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 = AutoDock305Scorer()
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
def __init__(self,atomset1,atomset2,func=None):
self.atomset1 =atomset1
self.atomset2 =atomset2
# save molecule instance of parent molecule
self.mol1 = self.atomset1.top.uniq()[0]
self.mol2 = self.atomset2.top.uniq()[0]
# dictionary to save the state of each molecule when the
# energy is calculated, will allow to retrieve the conformation
# use for the energy calculation
# keys are score,values is a list a 2 set of coords (mol1,mol2)
self.confcoords = {}
self.ms = ms = MolecularSystem()
self.cutoff = 1.0
self.score = 0.0
first = True
if verbose: print 'first is ', first
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 = "%12s%12s % 8.4f % 6.4f % 6.4f % 6.4f % 6.4f % 6.4f\n" %(receptor.name,ligand.name, score, estat, hb, vdw, dsolv, torsEnrg)
optr.write(ostr)
if verbose:
print 'wrote %s' %outputfilename
optr.close()
# 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()
