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)
