def __modifyParametersInp(self):
'''Modify the Parameters.inp file according the table information'''
# Creating new typeAtom line
newTypeAtomLine = "typeAtom=\""
typeatoms = []
for i in self.d_table:
typeatoms.extend(self.d_table[i].values())
daux = {i: None for i in typeatoms}
typeatoms = daux.keys()
typeatoms.sort()
for i, j in enumerate(typeatoms):
if i == len(typeatoms) - 1:
newTypeAtomLine += functions.formatAtomName(j)
else:
newTypeAtomLine += "%s ," % functions.formatAtomName(j)
newTypeAtomLine += " \"\n"
# Creating new line list for the new Parameters.inp file
l_newLines = []
for i, line in enumerate(open("Parameters.inp")):
if i == 0:
l_newLines.append(newTypeAtomLine)
else:
l_newLines.append(line)
# Writing new Parameters.inp file
f = open("Parameters.inp", "w")
for i in l_newLines:
f.write(i)
f.close()
def modifyPDBAtoms(self, inputs):
'''writes new PDB file with atomtypes modifications. The new file has the "Mod" word before .pdb extension.
If clickOutput flag is True, the pdb file will be modified with normal
IUPAC names for a standard PDB file'''
d_keywordRecord = {"ATOM": None, "HETATM": None, "ANISOU": None, "SIGUIJ": None}
l_newPDB = []
for line in open(self.pdb):
if line[:6].strip() in d_keywordRecord:
resname = line[17:20].strip()
atomname = line[12:16].strip()
chain = line[21]
resnum = line[22:26].strip()
# save line in original_lines list
self.original_lines.append(line)
# first we can modify a line just if the table has the right resname and atomname
if inputs.d_table.has_key(resname):
if inputs.d_table[resname].has_key(atomname):
if inputs.f:
# if -f flag is given, we use only the line with residue specified in d_pdbResnumTable
if self.name in inputs.d_pdbResnumTable and \
chain in inputs.d_pdbResnumTable[self.name] and \
resnum in inputs.d_pdbResnumTable[self.name][chain]:
l_newPDB.append(line[:12] + functions.formatAtomName(inputs.d_table[resname][atomname]) + line[16:])
else:
# ~ l_newPDB.append(line[:12] + formatAtomName(d_table[resname][atomname]) + line[16:])
l_newPDB.append(line)
else:
l_newPDB.append(line[:12] + functions.formatAtomName(inputs.d_table[resname][atomname]) + line[16:])
else:
l_newPDB.append(line)
else:
l_newPDB.append(line)
else:
l_newPDB.append(line)
#write modified pdb
f = open("%sMod.pdb" % self.pdb[:-4], "w")
for i in l_newPDB:
f.write(i)
f.close()