from rdkit import RDConfig import os import unittest from rdkit import Chem from rdkit.Chem import ChemicalForceFields from rdkit.Chem import rdMolTransforms class TestCase(unittest.TestCase): def setUp(self) : self.molB = """butane RDKit 3D butane 17 16 0 0 0 0 0 0 0 0999 V2000 0.0000 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.4280 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.7913 -0.2660 0.9927 H 0 0 0 0 0 0 0 0 0 0 0 0 1.9040 1.3004 -0.3485 C 0 0 0 0 0 0 0 0 0 0 0 0 1.5407 2.0271 0.3782 H 0 0 0 0 0 0 0 0 0 0 0 0 1.5407 1.5664 -1.3411 H 0 0 0 0 0 0 0 0 0 0 0 0 3.3320 1.3004 -0.3485 C 0 0 0 0 0 0 0 0 0 0 0 0 3.6953 1.5162 -1.3532 H 0 0 0 0 0 0 0 0 0 0 0 0 3.8080 0.0192 0.0649 C 0 0 0 0 0 0 0 0 0 0 0 0 3.4447 -0.7431 -0.6243 H 0 0 0 0 0 0 0 0 0 0 0 0 3.4447 -0.1966 1.0697 H 0 0 0 0 0 0 0 0 0 0 0 0 4.8980 0.0192 0.0649 H 0 0 0 0 0 0 0 0 0 0 0 0 3.6954 2.0627 0.3408 H 0 0 0 0 0 0 0 0 0 0 0 0 1.7913 -0.7267 -0.7267 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.3633 0.7267 0.7267 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.3633 -0.9926 0.2660 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.3633 0.2660 -0.9926 H 0 0 0 0 0 0 0 0 0 0 0 0 1 2 1 0 0 0 0 1 15 1 0 0 0 0 1 16 1 0 0 0 0 1 17 1 0 0 0 0 2 3 1 0 0 0 0 2 4 1 0 0 0 0 2 14 1 0 0 0 0 4 5 1 0 0 0 0 4 6 1 0 0 0 0 4 7 1 0 0 0 0 7 8 1 0 0 0 0 7 9 1 0 0 0 0 7 13 1 0 0 0 0 9 10 1 0 0 0 0 9 11 1 0 0 0 0 9 12 1 0 0 0 0 M END""" def testUFFDistanceConstraints(self) : m = Chem.MolFromMolBlock(self.molB, True, False) ff = ChemicalForceFields.UFFGetMoleculeForceField(m) self.failUnless(ff) ff.UFFAddDistanceConstraint(1, 3, False, 2.0, 2.0, 1.0e5) r = ff.Minimize() self.failUnless(r == 0) conf = m.GetConformer() dist = rdMolTransforms.GetBondLength(conf, 1, 3) self.failUnless(dist > 1.99) ff = ChemicalForceFields.UFFGetMoleculeForceField(m) self.failUnless(ff) ff.UFFAddDistanceConstraint(1, 3, True, -0.2, 0.2, 1.0e5) r = ff.Minimize() self.failUnless(r == 0) conf = m.GetConformer() dist = rdMolTransforms.GetBondLength(conf, 1, 3) self.failUnless(dist > 1.79) def testUFFAngleConstraints(self) : m = Chem.MolFromMolBlock(self.molB, True, False) ff = ChemicalForceFields.UFFGetMoleculeForceField(m) self.failUnless(ff) ff.UFFAddAngleConstraint(1, 3, 6, False, 90.0, 90.0, 1.0e5) r = ff.Minimize() self.failUnless(r == 0) conf = m.GetConformer() angle = rdMolTransforms.GetAngleDeg(conf, 1, 3, 6) self.failUnless(int(angle) == 90) ff = ChemicalForceFields.UFFGetMoleculeForceField(m) self.failUnless(ff) ff.UFFAddAngleConstraint(1, 3, 6, True, -10.0, 10.0, 1.0e5) r = ff.Minimize() self.failUnless(r == 0) conf = m.GetConformer() angle = rdMolTransforms.GetAngleDeg(conf, 1, 3, 6) self.failUnless(int(angle) == 100) def testUFFTorsionConstraints(self) : m = Chem.MolFromMolBlock(self.molB, True, False) ff = ChemicalForceFields.UFFGetMoleculeForceField(m) self.failUnless(ff) conf = m.GetConformer() rdMolTransforms.SetDihedralDeg(conf, 1, 3, 6, 8, 60.0); ff.UFFAddTorsionConstraint(1, 3, 6, 8, False, 30.0, 30.0, 1.0e5) r = ff.Minimize() self.failUnless(r == 0) dihedral = rdMolTransforms.GetDihedralDeg(conf, 1, 3, 6, 8) self.failUnless(int(dihedral) == 30) ff = ChemicalForceFields.UFFGetMoleculeForceField(m) self.failUnless(ff) ff.UFFAddTorsionConstraint(1, 3, 6, 8, True, -10.0, 10.0, 1.0e5) r = ff.Minimize() self.failUnless(r == 0) conf = m.GetConformer() dihedral = rdMolTransforms.GetDihedralDeg(conf, 1, 3, 6, 8) self.failUnless(int(dihedral) == 40) def testUFFPositionConstraints(self) : m = Chem.MolFromMolBlock(self.molB, True, False) ff = ChemicalForceFields.UFFGetMoleculeForceField(m) self.failUnless(ff) conf = m.GetConformer() p = conf.GetAtomPosition(1) ff.UFFAddPositionConstraint(1, 0.3, 1.0e5) r = ff.Minimize() self.failUnless(r == 0) q = conf.GetAtomPosition(1) self.failUnless((p - q).Length() < 0.3) def testUFFFixedAtoms(self) : m = Chem.MolFromMolBlock(self.molB, True, False) ff = ChemicalForceFields.UFFGetMoleculeForceField(m) self.failUnless(ff) conf = m.GetConformer() fp = conf.GetAtomPosition(1) ff.AddFixedPoint(1) r = ff.Minimize() self.failUnless(r == 0) fq = conf.GetAtomPosition(1) self.failUnless((fp - fq).Length() < 0.01) def testMMFFDistanceConstraints(self) : m = Chem.MolFromMolBlock(self.molB, True, False) mp = ChemicalForceFields.MMFFGetMoleculeProperties(m) ff = ChemicalForceFields.MMFFGetMoleculeForceField(m, mp) self.failUnless(ff) ff.MMFFAddDistanceConstraint(1, 3, False, 2.0, 2.0, 1.0e5) r = ff.Minimize() self.failUnless(r == 0) conf = m.GetConformer() dist = rdMolTransforms.GetBondLength(conf, 1, 3) self.failUnless(dist > 1.99) ff = ChemicalForceFields.MMFFGetMoleculeForceField(m, mp) self.failUnless(ff) ff.MMFFAddDistanceConstraint(1, 3, True, -0.2, 0.2, 1.0e5) r = ff.Minimize() self.failUnless(r == 0) conf = m.GetConformer() dist = rdMolTransforms.GetBondLength(conf, 1, 3) self.failUnless(dist > 1.79) def testMMFFAngleConstraints(self) : m = Chem.MolFromMolBlock(self.molB, True, False) mp = ChemicalForceFields.MMFFGetMoleculeProperties(m) ff = ChemicalForceFields.MMFFGetMoleculeForceField(m, mp) self.failUnless(ff) ff.MMFFAddAngleConstraint(1, 3, 6, False, 90.0, 90.0, 1.0e5) r = ff.Minimize() self.failUnless(r == 0) conf = m.GetConformer() angle = rdMolTransforms.GetAngleDeg(conf, 1, 3, 6) self.failUnless(int(angle) == 90) ff = ChemicalForceFields.MMFFGetMoleculeForceField(m, mp) self.failUnless(ff) ff.MMFFAddAngleConstraint(1, 3, 6, True, -10.0, 10.0, 1.0e5) r = ff.Minimize() self.failUnless(r == 0) conf = m.GetConformer() angle = rdMolTransforms.GetAngleDeg(conf, 1, 3, 6) self.failUnless(int(angle) == 100) def testMMFFTorsionConstraints(self) : m = Chem.MolFromMolBlock(self.molB, True, False) mp = ChemicalForceFields.MMFFGetMoleculeProperties(m) ff = ChemicalForceFields.MMFFGetMoleculeForceField(m, mp) self.failUnless(ff) conf = m.GetConformer() rdMolTransforms.SetDihedralDeg(conf, 1, 3, 6, 8, 60.0); ff.MMFFAddTorsionConstraint(1, 3, 6, 8, False, 30.0, 30.0, 1.0e5) r = ff.Minimize() self.failUnless(r == 0) dihedral = rdMolTransforms.GetDihedralDeg(conf, 1, 3, 6, 8) self.failUnless(int(dihedral) == 30) ff = ChemicalForceFields.MMFFGetMoleculeForceField(m, mp) self.failUnless(ff) ff.MMFFAddTorsionConstraint(1, 3, 6, 8, True, -10.0, 10.0, 1.0e5) r = ff.Minimize() self.failUnless(r == 0) conf = m.GetConformer() dihedral = rdMolTransforms.GetDihedralDeg(conf, 1, 3, 6, 8) self.failUnless(int(dihedral) == 40) def testMMFFPositionConstraints(self) : m = Chem.MolFromMolBlock(self.molB, True, False) mp = ChemicalForceFields.MMFFGetMoleculeProperties(m) ff = ChemicalForceFields.MMFFGetMoleculeForceField(m, mp) self.failUnless(ff) conf = m.GetConformer() p = conf.GetAtomPosition(1) ff.MMFFAddPositionConstraint(1, 0.3, 1.0e5) r = ff.Minimize() self.failUnless(r == 0) q = conf.GetAtomPosition(1) self.failUnless((p - q).Length() < 0.3) def testMMFFFixedAtoms(self) : m = Chem.MolFromMolBlock(self.molB, True, False) mp = ChemicalForceFields.MMFFGetMoleculeProperties(m) ff = ChemicalForceFields.MMFFGetMoleculeForceField(m, mp) self.failUnless(ff) conf = m.GetConformer() fp = conf.GetAtomPosition(1) ff.AddFixedPoint(1) r = ff.Minimize() self.failUnless(r == 0) fq = conf.GetAtomPosition(1) self.failUnless((fp - fq).Length() < 0.01) if __name__== '__main__': unittest.main()