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145 lines
3.8 KiB
Python
145 lines
3.8 KiB
Python
# $Id$
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#
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# Copyright (C) 2004 Rational Discovery LLC
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# All Rights Reserved
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#
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import os
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import sys
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import unittest
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from rdkit import Chem, Geometry, RDConfig
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from rdkit.Geometry import Point3D
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def feq(v1, v2, tol2=1e-4):
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return abs(v1 - v2) <= tol2
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def ptEq(pt1, pt2, tol=1e-4):
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return feq(pt1.x, pt2.x, tol) and feq(pt1.y, pt2.y, tol) and feq(pt1.z, pt2.z, tol)
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def addConf(mol):
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conf = Chem.Conformer(mol.GetNumAtoms())
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for i in range(mol.GetNumAtoms()):
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conf.SetAtomPosition(i, (0., 0., 0.))
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mol.AddConformer(conf)
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mb = Chem.MolToMolBlock(mol)
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mb = Chem.MolToMolBlock(mol)
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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 test0Conformers(self):
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"""Test the conformer data structure"""
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mol = Chem.MolFromSmiles("CC")
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conf = Chem.Conformer(2)
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conf.SetAtomPosition(0, (-0.5, 0.0, 0.0))
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conf.SetAtomPosition(1, (1.0, 0.0, 0.0))
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conf.SetId(0)
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cid = mol.AddConformer(conf)
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self.assertTrue(cid == 0)
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conf2 = mol.GetConformer(0)
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self.assertTrue(conf2.GetId() == cid)
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pt1 = conf2.GetAtomPosition(0)
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self.assertTrue(ptEq(pt1, Point3D(-0.5, 0.0, 0.0)))
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pt2 = conf2.GetAtomPosition(1)
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self.assertTrue(ptEq(pt2, Point3D(1.0, 0.0, 0.0)))
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#changing conf should not change conf2 - related to issue 217
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conf.SetAtomPosition(1, Point3D(2.0, 0.0, 0.0))
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pt2 = conf2.GetAtomPosition(1)
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self.assertTrue(feq(pt2[0], 1.0))
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conf = Chem.Conformer(2)
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conf.SetAtomPosition(0, Point3D(-0.5, 0.0, 0.0))
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conf.SetAtomPosition(1, Point3D(1.0, 0.0, 0.0))
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conf.SetId(2)
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cid = mol.AddConformer(conf, 0)
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self.assertTrue(cid == 2)
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conf3 = mol.GetConformer(2)
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def test0AddHds(self):
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mol = Chem.MolFromSmiles("CC")
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conf = Chem.Conformer(1)
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conf.SetAtomPosition(0, Point3D(-0.5, 0.0, 0.0))
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conf.SetAtomPosition(1, Point3D(1.0, 0.0, 0.0))
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cid = mol.AddConformer(conf)
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conf2 = mol.GetConformer()
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self.assertTrue(conf2.GetNumAtoms() == 2)
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nmol = Chem.AddHs(mol, 0, 1)
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conf3 = nmol.GetConformer()
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self.assertTrue(conf3.GetNumAtoms() == 8)
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self.assertTrue(conf2.GetNumAtoms() == 2)
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targetCoords = [[-0.5, 0.0, 0.0], [1.0, 0.0, 0.0], [-0.8667, 0.0, 1.03709],
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[-0.8667, 0.8981, -0.5185], [-0.8667, -0.8981, -0.5185], [1.3667, 0.0, -1.0371],
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[1.36667, 0.8981, 0.5185], [1.36667, -0.8981, 0.5185]]
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for i in range(8):
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pt = conf3.GetAtomPosition(i)
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self.assertTrue(ptEq(pt, Point3D(*tuple(targetCoords[i]))))
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def test2Issue217(self):
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smi = 'c1ccccc1'
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m = Chem.MolFromSmiles(smi)
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addConf(m)
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self.assertTrue(m.GetNumConformers() == 1)
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mb2 = Chem.MolToMolBlock(m)
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def test3Exceptions(self):
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smi = 'c1ccccc1'
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m = Chem.MolFromSmiles(smi)
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addConf(m)
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self.assertTrue(m.GetNumConformers() == 1)
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self.assertRaises(ValueError, lambda: m.GetConformer(2))
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def test4ConfTuple(self):
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smi = 'c1ccccc1'
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m = Chem.MolFromSmiles(smi)
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for i in range(10):
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addConf(m)
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confs = m.GetConformers()
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self.assertTrue(len(confs) == 10)
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for conf in confs:
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for i in range(6):
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pt = conf.GetAtomPosition(i)
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self.assertTrue(ptEq(pt, Point3D(0.0, 0.0, 0.0)))
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m.RemoveAllConformers()
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self.assertTrue(m.GetNumConformers() == 0)
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confs = m.GetConformers()
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self.assertEqual(len(confs), 0)
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def test5PositionsArray(self):
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smi = 'c1ccccc1'
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m = Chem.MolFromSmiles(smi)
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addConf(m)
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confs = m.GetConformers()
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self.assertTrue(len(confs) == 1)
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for conf in confs:
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pos = conf.GetPositions()
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self.assertTrue(pos.shape, (6, 3))
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m.RemoveAllConformers()
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self.assertTrue(m.GetNumConformers() == 0)
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confs = m.GetConformers()
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self.assertEqual(len(confs), 0)
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if __name__ == '__main__':
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unittest.main()
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