does not exist, this function will throw an error.

remove_constraint(*args, **kwargs)

Overloaded function.

1. remove_constraint(self : rosetta.core.pose.Pose, cst : core::scoring::constraints::Constraint) -> bool

re object_comparison see comment for ConstraintSet::remove_constraint function

2. remove_constraint(self : rosetta.core.pose.Pose, cst : core::scoring::constraints::Constraint, object_comparison : bool) -> bool

re object_comparison see comment for ConstraintSet::remove_constraint function

remove_constraints(*args, **kwargs)

Overloaded function.

1. remove_constraints(self : rosetta.core.pose.Pose, csts : rosetta.utility.vector1_std_shared_ptr_const_core_scoring_constraints_Constraint_t) -> bool

re object_comparison see comment for ConstraintSet::remove_constraint function

2. remove_constraints(self : rosetta.core.pose.Pose, csts : rosetta.utility.vector1_std_shared_ptr_const_core_scoring_constraints_Constraint_t, object_comparison : bool) -> bool

re object_comparison see comment for ConstraintSet::remove_constraint function

3. remove_constraints(rosetta.core.pose.Pose) -> bool

replace_residue(*args, **kwargs)

Overloaded function.

1. replace_residue(self : rosetta.core.pose.Pose, seqpos : int, new_rsd_in : rosetta.core.conformation.Residue, orient_backbone : bool) -> NoneType

Replaces the residue at <seqpos> with <new_rsd_in>

2. replace_residue(self : rosetta.core.pose.Pose, seqpos : int, new_rsd_in : rosetta.core.conformation.Residue, atom_pairs : rosetta.utility.vector1_std_pair_std_string_std_string_t) -> NoneType

Replaces the residue at <seqpos> with <new_rsd>

based on superposition on the specified input atom pairs NOTE: at the moment, only superposition on 3 atoms works This code sorely belongs in Pose.cc

residue(self : rosetta.core.pose.Pose, seqpos : int) → rosetta.core.conformation.Residue

Returns the Residue at position <seqpos> (read access)

Note: this method will trigger a refold if either the torsions or the coordinates are out-of-date

example(s):

pose.residue(4)

See also:

Pose Pose.sequence Pose.total_residue Residue ResidueType

residue_type(self : rosetta.core.pose.Pose, seqpos : int) → rosetta.core.chemical.ResidueType

Returns the ResidueType at position <seqpos> (read access)

Note: this method NOT will trigger a refold if either the torsions or the coordinates are out-of-date

example(s):

pose.residue_type(5)

See also:

Pose Pose.residue Pose.sequence Pose.total_residue Residue ResidueType

scoring_begin(self : rosetta.core.pose.Pose, info : core::scoring::ScoreFunction) → NoneType

Called by ScoreFunction at the beginning of scoring

scoring_end(self : rosetta.core.pose.Pose, scorefxn : core::scoring::ScoreFunction) → NoneType

Called by ScoreFunction at the end of scoring

secstruct(*args, **kwargs)

Overloaded function.

1. secstruct(self : rosetta.core.pose.Pose, seqpos : int) -> str

Returns the secondary structure of residue <seqpos>

this usually comes from fragments. The conformation object will not invoke DSSP to determine the secondary structure if e.g. it has not been made from fragments. ‘H’ = helical ‘S’ = strand or sheet ‘E’ = loop JKL: is this correct? DsspDesignOperations says that H = helix, E = strand, and L = loop

example(s):

pose.secstruct(3)

See also:

Pose Pose.residue Pose.set_secstruct Residue

2. secstruct(rosetta.core.pose.Pose) -> str

Returns a string representing pose secondary structure

example(s):

pose.secstruct()

See also:

Pose Pose.residue Pose.set_secstruct Residue

sequence(*args, **kwargs)

Overloaded function.

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

Returns a string representing the 1-letter-coded sequence of the pose conformation.

example(s):

pose.sequence()

See also:

Pose Pose.annotated_sequence Pose.chain Pose.chain_sequence Pose.residue Pose.total_residue

2. sequence(self : rosetta.core.pose.Pose, resnum_start : int, resnum_end : int) -> str

Returns a string representing the 1-letter-coded sequence of the pose conformation. From start to end.

example(s):

pose.sequence()

See also:

Pose Pose.annotated_sequence Pose.chain Pose.chain_sequence Pose.residue Pose.total_residue

set_alpha(self : rosetta.core.pose.Pose, seqpos : int, setting : float) → NoneType

Sets the alpha torsion angle of residue <seqpos> to <setting>

<setting> must be in degrees, assumes residue is an nucleic acid

example(s):

pose.set_alpha(1)

See also:

Pose Pose.alpha Pose.residue Residue

set_beta(self : rosetta.core.pose.Pose, seqpos : int, setting : float) → NoneType

Sets the beta torsion angle of residue <seqpos> to <setting>

<setting> must be in degrees, assumes residue is an nucleic acid

example(s):

pose.set_beta(2)

See also:

Pose Pose.beta Pose.residue Residue

set_chi(*args, **kwargs)

Overloaded function.

1. set_chi(self : rosetta.core.pose.Pose, chino : int, seqpos : int, setting : float) -> NoneType

Sets the <chino> chi torsion angle of residue <seqpos> to <setting>

<setting> must be in degrees, assumes residue is an amino acid or monosaccharide

example(s):

pose.set_chi(1,7,120)

See also:

Pose Pose.chi Pose.residue Residue

2. set_chi(self : rosetta.core.pose.Pose, seqpos : int, setting : float) -> NoneType

Sets the chi torsion angle of residue <seqpos> to <setting>

<setting> must be in degrees, assumes residue is an nucleic acid

example(s):

pose.set_chi(7)

See also:

Pose Pose.chi Pose.residue Residue

set_delta(self : rosetta.core.pose.Pose, seqpos : int, setting : float) → NoneType

Sets the delta torsion angle of residue <seqpos> to <setting>

<setting> must be in degrees, assumes residue is an nucleic acid

example(s):

pose.set_delta(4)

See also:

Pose Pose.delta Pose.residue Residue

set_dof(self : rosetta.core.pose.Pose, id : rosetta.core.id.DOF_ID, setting : float) → NoneType

Sets the value of the AtomTree DOF <id>

See also:

Pose DOF_ID

set_epsilon(self : rosetta.core.pose.Pose, seqpos : int, setting : float) → NoneType

Sets the epsilon torsion angle of residue <seqpos> to <setting>

<setting> must be in degrees, assumes residue is an nucleic acid

example(s):

pose.set_epsilon(5)

See also:

Pose Pose.epsilon Pose.residue Residue

set_gamma(self : rosetta.core.pose.Pose, seqpos : int, setting : float) → NoneType

Sets the gamma torsion angle of residue <seqpos> to <setting>

<setting> must be in degrees, assumes residue is an nucleic acid

example(s):

pose.set_gamma(3)

See also:

Pose Pose.gamma Pose.residue Residue

set_jump(*args, **kwargs)

Overloaded function.

1. set_jump(self : rosetta.core.pose.Pose, jump_number : int, new_jump : rosetta.core.kinematics.Jump) -> NoneType

Sets the pose FoldTree Jump <jump_number> to <new_jump>

example(s):

pose.set_jump(1,jump1)

See also:

Pose Pose.fold_tree Pose.jump FoldTree FoldTree.jump_edge Jump

2. set_jump(self : rosetta.core.pose.Pose, id : rosetta.core.id.AtomID, new_jump : rosetta.core.kinematics.Jump) -> NoneType

Sets the pose FoldTree Jump <id> to <new_jump>

example(s):

pose.set_jump(1,jump1)

See also:

Pose Pose.fold_tree Pose.jump FoldTree FoldTree.jump_edge AtomID

set_new_conformation(self : rosetta.core.pose.Pose, new_conformation : rosetta.core.conformation.Conformation) → NoneType

Now that the conformation_ member data is an owning pointer,

and we have derived classes of Conformation.

set_new_energies_object(self : rosetta.core.pose.Pose, energies : core::scoring::Energies) → NoneType

Now that the energies_ member data is an owning pointer,

and we have derived classes of Energies.

set_omega(self : rosetta.core.pose.Pose, seqpos : int, setting : float) → NoneType

Sets the omega torsion angle of residue <seqpos> to <setting>

<setting> must be in degrees, assumes residue is an amino acid or monosaccharide

example(s):

pose.set_omega(3, 180.0)

See also:

Pose Pose.omega Pose.residue Residue

set_phi(self : rosetta.core.pose.Pose, seqpos : int, setting : float) → NoneType

Sets the phi torsion angle of residue <seqpos> to <setting>

<setting> must be in degrees, assumes residue is an amino acid or monosaccharide

example(s):

pose.set_phi(1, -23.7)

See also:

Pose Pose.phi Pose.residue Residue

set_psi(self : rosetta.core.pose.Pose, seqpos : int, setting : float) → NoneType

Sets the psi torsion angle of residue <seqpos> to <setting>

<setting> must be in degrees, assumes residue is an amino acid or monosaccharide

example(s):

pose.set_psi(2, 45.3)

See also:

Pose Pose.psi Pose.residue Residue

set_ring_conformation(self : rosetta.core.pose.Pose, seqpos : int, ring_num : int, conformer : rosetta.core.chemical.rings.RingConformer) → NoneType

Set the given residue and ring’s ring conformation, if appropriate.

set_secstruct(self : rosetta.core.pose.Pose, seqpos : int, setting : str) → NoneType

Assign the secondary structure of residue <seqpos> to <setting>

example(s):

pose.set_secstruct(3,’H’)

See also:

Pose Pose.residue Pose.secstruct Residue

set_theta(self : rosetta.core.pose.Pose, seqpos : int, setting : float) → NoneType

Sets the theta torsion angle of beta-amino acid residue <seqpos> to <setting>

<setting> must be in degrees, assumes residue is a beta-amino acid.

example(s):

pose.set_theta(21, 58.9)

See also:

Pose Pose.theta Pose.residue Residue

Vikram K. Mulligan (vmullig.edu)

set_torsion(self : rosetta.core.pose.Pose, id : core::id::TorsionID, setting : float) → NoneType

Sets the Conformation torsion angle identified

by <id> to <setting>

See also:

Pose TorsionID

set_xyz(*args, **kwargs)

Overloaded function.

1. set_xyz(self : rosetta.core.pose.Pose, id : rosetta.core.id.AtomID, point : rosetta.numeric.xyzVector_double_t) -> NoneType

Sets the location (xyz) of pose AtomID <id> to

the PointPosition <point>

See also:

Pose Pose.residue Pose.xyz Residue

2. set_xyz(self : rosetta.core.pose.Pose, id : rosetta.core.id.NamedAtomID, point : rosetta.numeric.xyzVector_double_t) -> NoneType

Sets the location (xyz) of pose NamedAtomID <id>

to the PointPosition <point>

See also:

Pose Pose.residue Pose.xyz Residue

set_zeta(self : rosetta.core.pose.Pose, seqpos : int, setting : float) → NoneType

Sets the zeta torsion angle of residue <seqpos> to <setting>

<setting> must be in degrees, assumes residue is an nucleic acid

example(s):

pose.set_zeta(6)

See also:

Pose Pose.zeta Pose.residue Residue

split_by_chain(*args, **kwargs)

Overloaded function.

1. split_by_chain(rosetta.core.pose.Pose) -> rosetta.utility.vector1_std_shared_ptr_core_pose_Pose_t

Returns a vector of poses with one element per chain of the original pose

2. split_by_chain(self : rosetta.core.pose.Pose, chain_id : int) -> rosetta.core.pose.Pose

stub_from_id(self : rosetta.core.pose.Pose, id : core::id::NamedStubID) → rosetta.core.kinematics.Stub

theta(self : rosetta.core.pose.Pose, seqpos : int) → float

Returns the theta torsion angle of beta-amino acid residue <seqpos>

assumes residue is a beta-amino acid.

example(s):

pose.theta(21)

See also:

Pose Pose.set_theta Pose.residue Residue

Vikram K. Mulligan (vmullig.edu)

torsion(self : rosetta.core.pose.Pose, id : core::id::TorsionID) → float

Returns the Conformation torsion angle identified by <id>

See also:

Pose TorsionID

total_atoms(*args, **kwargs)

Overloaded function.

1. total_atoms(rosetta.core.pose.Pose) -> int

Returns the total number of atoms in the pose conformation

example:

pose.total_atoms()

2. total_atoms(self : rosetta.core.pose.Pose, nres : int) -> int

Returns the total number of atoms in the pose

up to a particular residue

total_residue(rosetta.core.pose.Pose) → int

Returns the number of residues in the pose conformation

example(s):

pose.total_residue()

See also:

Pose Pose.n_residue Pose.sequence

transfer_constraint_set(self : rosetta.core.pose.Pose, pose : rosetta.core.pose.Pose) → NoneType

update_actcoord(self : rosetta.core.pose.Pose, resid : int) → NoneType

Updates the action coordinates for pose residue <resid>

update_actcoords(rosetta.core.pose.Pose) → NoneType

Called by PairEPotential to update the action coordinates for all residues

update_orbital_coords(self : rosetta.core.pose.Pose, resid : int) → NoneType

update_pose_chains_from_pdb_chains(rosetta.core.pose.Pose) → NoneType

Updates the pose chain IDs to match the pdb chain IDs.

update_residue_neighbors(rosetta.core.pose.Pose) → NoneType

Updates neighbor links in the pose Energies object

xyz(*args, **kwargs)

Overloaded function.

1. xyz(self : rosetta.core.pose.Pose, id : rosetta.core.id.AtomID) -> rosetta.numeric.xyzVector_double_t

Returns the location (xyz) of pose AtomID <id>

example(s):

atom = AtomID(1,1) pose.xyz(atom)

See also:

Pose Pose.residue AtomID Residue Residue.xyz

2. xyz(self : rosetta.core.pose.Pose, id : rosetta.core.id.NamedAtomID) -> rosetta.numeric.xyzVector_double_t

Returns the location (xyz) of pose NamedAtomID <id>

Tutorial soon... See also:

Pose Pose.residue NamedAtomID Residue Residue.xyz

zero_reference_pose_mapping_at_seqpos(self : rosetta.core.pose.Pose, seqpos : int) → NoneType

Find all mappings in the new pose to seqpos in all ReferencePose objects, and set them to point to residue 0 (deletion signal).

If there is no ReferencePose object, do nothing.

zeta(self : rosetta.core.pose.Pose, seqpos : int) → float

Returns the zeta torsion angle of residue <seqpos>

assumes the residue is an nucleic acid

example(s):

pose.zeta(6)

See also:

Pose Pose.residue Pose.set_zeta Residue

class rosetta.core.pose.ResidueIndexDescription

Bases: object

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.

assign(self : rosetta.core.pose.ResidueIndexDescription, : rosetta.core.pose.ResidueIndexDescription) → rosetta.core.pose.ResidueIndexDescription

chain(rosetta.core.pose.ResidueIndexDescription) → str

insertion_code(rosetta.core.pose.ResidueIndexDescription) → str

pose_index(rosetta.core.pose.ResidueIndexDescription) → int

pose_numbered(rosetta.core.pose.ResidueIndexDescription) → bool

resindex(rosetta.core.pose.ResidueIndexDescription) → int

resolve_index(self : rosetta.core.pose.ResidueIndexDescription, p : rosetta.core.pose.Pose) → int

Turn the internal data into a pose index (in the range from 1 to total residue)

or throw an exception if the index cannot be resolved.

unassigned(rosetta.core.pose.ResidueIndexDescription) → bool

class rosetta.core.pose.ResidueIndexDescriptionFromFile

Bases: rosetta.core.pose.ResidueIndexDescription

%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.

assign(self : rosetta.core.pose.ResidueIndexDescriptionFromFile, : rosetta.core.pose.ResidueIndexDescriptionFromFile) → rosetta.core.pose.ResidueIndexDescriptionFromFile

fname(rosetta.core.pose.ResidueIndexDescriptionFromFile) → str

linenum(rosetta.core.pose.ResidueIndexDescriptionFromFile) → int

resolve_index(self : rosetta.core.pose.ResidueIndexDescriptionFromFile, p : rosetta.core.pose.Pose) → int

Turn the internal data into a pose index (in the range from 1 to total residue)

or throw an exception if the index cannot be resolved; the exception thrown by this class if the resolution fails includes a statement of the file name and the line number in that file.

class rosetta.core.pose.UnrecognizedAtomRecord

Bases: object

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

assign(self : rosetta.core.pose.UnrecognizedAtomRecord, : rosetta.core.pose.UnrecognizedAtomRecord) → rosetta.core.pose.UnrecognizedAtomRecord

atom_name(rosetta.core.pose.UnrecognizedAtomRecord) → str

coords(rosetta.core.pose.UnrecognizedAtomRecord) → rosetta.numeric.xyzVector_double_t

res_name(rosetta.core.pose.UnrecognizedAtomRecord) → str

res_num(rosetta.core.pose.UnrecognizedAtomRecord) → int

temp(rosetta.core.pose.UnrecognizedAtomRecord) → float

rosetta.core.pose.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.

2. 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.

rosetta.core.pose.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.

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

rosetta.core.pose.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.

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

rosetta.core.pose.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.

rosetta.core.pose.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.

rosetta.core.pose.annotated_to_oneletter_sequence(annotated_seq : str) → str

Returns the oneletter_sequence that corresponds to the given

annotated sequence.

rosetta.core.pose.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.

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

Append residues of pose2 to pose1.

rosetta.core.pose.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.

rosetta.core.pose.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.

2. 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.

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

rosetta.core.pose.canonical_atom_count(pose : rosetta.core.pose.Pose) → int

count the number of canonical amino acid atoms in the pose

rosetta.core.pose.canonical_residue_count(pose : rosetta.core.pose.Pose) → int

count the number of canonical residues in the pose

rosetta.core.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

rosetta.core.pose.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

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

compute last residue numbers of all chains

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

rosetta.core.pose.clearPoseExtraScores(pose : rosetta.core.pose.Pose) → NoneType

rosetta.core.pose.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

2. 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

rosetta.core.pose.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.

rosetta.core.pose.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

rosetta.core.pose.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

rosetta.core.pose.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

rosetta.core.pose.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.

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

rosetta.core.pose.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.

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

Deletes the entry in the STRING_MAP associated with the

given key.

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

dumps pose+ comments to pdb file

rosetta.core.pose.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

rosetta.core.pose.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.

rosetta.core.pose.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

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

rosetta.core.pose.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.

rosetta.core.pose.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.

rosetta.core.pose.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.

rosetta.core.pose.get_center_of_mass(pose : rosetta.core.pose.Pose) → rosetta.numeric.xyzVector_double_t

Get center of mass of a pose.

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

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

rosetta.core.pose.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

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

rosetta.core.pose.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

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

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

rosetta.core.pose.get_chains(pose : rosetta.core.pose.Pose) → rosetta.utility.vector1_int

Get all the chains from conformation

rosetta.core.pose.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.

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

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

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

rosetta.core.pose.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

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

rosetta.core.pose.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

rosetta.core.pose.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

rosetta.core.pose.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

rosetta.core.pose.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)

2. 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

rosetta.core.pose.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

rosetta.core.pose.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)

rosetta.core.pose.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.

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

rosetta.core.pose.get_sequence_len(sequence_in : str) → int

Get the real length of a annotated sequence

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

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

rosetta.core.pose.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

rosetta.core.pose.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

rosetta.core.pose.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

rosetta.core.pose.initialize_disulfide_bonds(*args, **kwargs)

Overloaded function.

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

detect and fix disulfide bonds

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

detect and fix disulfide bonds

rosetta.core.pose.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?

rosetta.core.pose.is_ideal_pose(pose : rosetta.core.pose.Pose) → bool

Returns true if the <pose> geometry is ideal

The Pose to check.

true if all pose positions have ideal bond lengths and angles

up to some very small epsilon

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

Returns true if the <pose> geometry is ideal in position <seqpos>

The Pose to check.

true if position seqpos has ideal bond lengths and angles

up to some very small epsilon

rosetta.core.pose.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

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

Returns true if <residue> is positionally conserved, false otherwise

rosetta.core.pose.is_referencepose_number(str : str, refpose_string : str, refpose_resnumber : int, refpose_offset : int) → bool

Is a string of the format “refpose(<refposename>,<refposenumber>)” or “refpose(<refposename>,<refposenumber>)+/-<number>”?

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)

rosetta.core.pose.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

rosetta.core.pose.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 <pose>, storing the result in <jumps>.

Jumps are keyed by their jump id.

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

rosetta.core.pose.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 <sequence> with ResidueTypeSet

<residue_set> and store it in <pose>.

2. 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 <sequence> with ResidueTypeSet

<residue_set> and store it in <pose>.

3. 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 <sequence> with ResidueTypeSet

<residue_set> and store it in <pose>.

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

Create a Pose from an annotated, linear, IUPAC polysaccharide sequence <sequence> with residue type set name

<type_set_name> and store it in <pose>.

5. 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 <sequence> with residue type set name

<type_set_name> and store it in <pose>.

6. 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 <sequence> with residue type set name

<type_set_name> and store it in <pose>.

7. 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 <sequence> with residue type set name

<type_set_name> and store it in <pose>.

rosetta.core.pose.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 <sequence>

with ResidueTypeSet <residue_set> and stores it in <pose>

: any existing data in <pose> 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

2. 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 <sequence>

with ResidueTypeSet <residue_set> and stores it in <pose>

: any existing data in <pose> 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

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

Creates a Pose from the annotated protein sequence <sequence>

with the desired <type_set_name> and stores it in <pose>

: any existing data in <pose> is cleared, auto_termini

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

8. 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 <sequence>

with the desired <type_set_name> and stores it in <pose>

: any existing data in <pose> is cleared, auto_termini

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

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

rosetta.core.pose.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

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

rosetta.core.pose.noncanonical_atom_count(pose : rosetta.core.pose.Pose) → int

count the number of non-canonical amino acids in thepose

rosetta.core.pose.noncanonical_chi_count(pose : rosetta.core.pose.Pose) → int

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

rosetta.core.pose.noncanonical_residue_count(pose : rosetta.core.pose.Pose) → int

count the number of non-canonical residues in the pose

rosetta.core.pose.nres_protein(pose : rosetta.core.pose.Pose) → int

Number of protein residues in the pose

No virtuals, membrane residues or embedding residues counted

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

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

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

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

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

rosetta.core.pose.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.

rosetta.core.pose.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

2. 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

rosetta.core.pose.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

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

rosetta.core.pose.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

2. 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

3. 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

4. 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

rosetta.core.pose.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.

2. 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.

rosetta.core.pose.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 <sequence> with residue type set name

<type_set_name>.

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

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

<type_set_name>.

3. 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 <sequence> with residue type set name

<type_set_name>.

4. 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 <sequence> with residue type set name

<type_set_name>.

rosetta.core.pose.pose_max_nbr_radius(pose : rosetta.core.pose.Pose) → float

returns a Distance

rosetta.core.pose.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

rosetta.core.pose.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

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

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

rosetta.core.pose.read_psipred_ss2_file(pose : rosetta.core.pose.Pose) → rosetta.utility.vector1_char

rosetta.core.pose.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.

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

rosetta.core.pose.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).

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

rosetta.core.pose.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.

rosetta.core.pose.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.

rosetta.core.pose.remove_virtual_residues(pose : rosetta.core.pose.Pose) → NoneType

Removes all virtual residues from <pose>

rosetta.core.pose.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

2. 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

3. 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

4. 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

5. 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

rosetta.core.pose.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.

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

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

Is residue number in this chain?

rosetta.core.pose.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

rosetta.core.pose.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.

rosetta.core.pose.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

2. 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

rosetta.core.pose.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

rosetta.core.pose.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.

rosetta.core.pose.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

rosetta.core.pose.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.

rosetta.core.pose.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

rosetta.core.pose.set_reasonable_fold_tree(pose : rosetta.core.pose.Pose) → NoneType

rosetta.core.pose.set_ss_from_phipsi(pose : rosetta.core.pose.Pose) → NoneType

Analyzes <pose> residue phi/psi sets and guesses the secondary

structure, ideally dssp should be used for that

rosetta.core.pose.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

rosetta.core.pose.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)

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

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

rosetta.core.pose.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 <pose>

rosetta.core.pose.tag_from_pose(pose : rosetta.core.pose.Pose) → str

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

rosetta.core.pose.total_energy_from_pose(pose : rosetta.core.pose.Pose) → float

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

rosetta.core.pose.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

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