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from rdkit import RDConfig
import os,sys
import unittest
from rdkit import DataStructs
from rdkit import Chem
from rdkit.Chem import rdMolAlign
from rdkit.Geometry import rdGeometry as geom
from rdkit.Chem import rdShapeHelpers as rdshp
from rdkit.Chem import rdMolTransforms as rdmt
import math
def feq(v1, v2, tol=1.0e-4):
return abs(v1-v2) < tol
class TestCase(unittest.TestCase):
def setUp(self) :
pass
def test1Shape(self):
fileN = os.path.join(RDConfig.RDBaseDir,'Code','GraphMol','ShapeHelpers',
'test_data','1oir.mol')
m = Chem.MolFromMolFile(fileN)
rdmt.CanonicalizeMol(m)
dims1, offset1 = rdshp.ComputeConfDimsAndOffset(m.GetConformer())
grd = geom.UniformGrid3D(30.0, 16.0, 10.0)
rdshp.EncodeShape(m, grd, 0);
ovect = grd.GetOccupancyVect()
self.failUnless(ovect.GetTotalVal() == 9250)
m = Chem.MolFromMolFile(fileN)
trans = rdmt.ComputeCanonicalTransform(m.GetConformer())
dims, offset = rdshp.ComputeConfDimsAndOffset(m.GetConformer(), trans=trans)
dims -= dims1
offset -= offset1;
self.failUnless(feq(dims.Length(), 0.0))
self.failUnless(feq(offset.Length(), 0.0))
grd1 = geom.UniformGrid3D(30.0, 16.0, 10.0)
rdshp.EncodeShape(m, grd1, 0, trans)
ovect = grd1.GetOccupancyVect()
self.failUnless(ovect.GetTotalVal() == 9250)
grd2 = geom.UniformGrid3D(30.0, 16.0, 10.0)
rdshp.EncodeShape(m, grd2, 0)
fileN2 = os.path.join(RDConfig.RDBaseDir,'Code','GraphMol','ShapeHelpers',
'test_data','1oir_conf.mol')
m2 = Chem.MolFromMolFile(fileN2)
rmsd = rdMolAlign.AlignMol(m, m2)
self.failUnless(feq(rdshp.ShapeTanimotoDist(m, m2),0.2813))
dist = rdshp.ShapeTanimotoDist(mol1=m, mol2=m2, confId1=0, confId2=0,
gridSpacing=0.25, stepSize=0.125)
self.failUnless(feq(dist,0.3021))
m = Chem.MolFromMolFile(fileN)
cpt = rdmt.ComputeCentroid(m.GetConformer())
dims, offset = rdshp.ComputeConfDimsAndOffset(m.GetConformer())
grd = geom.UniformGrid3D(dims.x, dims.y, dims.z,
0.5, DataStructs.DiscreteValueType.TWOBITVALUE,
offset)
dims -= geom.Point3D(13.927, 16.97, 9.775)
offset -= geom.Point3D(-4.353, 16.829, 2.782)
self.failUnless(feq(dims.Length(), 0.0))
self.failUnless(feq(offset.Length(), 0.0))
rdshp.EncodeShape(m, grd, 0)
ovect = grd.GetOccupancyVect()
self.failUnless(ovect.GetTotalVal() == 9275)
geom.WriteGridToFile(grd, '1oir_shape.grd')
m = Chem.MolFromMolFile(fileN)
lc, uc = rdshp.ComputeConfBox(m.GetConformer())
rdmt.CanonicalizeMol(m)
lc1, uc1 = rdshp.ComputeConfBox(m.GetConformer())
lc2, uc2 = rdshp.ComputeUnionBox((lc, uc), (lc1, uc1))
lc -= geom.Point3D(-4.353, 16.829, 2.782)
uc -= geom.Point3D(9.574, 33.799, 12.557)
self.failUnless(feq(lc.Length(), 0.0))
self.failUnless(feq(uc.Length(), 0.0))
lc1 -= geom.Point3D(-10.7519, -6.0778, -3.0123)
uc1 -= geom.Point3D(8.7163, 5.3279, 3.1621)
self.failUnless(feq(lc1.Length(), 0.0))
self.failUnless(feq(uc1.Length(), 0.0))
lc2 -= geom.Point3D(-10.7519, -6.0778, -3.01226)
uc2 -= geom.Point3D(9.574, 33.799, 12.557)
self.failUnless(feq(lc2.Length(), 0.0))
self.failUnless(feq(uc2.Length(), 0.0))
if __name__=='__main__':
print "Testing Shape Helpers wrapper"
unittest.main()
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