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 __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 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 __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)
def __init__(self, id):
"""Initialize the class."""
self.level = "S"
Entity.__init__(self, id)
