#fix number for problem files with alternative positions
mol.allAtoms.number = range(1, len(mol.allAtoms)+1)
#pdb_filename = mol.name + '.pdb'
writer = PdbqWriter()
#writer.write(pdbq_filename, mol.allAtoms, records=['ATOM', 'HETATM'])
fptr = open(pdbq_filename, 'w')
ctr = 0
for l in mol.parser.allLines:
if l.find('ATOM')==0 or l.find('HETATM')==0:
at = mol.allAtoms[ctr]
if at.autodock_element=='A':
if len(at.name)==1:
at.name='A'
else:
at.name = 'A' + at.name[1:]
writer.write_atom(fptr, mol.allAtoms[ctr])
ctr = ctr + 1
else:
fptr.write(l)
if verbose:
print "wrote ", ctr, " atoms to", pdbq_filename
# To execute this command type:
# pdbqt_to_pdb.py -f pdbqt_filename_stem [-o outputfilename] -v
mols = Read(pdbqt_filename)
if verbose: print('read ', pdbqt_filename)
mol = mols[0]
mol.buildBondsByDistance()
#fix number for problem files with alternative positions
mol.allAtoms.number = list(range(1, len(mol.allAtoms) + 1))
#pdb_filename = mol.name + '.pdb'
writer = PdbqWriter()
#writer.write(pdbq_filename, mol.allAtoms, records=['ATOM', 'HETATM'])
fptr = open(pdbq_filename, 'w')
ctr = 0
for l in mol.parser.allLines:
if l.find('ATOM') == 0 or l.find('HETATM') == 0:
at = mol.allAtoms[ctr]
if at.autodock_element == 'A':
if len(at.name) == 1:
at.name = 'A'
else:
at.name = 'A' + at.name[1:]
writer.write_atom(fptr, mol.allAtoms[ctr])
ctr = ctr + 1
else:
fptr.write(l)
if verbose:
print("wrote ", ctr, " atoms to", pdbq_filename)
# To execute this command type:
# pdbqt_to_pdb.py -f pdbqt_filename_stem [-o outputfilename] -v
