mirror of
https://github.com/rdkit/rdkit.git
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b53ee20b49
* Fix PEP8 [E101](https://github.com/PyCQA/pycodestyle/blob/2.8.0/docs/intro.rst#error-codes) * Fix PEP8 [E502](https://github.com/PyCQA/pycodestyle/blob/2.8.0/docs/intro.rst#error-codes) * Fix PEP8 [E703](https://github.com/PyCQA/pycodestyle/blob/2.8.0/docs/intro.rst#error-codes) * Fix PEP8 [E711](https://github.com/PyCQA/pycodestyle/blob/2.8.0/docs/intro.rst#error-codes) * Fix PEP8 [E712](https://github.com/PyCQA/pycodestyle/blob/2.8.0/docs/intro.rst#error-codes) * Fix PEP8 [E713](https://github.com/PyCQA/pycodestyle/blob/2.8.0/docs/intro.rst#error-codes) * Fix PEP8 [E722](https://github.com/PyCQA/pycodestyle/blob/2.8.0/docs/intro.rst#error-codes) * Fix PEP8 [W605](https://github.com/PyCQA/pycodestyle/blob/2.8.0/docs/intro.rst#error-codes)
298 lines
11 KiB
Python
298 lines
11 KiB
Python
from rdkit import RDConfig
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import os, sys, math
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import unittest
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import numpy as np
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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.assertTrue(ptEq(pt, geom.Point3D(4.0, 5.0, 6.0)))
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fileN = os.path.join(RDConfig.RDBaseDir, 'Code', 'GraphMol', 'MolTransforms', 'test_data',
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'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.assertTrue(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.assertTrue(feq(p1[0], p2[0]))
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self.assertTrue(feq(p1[1], p2[1]))
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self.assertTrue(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.assertTrue(feq(p1[0], p2[0]))
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self.assertTrue(feq(p1[1], p2[1]))
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self.assertTrue(feq(p1[2], p2[2]))
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def testComputePrincipalAxesAndMoments(self):
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if (not hasattr(rdmt, 'ComputePrincipalAxesAndMoments')):
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return
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molBlock = '''\
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RDKit 3D
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4 3 0 0 0 0 0 0 0 0999 V2000
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-0.1888 1.3224 -0.2048 F 0 0 0 0 0 0 0 0 0 0 0 0
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-0.0790 0.1671 0.6070 C 0 0 1 0 0 0 0 0 0 0 0 0
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-1.3083 -0.8939 -0.2236 Cl 0 0 0 0 0 0 0 0 0 0 0 0
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1.5761 -0.5956 -0.1786 Br 0 0 0 0 0 0 0 0 0 0 0 0
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2 1 1 6
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2 3 1 0
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2 4 1 0
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M END
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'''
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axesRef = (
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(-0.9997, -0.0246, 0.0009),
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( 0.0246, -0.9981, 0.0559),
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( 0.0004, -0.0559, -0.9984)
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)
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momentsRef = ( 3.4220, 4.7230, 7.1757)
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m = Chem.MolFromMolBlock(molBlock)
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axes, moments = rdmt.ComputePrincipalAxesAndMoments(m.GetConformer())
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self.assertIsNotNone(axes)
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self.assertIsNotNone(moments)
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for y in range(3):
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for x in range(3):
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self.assertAlmostEqual(axes[y][x], axesRef[y][x], 3)
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self.assertAlmostEqual(moments[y], momentsRef[y], 3)
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failed = False
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try:
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axes, moments = rdmt.ComputePrincipalAxesAndMoments(m.GetConformer(), weights = (0.5, 0.5))
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except Exception:
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failed = True
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self.assertTrue(failed)
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axesWeightedRef = (
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(-0.9998, -0.0114, -0.0189),
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(-0.0153, 0.9744, 0.2245),
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( 0.0158, 0.2247, -0.9743)
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)
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momentsWeightedRef = ( 0.5496, 1.5559, 1.9361)
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axesWeighted, momentsWeighted = rdmt.ComputePrincipalAxesAndMoments(
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m.GetConformer(), weights = (0.1, 0.2, 0.3, 0.4))
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self.assertIsNotNone(axesWeighted)
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self.assertIsNotNone(momentsWeighted)
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for y in range(3):
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for x in range(3):
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self.assertAlmostEqual(axesWeighted[y][x], axesWeightedRef[y][x], 3)
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self.assertAlmostEqual(momentsWeighted[y], momentsWeightedRef[y], 3)
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def testComputePrincipalAxesAndMomentsFromGyrationMatrix(self):
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if (not hasattr(rdmt, 'ComputePrincipalAxesAndMomentsFromGyrationMatrix')):
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return
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molBlock = '''\
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RDKit 3D
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4 3 0 0 0 0 0 0 0 0999 V2000
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-0.1888 1.3224 -0.2048 F 0 0 0 0 0 0 0 0 0 0 0 0
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-0.0790 0.1671 0.6070 C 0 0 1 0 0 0 0 0 0 0 0 0
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-1.3083 -0.8939 -0.2236 Cl 0 0 0 0 0 0 0 0 0 0 0 0
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1.5761 -0.5956 -0.1786 Br 0 0 0 0 0 0 0 0 0 0 0 0
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2 1 1 6
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2 3 1 0
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2 4 1 0
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M END
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'''
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axesRef = (
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(-0.0009, -0.0246, 0.9997),
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(-0.0559, -0.9981, -0.0246),
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( 0.9984, -0.0559, -0.0004)
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)
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momentsRef = ( 0.1212, 0.7343, 1.0596)
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m = Chem.MolFromMolBlock(molBlock)
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axes, moments = rdmt.ComputePrincipalAxesAndMomentsFromGyrationMatrix(m.GetConformer())
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self.assertIsNotNone(axes)
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self.assertIsNotNone(moments)
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for y in range(3):
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for x in range(3):
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self.assertAlmostEqual(axes[y][x], axesRef[y][x], 3)
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self.assertAlmostEqual(moments[y], momentsRef[y], 3)
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failed = False
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try:
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axes, moments = rdmt.ComputePrincipalAxesAndMomentsFromGyrationMatrix(m.GetConformer(), weights = (0.5, 0.5))
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except Exception:
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failed = True
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self.assertTrue(failed)
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axesWeightedRef = (
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( 0.0189, -0.0114, 0.9998),
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(-0.2245, 0.9744, 0.0153),
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( 0.9743, 0.2247, -0.0158)
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)
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momentsWeightedRef = ( 0.0847, 0.4649, 1.4712)
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axesWeighted, momentsWeighted = rdmt.ComputePrincipalAxesAndMomentsFromGyrationMatrix(
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m.GetConformer(), weights = (0.1, 0.2, 0.3, 0.4))
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self.assertIsNotNone(axesWeighted)
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self.assertIsNotNone(momentsWeighted)
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for y in range(3):
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for x in range(3):
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self.assertAlmostEqual(abs(axesWeighted[y][x]), abs(axesWeightedRef[y][x]), 3)
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self.assertAlmostEqual(abs(momentsWeighted[y]), abs(momentsWeightedRef[y]), 3)
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def testGetSetBondLength(self):
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file = os.path.join(RDConfig.RDBaseDir, 'Code', 'GraphMol', 'MolTransforms', 'test_data',
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'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.assertAlmostEqual(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.assertAlmostEqual(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.assertAlmostEqual(dist, 3.0, 1)
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def testGetSetAngle(self):
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file = os.path.join(RDConfig.RDBaseDir, 'Code', 'GraphMol', 'MolTransforms', 'test_data',
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'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.assertAlmostEqual(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.assertAlmostEqual(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.assertAlmostEqual(angle, math.pi / 2., 1)
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angle = rdmt.GetAngleDeg(conf, 0, 19, 21)
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self.assertAlmostEqual(angle, 90.0, 1)
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def testGetSetDihedral(self):
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file = os.path.join(RDConfig.RDBaseDir, 'Code', 'GraphMol', 'MolTransforms', 'test_data',
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'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.assertAlmostEqual(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.assertAlmostEqual(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.assertAlmostEqual(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.assertAlmostEqual(dihedral, -2. / 3. * math.pi, 1)
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dihedral = rdmt.GetDihedralDeg(conf, 8, 0, 19, 21)
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self.assertAlmostEqual(dihedral, -120.0, 1)
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def testGetSetDihedralThroughTripleBond(self):
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file = os.path.join(RDConfig.RDBaseDir, 'Code', 'GraphMol', 'MolTransforms', 'test_data',
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'github1262_2.mol')
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m = Chem.MolFromMolFile(file, True, False)
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conf = m.GetConformer()
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rdmt.SetDihedralDeg(conf, 6, 1, 2, 9, 0.0)
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dihedral = rdmt.GetDihedralDeg(conf, 6, 1, 2, 9)
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self.assertAlmostEqual(dihedral, 0.0, 1)
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dist = rdmt.GetBondLength(conf, 6, 9)
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rdmt.SetDihedralDeg(conf, 6, 1, 2, 9, 120.0)
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dihedral = rdmt.GetDihedralDeg(conf, 6, 1, 2, 9)
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self.assertAlmostEqual(dihedral, 120.0, 1)
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dist2 = rdmt.GetBondLength(conf, 6, 7)
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self.assertAlmostEqual(dist, dist2, 1)
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rdmt.SetDihedralDeg(conf, 6, 1, 2, 9, 180.0)
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dihedral = rdmt.GetDihedralDeg(conf, 6, 1, 2, 9)
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self.assertAlmostEqual(dihedral, 180.0, 1)
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dist3 = rdmt.GetBondLength(conf, 6, 9)
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self.assertNotAlmostEqual(dist, dist3, 1)
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exceptionRaised = False
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try:
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rdmt.SetDihedralDeg(conf, 6, 0, 3, 9, 0.0)
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except ValueError:
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exceptionRaised = True
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self.assertTrue(exceptionRaised)
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def testEigen3CanonicalTransformAgainstNumpy(self):
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def canonicalize_conf_rdkit(mol, conf_id=-1):
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mol = Chem.Mol(mol)
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conf = mol.GetConformer(conf_id)
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ctd = rdmt.ComputeCentroid(conf)
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canon_trans = rdmt.ComputeCanonicalTransform(conf, ctd)
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rdmt.TransformConformer(conf, canon_trans)
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return mol
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def canonicalize_conf_numpy(mol, conf_id=-1):
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mol = Chem.Mol(mol)
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conf = mol.GetConformer(conf_id)
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pos = conf.GetPositions()
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ctd = pos.mean(axis=0)
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trans_pos = pos - ctd
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cov_mat = np.cov(trans_pos, bias=1, rowvar=False) * conf.GetNumAtoms()
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eigval, eigvect = np.linalg.eig(cov_mat)
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eigval_sorted = sorted(enumerate(eigval), key=lambda x: x[1], reverse=True)
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eigvect_sorted = [eigvect[:, i] * (1.0 if eigvect[:, i].sum() > 0.0 else -1.0) for i, _ in eigval_sorted]
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canon_trans = np.array([
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[*eigvect_sorted[0], 0.],
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[*eigvect_sorted[1], 0.],
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[*eigvect_sorted[2], 0.],
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[0., 0., 0., 1.],
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], dtype=np.double)
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canon_trans[0:3, 3] = np.array([*ctd, 1.]).dot(canon_trans)[:3]
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rdmt.TransformConformer(conf, canon_trans)
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return mol
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file = os.path.join(RDConfig.RDBaseDir, 'Code', 'GraphMol', 'MolTransforms', 'test_data',
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'github4302.sdf')
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built_against_eigen3 = hasattr(rdmt, 'ComputePrincipalAxesAndMomentsFromGyrationMatrix')
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with Chem.SDMolSupplier(file) as suppl:
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for mol in suppl:
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mol_orig = Chem.Mol(mol)
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rdkit_canon = canonicalize_conf_rdkit(mol)
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numpy_canon = canonicalize_conf_numpy(mol)
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for i in range(mol.GetNumAtoms()):
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orig_coord = mol_orig.GetConformer().GetAtomPosition(i)
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rdkit_coord = rdkit_canon.GetConformer().GetAtomPosition(i)
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numpy_coord = numpy_canon.GetConformer().GetAtomPosition(i)
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self.assertLess(orig_coord.Distance(numpy_coord), 1.e-4)
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if built_against_eigen3:
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self.assertLess(orig_coord.Distance(rdkit_coord), 1.e-4)
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if __name__ == "__main__":
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unittest.main()
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