5.3 Saving aligned structures

OEBestOverlay does not actually move the fit molecule. Part of OEBestOverlayScore is the rotation matrix and translation matrix necessary to move the fit molecule into the final overlap position. It is up to the user to apply these transformations. The OpenEye standard is rotation then translation, but as a convenience, OEBestOverlayScore has a Transform() (section ) method that will apply the transforms in the proper order. This next example, expands from the previous. Now, not only can we choose the number of overlays to keep, we are also going to align each fit conformer to the ref conformer it was overlaid on, and then output the pair to an output file. If SD or OEB is used as the output file type, then scores will also be stored in SD tags.

 1 #!/usr/bin/env python
 2 # Copyright (C) 2005,2006 OpenEye Scientific Software, Inc.
 3 import os, sys
 4 from openeye.oechem import *
 5 from openeye.oeshape import *
 6
 7 if len(sys.argv)!=5:
 8     OEThrow.Usage("bestoverlay4.py <reffile> <rocs_hits_file> <out.sdf> <keepsize>")
 9
10 reffs = oemolistream(sys.argv[1])
11 fitfs = oemolistream(sys.argv[2])
12 outfs = oemolostream(sys.argv[3])
13 keepsize = int(sys.argv[4])
14
15 refmol=OEMol()
16 OEReadMolecule(reffs, refmol)
17
18 best=OEBestOverlay()
19 best.SetRefMol(refmol)
20
21 print "Ref. Title:", refmol.GetTitle(),
22 print "Num Confs:", refmol.NumConfs()
23
24 resCount = 0
25 fitmol = OEMol()
26 while OEReadMolecule(fitfs, fitmol):
27     print "Fit Title:", fitmol.GetTitle(),
28     print "Num Confs:", fitmol.NumConfs()
29
30     scoreiter = OEBestOverlayScoreIter()
31     OESortOverlayScores(scoreiter, best.Overlay(fitmol), OEHighestTanimoto())
32     for score in scoreiter:
33         outmol = OEGraphMol(fitmol.GetConf(OEHasConfIdx(score.fitconfidx)))
34         score.Transform(outmol)
35
36         OESetSDData(outmol, "RefConfIdx", "%-d"%score.refconfidx)
37         OESetSDData(outmol, "Tanimoto", "%-.3f"%score.tanimoto)
38
39         OEWriteMolecule(outfs, refmol.GetConf(OEHasConfIdx(score.refconfidx)))
40         OEWriteMolecule(outfs, outmol)
41
42         resCount +=1
43         if resCount==keepsize:
44             break
45
46 print resCount,"results returned"
47

Listing:5.4 Writing aligned structures from OEBestOverlay.

				Shape Toolkit Python Programming Manual

				Shape Toolkit Python Programming Manual