pestifer.molecule.segment module

Defines the Segment class for generating and managing segments declared for psfgen

class pestifer.molecule.segment.Segment(*args, segtype: str, segname: str, chainID: str, residues: ResidueList = <factory>, subsegments: StateIntervalList, parent_chain: str, specs: dict, mutations: MutationList | None = None, deletions: DeletionList | None = None, grafts: GraftList | None = None, patches: PatchList | None = None, attachments: List | None = None, psfgen_segname: str | None = None, objmanager: ObjManager = <factory>, parent_molecule: Molecule = None)

Bases: BaseObj

This class represents a segment defined by a list of residue indices and provides methods to check if a bond intersects the segment. It also provides methods to yield treadmilled versions of the segment and to check for equality with another segment.

A segment represents a set of residues in which there are not repeated resids.

attachments: List | None

chainID: str

cleave(clv: CleavageSite, daughter_chainID)

Cleave the segment at a specified cut location, creating a daughter segment.

Parameters:

• clv (Cleavage) – The cut location specifying where to cleave the segment.

• daughter_chainID (str) – The chain ID to assign to the daughter segment.

deletions: DeletionList | None

grafts: GraftList | None

model_config = {'arbitrary_types_allowed': True, 'extra': 'forbid', 'frozen': False}

Configuration for pydantic.BaseModel.

model_post_init(context: Any, /) → None

This function is meant to behave like a BaseModel method to initialize private attributes.

It takes context as an argument since that’s what pydantic-core passes when calling it.

Parameters:

• self – The BaseModel instance.

• context – The context.

mutations: MutationList | None

objmanager: ObjManager

parent_chain: str

parent_molecule: Molecule

patches: PatchList | None

psfgen_segname: str | None

residues: ResidueList

segname: str

segtype: str

set_parent_molecule(parent_molecule)

Set the parent molecule for this segment.

Parameters:

parent_molecule (object) – The parent molecule to which this segment belongs.

specs: dict

subsegments: StateIntervalList

class pestifer.molecule.segment.SegmentList(data)

Bases: BaseObjList[Segment]

A list of segments in a molecular structure. This class represents a collection of segments and provides methods to manage and manipulate them. It inherits from AncestorAwareObjList to maintain the context of the parent molecule.

build_from_only_pdb_data()

Build the segment list given residues that were populated only from PDB data

build_from_psf_and_pdb_data()

Build the segment list using the pre-populated PSF segment list and PDB-derived residues

chainIDmanager: ChainIDManager

collect_residues()

Collect all residues from the segments in the list.

Returns:

A list of all residues associated with the segments.

Return type:

ResidueList

describe() → str

Abstract method to describe the contents of the BaseObjList. Subclasses should implement this method to provide a meaningful description.

generate_from_residues(seq_spec: dict = {}, residues: ResidueList = [], chainIDmanager: ChainIDManager = None, psfcompanion: PSFSegmentList = None, links=None)

Generate a SegmentList from a sequence specification and a list of residues extracted from a structure file.

Parameters:

• seq_spec (dict) – A dictionary containing sequence specifications.

• residues (ResidueList) – A list of residues to be processed into segments.

• chainIDmanager (ChainIDManager) – An object managing chain IDs to ensure uniqueness.

• psfcompanion (PSFSegmentList) – A companion PSF segment list to provide additional context.

Returns:

A new SegmentList instance containing the generated segments.

Return type:

SegmentList

get_residue_to_segname_map() → dict

Return a mapping from id(residue) → segname for all residues in all segments.

get_segment_of_residue(residue: Residue) → Segment | None

Get the segment that contains a specified residue.

Parameters:

residue (Residue) – The residue for which to find the containing segment.

Returns:

The segment containing the specified residue, or None if not found.

Return type:

Segment or None

glycan_segment_parents: dict[str, str]

inherit_objs(objmanager: ObjManager)

Inherit objects from the object manager for each segment in the list. This method updates the object manager for each segment with inherited objects such as mutations, grafts, and patches.

Parameters:

objmanager (ObjectManager) – The object manager from which to inherit objects.

prune_topology(mutations: MutationList, links: LinkList, ssbonds: SSBondList)

Prunes links, ssbonds, and even whole segments based on mutations

psfcompanion: PSFSegmentList

remove(item)

Remove a segment from the list and update associated attributes.

Parameters:

item (Segment) – The segment to remove from the list.

residues: ResidueList