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from rdkit import RDConfig
import os,sys
import unittest
from rdkit import DataStructs
from rdkit import Chem
from rdkit.Geometry import rdGeometry as geom
from rdkit.Chem import rdMolTransforms as rdmt
def feq(v1, v2, tol=1.0e-4):
return abs(v1-v2) < tol
def ptEq(pt, tpt, tol=0.0001):
pt -= tpt
return feq(pt.Length(), 0.0)
class TestCase(unittest.TestCase):
def setUp(self) :
pass
def test1Canonicalization(self) :
mol = Chem.MolFromSmiles("C")
conf = Chem.Conformer(1)
conf.SetAtomPosition(0, (4.0, 5.0, 6.0))
mol.AddConformer(conf,1)
conf = mol.GetConformer()
pt = rdmt.ComputeCentroid(conf)
self.failUnless(ptEq(pt, geom.Point3D(4.0, 5.0, 6.0)))
fileN = os.path.join(RDConfig.RDBaseDir,'Code','GraphMol','MolTransforms',
'test_data','1oir.mol')
m = Chem.MolFromMolFile(fileN)
cpt = rdmt.ComputeCentroid(m.GetConformer())
trans = rdmt.ComputeCanonicalTransform(m.GetConformer(), cpt)
trans2 = rdmt.ComputeCanonicalTransform(m.GetConformer())
for i in range(4):
for j in range(4) :
self.failUnless(feq(trans[i,j], trans2[i, j]))
rdmt.TransformConformer(m.GetConformer(), trans2)
m2 = Chem.MolFromMolFile(fileN)
rdmt.CanonicalizeConformer(m2.GetConformer())
nats = m.GetNumAtoms()
cnf1 = m.GetConformer()
cnf2 = m2.GetConformer()
for i in range(nats):
p1 = list(cnf1.GetAtomPosition(i))
p2 = list(cnf2.GetAtomPosition(i))
self.failUnless(feq(p1[0],p2[0]))
self.failUnless(feq(p1[1],p2[1]))
self.failUnless(feq(p1[2],p2[2]))
m3 = Chem.MolFromMolFile(fileN)
rdmt.CanonicalizeMol(m3)
cnf1 = m.GetConformer()
cnf2 = m3.GetConformer()
for i in range(nats):
p1 = list(cnf1.GetAtomPosition(i))
p2 = list(cnf2.GetAtomPosition(i))
self.failUnless(feq(p1[0],p2[0]))
self.failUnless(feq(p1[1],p2[1]))
self.failUnless(feq(p1[2],p2[2]))
if __name__=="__main__":
unittest.main()
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