def parsepdb(self,lines):
"""
Parses a PDB file, which is contained in lines (a list of lines)
"""
import PDBparser
Y=PDBparser.PDBparser(lines,self.parse_terms)
Y.parse()
self.atoms=Y.atoms
self.Update()
self.attribute=Y.attribute
return
def readpdb(self,filename=None,data=None,parse=1,readmodels=1,use_NMRnumber=True):
"""
# Reads a pdb file and lets PDBparser.parse do the parsing
"""
import os
if data != None:
import StringIO
stream = StringIO.StringIO(data)
self.lines = stream.readlines()
elif os.path.isfile(filename):
if not silent:
print 'Reading: ',filename
fd=open(filename)
self.lines=fd.readlines()
fd.close()
else:
raise FileNotFoundError(filename)
if parse:
import PDBparser
Y=PDBparser.PDBparser(self.lines,self.parse_terms)
Y.readmodels=readmodels
if not use_NMRnumber:
Y.ignore_NMRmodel=True
#
Y.parse()
self.atoms=Y.atoms
if hasattr(Y,'spacegroup'):
self.spacegroup=Y.spacegroup # Transfer spacegroup info
else:
self.spacegroup='Unknown'
self.header=''
if hasattr(Y,'header'):
self.header=Y.header
#
# Transfer crystal symmetry info
#
self.scale=Y.scale
self.orig=Y.orig
self.cryst=Y.cryst
#
# Update
#
self.Update()
self.attribute=Y.attribute
if not silent:
print 'Read file with %3d residues and %5d atoms' %(len(self.residues.keys()),len(self.atoms.keys()))
return
def addpdblines(self,lines):
"""Add the atoms in lines to the current set of atoms"""
import PDBparser
Y=PDBparser.PDBparser(lines,self.parse_terms)
Y.parse()
error=False
for atom in Y.atoms.keys():
if not self.atoms.has_key(atom):
self.atoms[atom]=Y.atoms[atom]
else:
print 'Name clash for',atom
error=True
if not error:
self.Update()
self.attribute=Y.attribute
return
else:
print 'Protool does not allow name clashes'
import os
os._exit(0)
