pestifer.objs.ssbonddelete module

One modification a user might want to make is reducing a disulfide bond to free cysteine residues. This is handled by the SSBondDelete class.

class pestifer.objs.ssbonddelete.SSBondDelete(*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 = '')

Bases: SSBond

A class for handling deletion of SSBonds.

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

Configuration for pydantic.BaseModel.

class pestifer.objs.ssbonddelete.SSBondDeleteList(initlist: Iterable[T] = ())

Bases: SSBondList

A class for handling a list of deleted SSBonds.

is_deleted(a_SSBond: SSBond) → bool

Check if a given SSBond is deleted in this list.

Parameters:

a_SSBond (SSBond) – The SSBond to check for deletion.

Returns:

True if the SSBond is deleted, False otherwise.

Return type:

bool