a._coords[0][1] = -1. * a._coords[0][1]
elif rotation == 'y':
#for rotation around y-axis:
for a in mol.allAtoms:
a._coords[0][0] = -1. * a._coords[0][0]
a._coords[0][2] = -1. * a._coords[0][2]
elif rotation == 'x':
#for rotation around x-axis:
for a in mol.allAtoms:
a._coords[0][1] = -1. * a._coords[0][1]
a._coords[0][2] = -1. * a._coords[0][2]
ncrds = numpy.array(mol.allAtoms.coords)
ncrds = ncrds + center
ncrds = ncrds.tolist()
mol.allAtoms.updateCoords(ncrds)
if writer:
outptr = open(outputfilename, 'w')
liglines = mol.parser.allLines
ctr = 0
for l in liglines:
if l.find("ATOM") != 0 and l.find("HETATM") != 0:
outptr.write(l)
else:
writer.write_atom(outptr, mol.allAtoms[ctr])
ctr += 1
outptr.close()
# To execute this command type:
# rotate_molecule.py -f filename [-o outputfilename -u axis -a angle to rotate] -v
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:
# pdbqs_to_pdbqt.py -s pdbqs_filename_stem -v
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
#for rotation around y-axis:
for a in mol.allAtoms:
a._coords[0][0] = -1.*a._coords[0][0]
a._coords[0][2] = -1.*a._coords[0][2]
elif rotation=='x':
#for rotation around x-axis:
for a in mol.allAtoms:
a._coords[0][1] = -1.*a._coords[0][1]
a._coords[0][2] = -1.*a._coords[0][2]
ncrds = Numeric.array(mol.allAtoms.coords)
ncrds = ncrds + center
ncrds = ncrds.tolist()
mol.allAtoms.updateCoords(ncrds)
if writer:
outptr = open(outputfilename, 'w')
liglines = mol.parser.allLines
ctr = 0
for l in liglines:
if l.find("ATOM")!=0 and l.find("HETATM")!=0:
outptr.write(l)
else:
writer.write_atom(outptr, mol.allAtoms[ctr])
ctr += 1
outptr.close()
# To execute this command type:
# rotate_molecule.py -f filename [-o outputfilename -u axis -a angle to rotate] -v
