s1 = b.GenerateSubshapeShape(m1)
cPickle.dump(s1,file('test_data/square1.shp.pkl','wb+'))
print 'm2:'
s2 = b.GenerateSubshapeShape(m2)
cPickle.dump(s2,file('test_data/square2.shp.pkl','wb+'))
ns1 = b.CombineSubshapes(s1,s2)
b.GenerateSubshapeSkeleton(ns1)
cPickle.dump(ns1,file('test_data/combined.shp.pkl','wb+'))
else:
s1 = cPickle.load(file('test_data/square1.shp.pkl','rb'))
s2 = cPickle.load(file('test_data/square2.shp.pkl','rb'))
#ns1 = cPickle.load(file('test_data/combined.shp.pkl','rb'))
ns1=cPickle.load(file('test_data/combined.shp.pkl','rb'))
v = MolViewer()
SubshapeObjects.DisplaySubshape(v,s1,'shape1')
SubshapeObjects.DisplaySubshape(v,ns1,'ns1')
#SubshapeObjects.DisplaySubshape(v,s2,'shape2')
a = SubshapeAligner.SubshapeAligner()
pruneStats={}
algs =a.GetSubshapeAlignments(None,ns1,m1,s1,b,pruneStats=pruneStats)
print len(algs)
print pruneStats
import os,tempfile
from rdkit import Geometry
fName = tempfile.mktemp('.grd')
Geometry.WriteGridToFile(ns1.coarseGrid.grid,fName)
v.server.loadSurface(fName,'coarse','',2.5)
os.unlink(fName)
targetConf=tgtConf,
queryConf=queryConf,
pruneStats=pruneStats):
continue
# if we made it this far, it's a good alignment
yield alignment
if __name__ == '__main__':
from rdkit.six.moves import cPickle
tgtMol, tgtShape = cPickle.load(file('target.pkl', 'rb'))
queryMol, queryShape = cPickle.load(file('query.pkl', 'rb'))
builder = cPickle.load(file('builder.pkl', 'rb'))
aligner = SubshapeAligner()
algs = aligner.GetSubshapeAlignments(tgtMol, tgtShape, queryMol,
queryShape, builder)
print(len(algs))
from rdkit.Chem.PyMol import MolViewer
v = MolViewer()
v.ShowMol(tgtMol, name='Target', showOnly=True)
v.ShowMol(queryMol, name='Query', showOnly=False)
SubshapeObjects.DisplaySubshape(v,
tgtShape,
'target_shape',
color=(.8, .2, .2))
SubshapeObjects.DisplaySubshape(v,
queryShape,
'query_shape',
color=(.2, .2, .8))
