def __init__(self,atomset1,atomset2):
""" """
EnergyScorer.__init__(self,atomset1,atomset2)
self.weight = None
self.weightLabel = None
self.scorer = AutoDock4Scorer()
self.prop = self.scorer.prop
self.r = self.ms.add_entities(atomset1)
self.l = self.ms.add_entities(atomset2)
self.scorer.set_molecular_system(self.ms)
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 = AutoDock4Scorer()
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
cl.make_clustering(rms_tolerance)
ref_coords = cl.clustering_dict[rms_tolerance][0][0].getCoords()[:]
# for building hydrogen bonds or reporting energy breakdown
# setup receptor:
if build_hydrogen_bonds or report_energy_breakdown:
ligMol.buildBondsByDistance()
receptor = Read(receptor_filename)[0]
receptor.buildBondsByDistance()
if build_hydrogen_bonds:
hbondBuilder = HydrogenBondBuilder()
if report_energy_breakdown:
ms = MolecularSystem()
ms.add_entities(receptor.allAtoms)
ms.add_entities(ligMol.allAtoms)
adscorer = AutoDock4Scorer()
adscorer.set_molecular_system(ms)
mode = 'w'
if append_to_outputfile:
mode = 'a'
fptr = open(outputfilename, mode)
if mode=='w':
if build_hydrogen_bonds and report_energy_breakdown:
titles = "#clust binding_nrg rmsd_v_0 Ki int_nrg hbnds sum_py_nrg estat_nrg hbnd_nrg vdw_nrg dsolv_nrg#ats #t\n"
elif build_hydrogen_bonds:
titles = "#clust binding_nrg rmsd_v_0 Ki int_nrg hbnds #ats #t\n"
elif report_energy_breakdown:
titles = "#clust binding_nrg rmsd_v_0 Ki int_nrg sum_py_nrg estat_nrg hbnd_nrg vdw_nrg dsolv_nrg#ats #t\n"
else:
titles = "#clust binding_nrg rmsd_v_0 Ki int_nrg #ats #t\n"
mode = 'w'
first = True
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