def test_write(self):
"""
test writing a pdbqs file
"""
writer = PdbqtWriter()
writer.write('test_pdbqtWriter.pdbqt', self.mol, bondOrigin=('File',))
ans, errors = self.compare('Data/hsg1.pdbqt', 'test_pdbqtWriter.pdbqt')
self.assertEquals(errors, None)
self.assertEquals(ans, True)
if o in ('-h', '--'):
usage()
sys.exit()
if not filename:
print('rotate_molecule: filename must be specified.')
usage()
sys.exit()
mol = Read(filename)[0]
if verbose: print('read ', filename)
filetype = os.path.splitext(os.path.basename(filename))[1]
if verbose: print("filetype=", filetype)
writer = None
if filetype == '.pdbqt':
writer = PdbqtWriter()
elif filetype == '.pdbq':
writer = PdbqWriter()
elif filetype == '.pdbqs':
writer = PdbqsWriter()
elif filetype == '.pdb':
writer = PdbWriter()
else:
print('Sorry! Unable to write this filetype->', filetype)
center = numpy.add.reduce(mol.allAtoms.coords) / len(mol.allAtoms)
crds = numpy.array(mol.allAtoms.coords)
center = numpy.add.reduce(crds) / len(mol.allAtoms)
crds = crds - center
crds = crds.tolist()
mol.allAtoms.updateCoords(crds)
ats = mol.allAtoms.get(lambda x: x.autodock_element==t)
for a in ats:
if a.chargeSet is not None:
preserved[a] = [a.chargeSet, a.charge]
if charges_to_add=='gasteiger':
GasteigerChargeCalculator().addCharges(mol.allAtoms)
if charges_to_add is not None:
#restore any previous charges
for atom, chargeList in preserved.items():
atom._charges[chargeList[0]] = chargeList[1]
atom.chargeSet = chargeList[0]
#pdbqt_filename = mol.name + '.pdbqt'
writer = PdbqtWriter()
fptr = open(pdbqt_filename, 'w')
ctr = 0
for line in mol.parser.allLines:
if find(line, 'ATOM')<0 and find(line, "HETA")<0:
fptr.write(line)
else:
this_atom = mol.allAtoms[ctr]
writer.write_atom(fptr, this_atom)
ctr = ctr + 1
fptr.close()
if verbose:
print "wrote ", ctr, " atoms to", pdbqt_filename
# To execute this command type:
ats = mol.allAtoms.get(lambda x: x.autodock_element == t)
for a in ats:
if a.chargeSet is not None:
preserved[a] = [a.chargeSet, a.charge]
if charges_to_add == 'gasteiger':
GasteigerChargeCalculator().addCharges(mol.allAtoms)
if charges_to_add is not None:
#restore any previous charges
for atom, chargeList in list(preserved.items()):
atom._charges[chargeList[0]] = chargeList[1]
atom.chargeSet = chargeList[0]
#pdbqt_filename = mol.name + '.pdbqt'
writer = PdbqtWriter()
fptr = open(pdbqt_filename, 'w')
ctr = 0
for line in mol.parser.allLines:
if find(line, 'ATOM') < 0 and find(line, "HETA") < 0:
fptr.write(line)
else:
this_atom = mol.allAtoms[ctr]
writer.write_atom(fptr, this_atom)
ctr = ctr + 1
fptr.close()
if verbose:
print("wrote ", ctr, " atoms to", pdbqt_filename)
# To execute this command type:
# pdbqs_to_pdbqt.py -s pdbqs_filename_stem -v
usage()
sys.exit()
if not filename:
print 'rotate_molecule: filename must be specified.'
usage()
sys.exit()
mol = Read(filename)[0]
if verbose: print 'read ', filename
filetype = os.path.splitext(os.path.basename(filename))[1]
if verbose: print "filetype=", filetype
writer = None
if filetype=='.pdbqt':
writer = PdbqtWriter()
elif filetype=='.pdbq':
writer = PdbqWriter()
elif filetype=='.pdbqs':
writer = PdbqsWriter()
elif filetype=='.pdb':
writer = PdbWriter()
else:
print 'Sorry! Unable to write this filetype->', filetype
center = Numeric.add.reduce(mol.allAtoms.coords)/len(mol.allAtoms)
crds = Numeric.array(mol.allAtoms.coords)
center = Numeric.add.reduce(crds)/len(mol.allAtoms)
crds = crds - center
crds = crds.tolist()
mol.allAtoms.updateCoords(crds)
