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865175104b
in the MolTransforms namespace:
* getBondLength(conf, iAtomId, jAtomId)
(only in this case, atoms need not be covalently bonded)
* setBondLength(conf, iAtomId, jAtomId, value)
* getAngleRad(conf, iAtomId, jAtomId, kAtomId)
* setAngleRad(conf, iAtomId, jAtomId, kAtomId, value)
* getAngleDeg(conf, iAtomId, jAtomId, kAtomId)
* setAngleDeg(conf, iAtomId, jAtomId, kAtomId, value)
* getDihedralRad(conf, iAtomId, jAtomId, kAtomId, lAtomId)
* setDihedralRad(conf, iAtomId, jAtomId, kAtomId, lAtomId, value)
* getDihedralDeg(conf, iAtomId, jAtomId, kAtomId, lAtomId)
* setDihedralDeg(conf, iAtomId, jAtomId, kAtomId, lAtomId, value)
- added the corresponding Python wrappers in rdMolTransforms
(same prototype as C++; as usual all Python methods
have an uppercase initial)
- added relevant C++/Python tests
117 lines
4.6 KiB
Python
117 lines
4.6 KiB
Python
from rdkit import RDConfig
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import os,sys,math
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import unittest
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from rdkit import DataStructs
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from rdkit import Chem
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from rdkit.Geometry import rdGeometry as geom
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from rdkit.Chem import rdMolTransforms as rdmt
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def feq(v1, v2, tol=1.0e-4):
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return abs(v1-v2) < tol
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def ptEq(pt, tpt, tol=0.0001):
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pt -= tpt
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return feq(pt.Length(), 0.0)
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class TestCase(unittest.TestCase):
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def setUp(self) :
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pass
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def test1Canonicalization(self) :
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mol = Chem.MolFromSmiles("C")
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conf = Chem.Conformer(1)
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conf.SetAtomPosition(0, (4.0, 5.0, 6.0))
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mol.AddConformer(conf,1)
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conf = mol.GetConformer()
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pt = rdmt.ComputeCentroid(conf)
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self.failUnless(ptEq(pt, geom.Point3D(4.0, 5.0, 6.0)))
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fileN = os.path.join(RDConfig.RDBaseDir,'Code','GraphMol','MolTransforms',
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'test_data','1oir.mol')
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m = Chem.MolFromMolFile(fileN)
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cpt = rdmt.ComputeCentroid(m.GetConformer())
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trans = rdmt.ComputeCanonicalTransform(m.GetConformer(), cpt)
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trans2 = rdmt.ComputeCanonicalTransform(m.GetConformer())
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for i in range(4):
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for j in range(4) :
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self.failUnless(feq(trans[i,j], trans2[i, j]))
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rdmt.TransformConformer(m.GetConformer(), trans2)
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m2 = Chem.MolFromMolFile(fileN)
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rdmt.CanonicalizeConformer(m2.GetConformer())
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nats = m.GetNumAtoms()
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cnf1 = m.GetConformer()
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cnf2 = m2.GetConformer()
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for i in range(nats):
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p1 = list(cnf1.GetAtomPosition(i))
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p2 = list(cnf2.GetAtomPosition(i))
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self.failUnless(feq(p1[0],p2[0]))
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self.failUnless(feq(p1[1],p2[1]))
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self.failUnless(feq(p1[2],p2[2]))
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m3 = Chem.MolFromMolFile(fileN)
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rdmt.CanonicalizeMol(m3)
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cnf1 = m.GetConformer()
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cnf2 = m3.GetConformer()
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for i in range(nats):
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p1 = list(cnf1.GetAtomPosition(i))
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p2 = list(cnf2.GetAtomPosition(i))
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self.failUnless(feq(p1[0],p2[0]))
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self.failUnless(feq(p1[1],p2[1]))
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self.failUnless(feq(p1[2],p2[2]))
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def testGetSetBondLength(self):
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file = os.path.join(RDConfig.RDBaseDir, 'Code', 'GraphMol', 'MolTransforms',
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'test_data', '3-cyclohexylpyridine.mol')
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m = Chem.MolFromMolFile(file, True, False)
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conf = m.GetConformer()
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dist = rdmt.GetBondLength(conf, 0, 19)
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self.failUnlessAlmostEqual(dist, 1.36, 2)
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rdmt.SetBondLength(conf, 0, 19, 2.5)
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dist = rdmt.GetBondLength(conf, 0, 19)
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self.failUnlessAlmostEqual(dist, 2.5, 1)
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rdmt.SetBondLength(conf, 19, 0, 3.0)
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dist = rdmt.GetBondLength(conf, 0, 19)
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self.failUnlessAlmostEqual(dist, 3.0, 1)
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def testGetSetAngle(self):
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file = os.path.join(RDConfig.RDBaseDir, 'Code', 'GraphMol', 'MolTransforms',
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'test_data', '3-cyclohexylpyridine.mol')
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m = Chem.MolFromMolFile(file, True, False)
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conf = m.GetConformer()
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angle = rdmt.GetAngleDeg(conf, 0, 19, 21)
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self.failUnlessAlmostEqual(angle, 109.7, 1)
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rdmt.SetAngleDeg(conf, 0, 19, 21, 125.0)
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angle = rdmt.GetAngleDeg(conf, 0, 19, 21);
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self.failUnlessAlmostEqual(angle, 125.0, 1)
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rdmt.SetAngleRad(conf, 21, 19, 0, math.pi / 2.)
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angle = rdmt.GetAngleRad(conf, 0, 19, 21)
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self.failUnlessAlmostEqual(angle, math.pi / 2., 1)
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angle = rdmt.GetAngleDeg(conf, 0, 19, 21)
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self.failUnlessAlmostEqual(angle, 90.0, 1)
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def testGetSetDihedral(self):
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file = os.path.join(RDConfig.RDBaseDir, 'Code', 'GraphMol', 'MolTransforms',
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'test_data', '3-cyclohexylpyridine.mol')
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m = Chem.MolFromMolFile(file, True, False)
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conf = m.GetConformer()
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dihedral = rdmt.GetDihedralDeg(conf, 0, 19, 21, 24)
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self.failUnlessAlmostEqual(dihedral, 176.05, 2)
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rdmt.SetDihedralDeg(conf, 8, 0, 19, 21, 65.0)
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dihedral = rdmt.GetDihedralDeg(conf, 8, 0, 19, 21)
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self.failUnlessAlmostEqual(dihedral, 65.0, 1)
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rdmt.SetDihedralDeg(conf, 8, 0, 19, 21, -130.0)
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dihedral = rdmt.GetDihedralDeg(conf, 8, 0, 19, 21)
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self.failUnlessAlmostEqual(dihedral, -130.0, 1)
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rdmt.SetDihedralRad(conf, 21, 19, 0, 8, -2. / 3. * math.pi)
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dihedral = rdmt.GetDihedralRad(conf, 8, 0, 19, 21)
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self.failUnlessAlmostEqual(dihedral, -2. / 3. * math.pi, 1)
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dihedral = rdmt.GetDihedralDeg(conf, 8, 0, 19, 21)
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self.failUnlessAlmostEqual(dihedral, -120.0, 1)
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if __name__=="__main__":
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unittest.main()
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