path = os.path.join(drug, "ca_%s_%s.pdb" % (protein, drug))
print "Working with", path
pdb = parsePDB(path, subset="ca", csets=range(1000))
print "Loaded"
for motif in ordered_motifs:
if motif in motifs[protein]:
cas = pdb.select("name CA")
motif_cas = pdb.select(
"resid %d to %d" % (motifs[protein][motif][0], motifs[protein][motif][1])
)
calculator = RMSDCalculator(
calculatorType="QCP_OMP_CALCULATOR",
fittingCoordsets=cas.getCoordsets(),
calculationCoordsets=motif_cas.getCoordsets(),
)
rmsds = calculator.oneVsFollowing(0)
rmsd_results[protein]["RMSD"].extend(rmsds)
rmsd_results[protein]["Drug"].extend([drug] * len(rmsds))
rmsd_results[protein]["Motif"].extend([motif] * len(rmsds))
del cas
del motif_cas
del pdb
pickle.dump(rmsd_results, open(os.path.join(options.results, "rmsd_results.pickle"), "w"))
else:
rmsd_results = pickle.load(open(options.data))
f, axes = plt.subplots(3, 2, sharey="row")
f.subplots_adjust(hspace=0.4, wspace=0.1)
f.set_size_inches(10, 18, forward=True)