def autodock_scoring(receptor, ligand):
receptorfilename = receptor
ligandfilename = ligand
write_file_mode = False
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()
ligand = Read(ligandfilename)[0]
ligand.buildBondsByDistance()
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
output_score = {
'score': score,
'estat': estat,
'hb': hb,
'vdw': vdw,
'dsolv,': dsolv,
'torsEnrg': torsEnrg
}
return output_score
def get_energy_breakdown(receptor_atoms, ligand_atoms, coords_to_use):
ms = MolecularSystem()
ms.add_entities(receptor_atoms)
ms.add_entities(ligand_atoms)
ms.set_coords(1, coords_to_use)
#ms.set_coords(1, c.getCoords()[:])
ad_scorer = AutoDock41Scorer()
ad_scorer.set_molecular_system(ms)
score_list = ad_scorer.get_score_per_term()
ostr = ""
for score in score_list:
ostr = ostr + "% 8.4f," % score
return ostr[:-1]
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:]:
rec_non_std = rec_non_std + '_' + t
#check format of receptor
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()
usage()
sys.exit()
#1: create the python molecules
rec = Read(receptor_file)[0]
recbnds = rec.buildBondsByDistance()
lig = Read(ligand_file)[0]
ligbnds = lig.buildBondsByDistance()
#2: setup python scorers for your molecules:
ms = MolecularSystem()
ms.add_entities(rec.allAtoms)
ms.add_entities(lig.allAtoms)
#3: setup python scorers
scorer = AutoDock41Scorer()
scorer.set_molecular_system(ms)
estat_scores = numpy.add.reduce(scorer.terms[0][0].get_score_array())
dsolv_scores = numpy.add.reduce(scorer.terms[1][0].get_score_array())
vdw_scores = numpy.add.reduce(scorer.terms[2][0].get_score_array())
hbond_scores = numpy.add.reduce(scorer.terms[3][0].get_score_array())
wts = AutoDockTermWeights41()
#4: open outputfile for writing scores
if output_file is not None:
fptr = open(output_file, 'w')
#5. score the docked pose outputting individual terms for each atom:
all_estat = []
all_VHD = []
for i in range(len(lig.allAtoms)):