pestifer.objs.link module

A Link is a covalent bond between two residues in a protein structure.

class pestifer.objs.link.Link(*args, chainID1: str, resid1: ResID, name1: str, chainID2: str, resid2: ResID, name2: str, altloc1: str | None = None, altloc2: str | None = None, resname1: str | None = None, resname2: str | None = None, sym1: str | None = None, sym2: str | None = None, link_distance: float | None = None, segname1: str | None = None, segname2: str | None = None, residue1: Residue = None, residue2: Residue = None, atom1: Atom = None, atom2: Atom = None, empty: bool | None = None, segtype1: str | None = None, segtype2: str | None = None, ptnr1_label_asym_id: str | None = None, ptnr2_label_asym_id: str | None = None, ptnr1_label_seq_id: str | None = None, ptnr2_label_seq_id: str | None = None, ptnr1_label_comp_id: str | None = None, ptnr2_label_comp_id: str | None = None, ptnr1_auth_asym_id: str | None = None, ptnr2_auth_asym_id: str | None = None, ptnr1_auth_seq_id: str | None = None, ptnr2_auth_seq_id: str | None = None, ptnr1_auth_comp_id: str | None = None, ptnr2_auth_comp_id: str | None = None, patchname: str | None = None, patchhead: int | None = None)

Bases: BaseObj

A class for handling covalent bonds between residues where at least one residue is non-protein

altloc1: str | None

altloc2: str | None

atom1: Atom

atom2: Atom

chainID1: str

chainID2: str

empty: bool | None

link_distance: float | 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.

name1: str

name2: str

Required attributes for a Link object. These attributes must be provided when creating a Link object.

• chainID1: The chain ID of the first residue in the link.

• resid1: The residue ID of the first residue in the link.

• name1: The name of the first atom in the link.

• chainID2: The chain ID of the second residue in the link.

• resid2: The residue ID of the second residue in the link.

• name2: The name of the second atom in the link.

patchhead: int | None

Optional attributes for a Link object. These attributes can be provided to modify the behavior of the link. - residue1: The first residue object in the link. - residue2: The second residue object in the link. - atom1: The first atom object in the link. - atom2: The second atom object in the link. - empty: A boolean indicating if the link is empty. - segtype1: The segment type of the first residue. - segtype2: The segment type of the second residue. - ptnr1_label_asym_id: The asym ID of the first partner in the link (mmCIF). - ptnr2_label_asym_id: The asym ID of the second partner in the link (mmCIF). - ptnr1_label_seq_id: The sequence ID of the first partner in the link (mmCIF). - ptnr2_label_seq_id: The sequence ID of the second partner in the link (mmCIF). - ptnr1_label_comp_id: The component ID of the first partner in the link (mmCIF). - ptnr2_label_comp_id: The component ID of the second partner in the link (mmCIF). - ptnr1_auth_asym_id: The author asym ID of the first partner in the link (mmCIF). - ptnr2_auth_asym_id: The author asym ID of the second partner in the link (mmCIF). - ptnr1_auth_seq_id: The author sequence ID of the first partner in the link (mmCIF). - ptnr2_auth_seq_id: The author sequence ID of the second partner in the link (mmCIF). - ptnr1_auth_comp_id: The author component ID of the first partner in the link (mmCIF). - ptnr2_auth_comp_id: The author component ID of the second partner in the link (mmCIF). - patchname: The name of the patch applied to the link. - patchhead: 1 = residue1 is the first residue in the link, 2 = residue2 is the first residue in the link.

patchname: str | None

ptnr1_auth_asym_id: str | None

ptnr1_auth_comp_id: str | None

ptnr1_auth_seq_id: str | None

ptnr1_label_asym_id: str | None

ptnr1_label_comp_id: str | None

ptnr1_label_seq_id: str | None

ptnr2_auth_asym_id: str | None

ptnr2_auth_comp_id: str | None

ptnr2_auth_seq_id: str | None

ptnr2_label_asym_id: str | None

ptnr2_label_comp_id: str | None

ptnr2_label_seq_id: str | None

resid1: ResID

resid2: ResID

residue1: Residue

residue2: Residue

resname1: str | None

resname2: str | None

segname1: str | None

segname2: str | None

segtype1: str | None

segtype2: str | None

set_patchname(force=False)

Set the charmmff patch name for this link. This method assigns a patch name based on the residues involved in the link. If the patch name is already set and force is False, it will not change the patch name. This method does not return any value. It modifies the patchname attribute of the Link object. It checks the residues involved in the link and assigns a patch name based on predefined mappings.

Parameters:

force (bool, optional) – If True, forces the patch name to be set even if it is already assigned. Default is False.

shortcode() → str

Returns a string representation of the link in the format ‘C1_R1_A1-C2_R2_A2’.

sym1: str | None

sym2: str | None

update_residue(idx, **fields)

Updates the chainID of the residue in the link based on the index provided

Parameters:

• idx (int) – 1 for residue1, 2 for residue2

• fields (dict) – a dictionary of fields to update; currently only ‘chainID’ is supported

class pestifer.objs.link.LinkList(initlist: Iterable[T] = ())

Bases: BaseObjList[Link]

A class for handling lists of Links

apply_segtypes(map)

Apply segtype values to each of the two residues using the map

Parameters:

map (dict) – map of segtypes for given resnames

assign_residues(Residues: ResidueList) → tuple['ResidueList', 'LinkList']

Assigns residue and atom pointers to each link; sets up the up and down links of both residues so that linked residue objects can reference one another; flags residues from list of residues passed in that are not assigned to any links

Parameters:

Residues (ResidueList) – list of residues to assign to links; this is typically a list of all residues in the structure, but it can also be a list of residues that are not linked to any other residues, such as when reading in a set of links from a pre-built psf file.

Returns:

Residues – list of residues from Residues that are not used for any assignments

Return type:

ResidueList

describe() → str

Returns a string description of the LinkList.

Returns:

A string describing the number of links in the list.

Return type:

str

classmethod from_cif(dc: DataContainer) → LinkList

Create a LinkList from a CIF DataContainer.

Parameters:

dc (DataContainer) – A CIF DataContainer containing the necessary fields to create Link objects.

Returns:

An instance of LinkList created from the CIF DataContainer.

Return type:

LinkList

classmethod from_pdb(pdb: PDBRecordDict) → LinkList

Create a LinkList from a PDBRecordDict.

remove_links_to(r) → LinkList

Remove all links to a specific residue.

Parameters:

Residue (Residue) – The residue to remove links to.

Returns:

A new LinkList containing the removed links.

Return type:

LinkList

report() → str

Report the string representation of each link in the list.

pestifer.objs.link.ic_reference_closest(res12: list['Residue'], ICmaps: list[dict]) → str

Given the two Residues in res12 and the maps in ICmaps, return the mapping key to which the given IC values are closest in a Euclidean sense.

This method will identify the four atoms of the IC and reference them directly when calling the measure_dihedral function.

The list of computed dihedral values from the set of atoms is a “point” in “IC-space”, and each patch has its own “reference point” in this space.

The reference point to which the point is closest is identified as the desired result.

Parameters:

• res12 (list) – exactly two Residue objects which must have lists of atoms attributes

• ICMaps (list of dict) –

  A list of dictionaries, each with the following structure:

  Key	Description
  ICatomnames	List of 4 atom names as they appear in the CHARMM FF IC.
  mapping	Dictionary mapping patch names to IC values.