def get_energy_breakdown(receptor_atoms, ligand_atoms, c):
ms = MolecularSystem()
ms.add_entities(receptor_atoms)
ms.add_entities(ligand_atoms)
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
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
if print_best_only:
clust0 = d.clusterer.clustering_dict[rms_tolerance][0]
c = clust0[0]
#find the filename of the best result
#for k in d.dlo_list:
# if c in k.conformations:
# dlo_filename = os.path.splitext(k.parser.filename)[0]
# print "set dlo_filename to ", dlo_filename
# ostr = dlo_filename + ", "
# fptr.write(ostr)
score_list = []
#update the coords if you need to
if build_hydrogen_bonds or report_energy_breakdown:
d.ch.set_conformation(c)
if report_energy_breakdown:
ms.set_coords(1, c.getCoords()[:])
score_list = adscorer.get_score_per_term()
total_score = Numeric.add.reduce(score_list) + c.internal_energy + tors_penalty
#total_score = Numeric.add.reduce(score_list)
ostr = "% 4d, % 4d, % 12.4f, % 6.4f, % 8.6e,% 9.6f" %(len(d.clusterer.data), len(clust0), c.binding_energy, c.getRMSD(ref_coords), c.Ki, c.internal_energy)
if build_hydrogen_bonds:
atDict = hbondBuilder.build(receptor.allAtoms, ligMol.allAtoms)
num_hbonds = len(atDict)
ostr = ostr + ", % 2d" %(num_hbonds)
if report_energy_breakdown:
ostr = ostr + ", % 12.4f" %total_score
#for score in score_list:
# ostr = ostr + ", % 12.4f" %score
ostr = ostr + ", % 6.4f, % 12.4f, % 12.4f,% 6.4f," %(score_list[0],
score_list[1], score_list[2], score_list[3])
#add the number of atoms and the number of active torsions in the ligand
