def test_write(self):
"""
test writing a pdbqs file
"""
writer = PdbqsWriter()
writer.write('test_pdbqsWriter.pdbqs', self.mol, bondOrigin=('File',))
ans, errors = self.compare('Data/1crn.pdbqs', 'test_pdbqsWriter.pdbqs')
self.assertEquals(errors, None)
self.assertEquals(ans, True)
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)
lenCoords = len(crds)
#rotate the atoms here
if axis is not None and angle is not None:
rot = (float(angle) * 3.14159 / 180.) % (2 * numpy.pi)
mols = Read(pdbqt_filename)
if verbose:
print "read ", pdbqt_filename
mol = mols[0]
# fix number for problem files with alternative positions
mol.allAtoms.number = range(1, len(mol.allAtoms) + 1)
# possible clean-up???
# need to type atoms + assign babel_types
solparer = SolvationParameterizer()
solparer.addParameters(mol.allAtoms)
if verbose:
print "set autodock3 solvation parameters for ", mol.name
# pdbqs_filename = mol.name + '.pdbqs'
writer = PdbqsWriter()
fptr = open(pdbqs_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", pdbqs_filename
# To execute this command type:
if len(item.name) == 1:
item.name = 'A'
else:
item.name = 'A' + item.name[1:]
elif hasattr(item, 'autodock_element'):
item.autodock_element = item.autodock_element
if splitAcceptors and item.autodock_element in self.acceptorList:
#if item has a bond to a hydrogen:
# change acceptor type 'XA' to 'XB' for 'B'oth 'A'cceptor and 'D'onor
if 'H' in item.bonds.getAtoms().element:
#O->OB;N->NB;S->SB
item.autodock_element = item.element + 'B'
d[item.autodock_element] = 1
type_list = d.keys()
type_list.sort()
mol.types = type_list
if __name__ == "__main__":
from MolKit import Read
m = Read("/mgl/work4/rhuey/dev23/hsg1_no_conects.pdbq")[0]
solP = SolvationParameterizer()
ll = solP.addParameters(m.allAtoms)
#NB: hydrogens get 0.0 0.0
print "len(notfound) = ", len(ll)
for i in ll:
print i.full_name(),
from MolKit.pdbWriter import PdbqsWriter
writer = PdbqsWriter()
writer.write("/mgl/work4/rhuey/dev23/test_hsg1.pdbqs", m.allAtoms)
mols = Read(pdbqt_filename)
if verbose: print 'read ', pdbqt_filename
mol = mols[0]
#fix number for problem files with alternative positions
mol.allAtoms.number = range(1, len(mol.allAtoms) + 1)
#possible clean-up???
#need to type atoms + assign babel_types
solparer = SolvationParameterizer()
solparer.addParameters(mol.allAtoms)
if verbose:
print "set autodock3 solvation parameters for ", mol.name
#pdbqs_filename = mol.name + '.pdbqs'
writer = PdbqsWriter()
fptr = open(pdbqs_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", pdbqs_filename
# To execute this command type:
# pdbqt_to_pdbqs.py -s pdbqt_filename_stem -v
item.name = 'A'
else:
item.name = 'A' + item.name[1:]
elif hasattr(item, 'autodock_element'):
item.autodock_element = item.autodock_element
if splitAcceptors and item.autodock_element in self.acceptorList:
#if item has a bond to a hydrogen:
# change acceptor type 'XA' to 'XB' for 'B'oth 'A'cceptor and 'D'onor
if 'H' in item.bonds.getAtoms().element:
#O->OB;N->NB;S->SB
item.autodock_element = item.element + 'B'
d[item.autodock_element] = 1
type_list = d.keys()
type_list.sort()
mol.types = type_list
if __name__ == "__main__":
from MolKit import Read
m = Read("/mgl/work4/rhuey/dev23/hsg1_no_conects.pdbq")[0]
solP = SolvationParameterizer()
ll = solP.addParameters(m.allAtoms)
#NB: hydrogens get 0.0 0.0
print "len(notfound) = ", len(ll)
for i in ll:
print i.full_name(),
from MolKit.pdbWriter import PdbqsWriter
writer = PdbqsWriter()
writer.write("/mgl/work4/rhuey/dev23/test_hsg1.pdbqs", m.allAtoms)