def __init__(self, id): self.level="I" self.id=id self.neighbors = {} self.uniq_pairs = [] Entity.__init__(self, id)
def __init__(self, id, resname, segid): """Initialize the class.""" self.level = "R" self.disordered = 0 self.resname = resname self.segid = segid Entity.__init__(self, id)
def __init__(self,id): Entity.__init__(self, id) #Store the SEQRES protein. Whole its SEQRES will be record it self._SeqRes={} self._iSeq = -1 #Store chain and its residue number. Because this value is very used. Thus, this dictionary help to get it self._ChainNumRes = {}
def add(self, atom): """Add an Atom object. Checks for adding duplicate atoms, and raises a PDBConstructionException if so. """ atom_id=atom.get_id() if self.has_id(atom_id): raise PDBConstructionException( \ "Atom %s defined twice in residue %s" % (atom_id, self)) Entity.add(self, atom)
def add(self, atom): """Add an Atom object. Checks for adding duplicate atoms, and raises a PDBConstructionException if so. """ atom_id = atom.get_id() if self.has_id(atom_id): raise PDBConstructionException( "Atom %s defined twice in residue %s" % (atom_id, self)) Entity.add(self, atom)
def __init__(self, id, serial_num=None): """Arguments: o id - int o serial_num - int """ self.level = "M" if serial_num is None: self.serial_num = id else: self.serial_num = serial_num Entity.__init__(self, id)
def __init__(self, id, serial_num=None): """ Arguments: o id - int o serial_num - int """ self.level = "M" if serial_num is None: self.serial_num = id else: self.serial_num = serial_num Entity.__init__(self, id)
def __init__(self, id, serial_num=None): """Initialize. Arguments: - id - int - serial_num - int """ self.level = "M" if serial_num is None: self.serial_num = id else: self.serial_num = serial_num Entity.__init__(self, id)
def __delitem__(self, id): """ Arguments: o id - (string, int, string) or int """ id=self._translate_id(id) return Entity.__delitem__(self, id)
def __delitem__(self, id): """ Arguments: o id - (string, int, string) or int """ id = self._translate_id(id) return Entity.__delitem__(self, id)
def __contains__(self, id): """True if a residue with given id is present in this chain. Arguments: o id - (string, int, string) or int """ id = self._translate_id(id) return Entity.__contains__(self, id)
def __contains__(self, id): """True if a residue with given id is present in this chain. Arguments: o id - (string, int, string) or int """ id=self._translate_id(id) return Entity.__contains__(self, id)
def get_hetero_atom_residues(struct: Entity) -> Iterator[Residue]: """ non-polymer ligands, excl. water BioPython's residue is a group of atoms belonging to the same molecule (made possible by mmcifs author_seq_id of heteroatoms, label_seq_id is '.' because a heterocompound does not belong to the poly-chain) scans all chains (we deliberately ignore author chain assignment in case of a heteroatom)""" return filter(lambda res: res.id[0].startswith('H_'), struct.get_residues()) # .id[0] is a residue's hetatm flag
def __getitem__(self, id): """Return the residue with given id. The id of a residue is (hetero flag, sequence identifier, insertion code). If id is an int, it is translated to (" ", id, " ") by the _translate_id method. Arguments: o id - (string, int, string) or int """ id=self._translate_id(id) return Entity.__getitem__(self, id)
def __getitem__(self, id): """Return the residue with given id. The id of a residue is (hetero flag, sequence identifier, insertion code). If id is an int, it is translated to (" ", id, " ") by the _translate_id method. Arguments: o id - (string, int, string) or int """ id = self._translate_id(id) return Entity.__getitem__(self, id)
def __init__(self, id): """Initialize the class.""" self.level = "C" self.internal_coord = None Entity.__init__(self, id)
def get_short_peptide_ligands(struct: Entity, peptide_length_limit: int) -> Iterator[Chain]: return filter( lambda chain: sum(is_aa(residue) for residue in chain) <= peptide_length_limit, struct.get_chains())
def __init__(self, id): """Initialize the class.""" self.level = "S" Entity.__init__(self, id)
def __init__(self,id): Entity.__init__(self, id) #Store the structure errors. self._dicStructureErrors= {}
def __init__(self, id, resname, segid): self.level="R" self.disordered=0 self.resname=resname self.segid=segid Entity.__init__(self, id)
def __init__(self,id): Entity.__init__(self, id) self._SeqRes = None self._SSBonds = None self._structureErrors = None
def __init__(self,id): Entity.__init__(self, id) #Store the SSBONDS protein. self._SSBonds= {}
def __init__(self, id): self.level = "S" Entity.__init__(self, id)