if verbose: print('set parameter_library_filename to ', a)
if o in ('-h', '--'):
usage()
sys.exit()
if not receptorfilename:
print('compute_AutoDock41_score: receptorfilename must be specified.')
usage()
sys.exit()
if not ligandfilename:
print('compute_AutoDock41_score: ligandfilename must be specified.')
usage()
sys.exit()
ad_scorer = AutoDock41Scorer(exclude_torsFreeEnergy=exclude_torsFreeEnergy)
if parameter_library_filename is not None:
ad_scorer.read_parameter_file(parameter_library_filename)
supported_types = ad_scorer.supported_types
receptor = Read(receptorfilename)[0]
assert os.path.splitext(
receptor.parser.filename
)[-1] == '.pdbqt', "receptor file not in required '.pdbqt' format"
if verbose: print('read ', receptorfilename)
receptor.buildBondsByDistance()
rec_non_std = ""
non_std_types = check_types(receptor, supported_types)
if len(non_std_types):
rec_non_std = non_std_types[0]
if len(non_std_types) > 1:
for t in non_std_types[1:]:
if append_to_outputfile:
mode = 'a'
first = not os.path.exists(outputfilename)
if verbose: print 'first is ', first
optr = open(outputfilename, mode)
if first:
tstr = "RECEPTOR_LIGAND #ESTAT #HB #VDW #DSOLV #TORSDOF #ATS #TORS\n"
optr.write(tstr)
#get the scores
ms = MolecularSystem()
ms.add_entities(receptor.allAtoms)
ms.add_entities(ligand.allAtoms)
if use_autodock40_weights:
ad_scorer = AutoDock4Scorer()
else:
ad_scorer = AutoDock41Scorer()
ad_scorer.set_molecular_system(ms)
score_list = ad_scorer.get_score_per_term()
ostr = "%8s_%6s," % (receptor.name, ligand.name)
for score in score_list:
ostr = ostr + " % 8.4f," % score
ostr = ostr + " % 8d," % ligand.TORSDOF
ostr = ostr + " % 8d," % len(ligand.allAtoms)
ostr = ostr + " % 8d," % len(ligand.torTree.torsionMap)
ostr = ostr + "\n"
optr.write(ostr)
optr.close()
if verbose:
print 'wrote %s' % outputfilename
# To execute this command type:
def autodock_scoring(receptor, ligand):
receptorfilename = receptor
ligandfilename = ligand
write_file_mode = False
outputfilename = dirname+'/Alanine_Scanning_Binding_Energies_Result.csv'
parameter_library_filename = None
exclude_torsFreeEnergy = False
verbose = None
ad_scorer = AutoDock41Scorer(exclude_torsFreeEnergy=exclude_torsFreeEnergy)
supported_types = ad_scorer.supported_types
receptor = Read(receptorfilename)[0]
receptor.buildBondsByDistance()
rec_non_std = ""
non_std_types = check_types(receptor, supported_types)
#Checking the format of receptor
if len(non_std_types):
rec_non_std = non_std_types[0]
if len(non_std_types)>1:
for t in non_std_types[1:]:
rec_non_std = rec_non_std + '_' + t
ligand = Read(ligandfilename)[0]
ligand.buildBondsByDistance()
lig_non_std = ""
non_std_types = check_types(ligand, supported_types)
#Checking the format of ligand
if len(non_std_types):
lig_non_std = non_std_types[0]
if len(non_std_types)>1:
for t in non_std_types[1:]:
lig_non_std = lig_non_std + '_' + t
mode = 'a'
first = not os.path.exists(outputfilename)
if write_file_mode:
mode = 'w'
first = True
optr = open(outputfilename, mode)
if first:
tstr = "Receptor,Ligand,AutoDock4.1Score,estat,hb,vdw,dsolv,tors\n"
optr.write(tstr)
#setup the molecular system
ostr = ""
if len(lig_non_std):
ostr = 'ERROR: unable to score ligand "%s" due to presence of non-standard atom type(s): %s\n' %(ligand.name, lig_non_std)
optr.write(ostr)
elif len(rec_non_std):
ostr = 'ERROR: unable to score receptor "%s" due to non-standard atom type(s): %s\n' %(receptor.name, rec_non_std)
optr.write(ostr)
else:
ms = MolecularSystem()
ms.add_entities(receptor.allAtoms)
ms.add_entities(ligand.allAtoms)
ad_scorer.set_molecular_system(ms)
#get the scores
#score per term
estat, hb,vdw,dsolv = ad_scorer.get_score_per_term()
torsEnrg = ligand.TORSDOF * ad_scorer.tors_weight
score = estat + hb + vdw + dsolv + torsEnrg
ostr = "%19s,%3s,%8.4f,%6.4f,%6.4f,%6.4f,%6.4f,%6.4f\n" %(receptor.name, uniq_ligand[0], score, estat, hb, vdw, dsolv, torsEnrg)
optr.write(ostr)
optr.close()