def get(self, name):
"""
Get a member of the Atom class
Parameters
name: The name of the member (string)
Possible Values
type: The type of Atom (either ATOM or HETATM)
serial: Atom serial number
name: Atom name
altLoc: Alternate location
resName: Residue name
chainID: Chain identifier
resSeq: Residue sequence number
iCode: Code for insertion of residues
x: Orthogonal coordinates for X in Angstroms.
y: Orthogonal coordinates for Y in Angstroms.
z: Orthogonal coordinates for Z in Angstroms.
occupancy: Occupancy
tempFactor: Temperature Factor
segID: Segment identifier
element: Element symbol
charge: Charge on the atom
bonds: The bonds associated with the atom
interbonds: The intrabonds associated with the atom
extrabonds: The extrabonds assocaited with the atom
residue: The parent residue of the atom
radius: The radius of the atom
ffcharge: The forcefield charge on the atom
hdonor: Whether the atom is a hydrogen donor
hacceptor: Whether the atom is a hydrogen acceptor
Returns
item: The value of the member
"""
try:
item = getattr(self, name)
return item
except AttributeError:
message = "Unable to access object \"%s\" in class Atom" % name
raise PDBInternalError(message)
def endElement(self, name):
if name == "residue": # Complete Residue object
residue = self.curholder
if not isinstance(residue, DefinitionResidue):
raise PDBInternalError("Internal error parsing XML!")
resname = residue.name
if resname == "":
raise PDBInternalError("Residue name not set in XML!")
else:
self.map[resname] = residue
self.curholder = None
self.curobj = None
elif name == "patch": # Complete patch object
patch = self.curholder
if not isinstance(patch, Patch):
raise PDBInternalError("Internal error parsing XML!")
patchname = patch.name
if patchname == "":
raise PDBInternalError("Residue name not set in XML!")
else:
self.patches.append(patch)
self.curholder = None
self.curobj = None
elif name == "atom": # Complete atom object
atom = self.curatom
if not isinstance(atom, DefinitionAtom):
raise PDBInternalError("Internal error parsing XML!")
atomname = atom.name
if atomname == "":
raise PDBInternalError("Atom name not set in XML!")
else:
self.curholder.map[atomname] = atom
self.curatom = None
self.curobj = self.curholder
else: # Just free the current element namespace
self.curelement = ""
return self.map