pestifer.objs.ssbond module¶

Disufulfide bonds are covalent linkages between two CYS residues in a protein. These are represented in PDB files as SSBOND records, and in mmCIF files as struct_conn records.

class pestifer.objs.ssbond.SSBond(*args, chainID1: str, resid1: ResID, chainID2: str, resid2: ResID, serial_number: int = 0, residue1: Residue = None, residue2: Residue = None, resname1: str = 'CYS', resname2: str = 'CYS', sym1: str = '', sym2: str = '', length: float = 0.0, ptnr1_auth_asym_id: str = '', ptnr2_auth_asym_id: str = '', ptnr1_auth_seq_id: str = '', ptnr2_auth_seq_id: str = '')[source]¶

Bases: BaseObj

A class for handling disulfide bonds between two CYS residues in a protein.

chainID1: str¶

chainID2: str¶

length: float¶

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.

pdb_line() → str[source]¶

Write the SSBond as it would appear in a PDB file.

Returns:: The PDB line for the SSBOND record.
Return type:: str

ptnr1_auth_asym_id: str¶

ptnr1_auth_seq_id: str¶

ptnr2_auth_asym_id: str¶

ptnr2_auth_seq_id: str¶

resid1: ResID¶

resid2: ResID¶

residue1: Residue¶

residue2: Residue¶

resname1: str¶

resname2: str¶

serial_number: int¶

shortcode() → str[source]¶

Convert the SSBond object to a shortcode string representation.

Returns:: A shortcode string representation of the SSBond object in the format C_RRR-D_SSS. Where C and D are chain IDs, and RRR and SSS are residue sequence numbers with insertion codes.
Return type:: str

sym1: str¶

sym2: str¶

class pestifer.objs.ssbond.SSBondList(initlist: Iterable[T] = ())[source]¶

Bases: BaseObjList[SSBond]

A class for handling a list of SSBond objects. This class inherits from BaseObjList and provides methods to manage a list of SSBond objects.

assign_residues(Residues: ResidueList)[source]¶

Assigns a list of Residue objects to the SSBond residues.

Parameters:: Residues (list of Residue) – A list of Residue objects to be assigned to the SSBond residues.
Returns:: A new SSBondList object containing the residues that were not assigned because no applicable residues were found.
Return type:: SSBondList

describe()[source]¶: Abstract method to describe the contents of the BaseObjList. Subclasses should implement this method to provide a meaningful description.

classmethod from_cif(dc: DataContainer) → SSBondList[source]¶

Create a SSBondList from a CIF DataContainer.

Parameters:: dc (DataContainer) – A CIF DataContainer containing the necessary fields to create SSBond objects.
Returns:: An instance of SSBondList created from the CIF DataContainer.
Return type:: SSBondList

classmethod from_pdb(pdb: PDBRecordDict) → SSBondList[source]¶: Create a SSBondList from a PDBRecordDict.