def prepare_receptor(self, molecule):
path = '{}_receptor.pdb'.format(self.tmpfile)
pathqt = path + 'qt'
pdb = molecule.write(absolute=path, filetype='pdb')
self._paths.append(path)
mol = MolKit.Read(path)[0]
mol.buildBondsByDistance()
RPO = AD4ReceptorPreparation(mol, outputfilename=pathqt)
self._paths.append(pathqt)
return pathqt
def receptor_preparation(receptor, output): receptor_filename = receptor verbose = None repairs = 'checkhydrogens' charges_to_add = 'gasteiger' preserve_charge_types=None cleanup = "nphs_lps_waters_nonstdres" mode = 'automatic' delete_single_nonstd_residues = None dictionary = None mols = Read(receptor) mol = mols[0] RPO = AD4ReceptorPreparation(mol, mode, repairs, charges_to_add, cleanup, outputfilename=output, delete_single_nonstd_residues=delete_single_nonstd_residues,dict=dictionary)
def preprocess_receptor(receptor_filename, outputfilename):
repairs = ''
charges_to_add = 'gasteiger'
preserve_charge_types=None
cleanup = ""
mode = "automatic"
delete_single_nonstd_residues = False
dictionary = None
mols = Read(receptor_filename)
mol = mols[0]
preserved = {}
if charges_to_add is not None and preserve_charge_types is not None:
preserved_types = preserve_charge_types.split(',')
for t in preserved_types:
if not len(t): continue
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 len(mols)>1:
ctr = 1
for m in mols[1:]:
ctr += 1
if len(m.allAtoms)>len(mol.allAtoms):
mol = m
mol.buildBondsByDistance()
RPO = AD4ReceptorPreparation(mol, mode, repairs, charges_to_add,
cleanup, outputfilename=outputfilename,
preserved=preserved,
delete_single_nonstd_residues=delete_single_nonstd_residues,
dict=dictionary)
if charges_to_add is not None:
for atom, chargeList in preserved.items():
atom._charges[chargeList[0]] = chargeList[1]
atom.chargeSet = chargeList[0]
if verbose:
print "mol set to ", ctr, "th molecule with", len(
mol.allAtoms), "atoms"
mol.buildBondsByDistance()
if verbose:
print "setting up RPO with mode=", mode,
print "and outputfilename= ", outputfilename
print "charges_to_add=", charges_to_add
print "delete_single_nonstd_residues=", delete_single_nonstd_residues
RPO = AD4ReceptorPreparation(
mol,
mode,
repairs,
charges_to_add,
cleanup,
outputfilename=outputfilename,
preserved=preserved,
delete_single_nonstd_residues=delete_single_nonstd_residues,
dict=dictionary)
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]
# To execute this command type:
# prepare_receptor4.py -r pdb_file -o outputfilename -A checkhydrogens