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#
# Copyright (C) 2022 Greg Landrum
# @@ All Rights Reserved @@
#
# This file is part of the RDKit.
# The contents are covered by the terms of the BSD license
# which is included in the file license.txt, found at the root
# of the RDKit source tree.
import glob
import os
import unittest
from rdkit import Chem, RDConfig
from rdkit.Chem import rdDetermineBonds
class TestCase(unittest.TestCase):
def testVdWConnectivity(self):
testDir = os.path.join(RDConfig.RDBaseDir, 'Code', 'GraphMol', 'DetermineBonds', 'test_data',
'connectivity')
for fn in glob.glob(os.path.join(testDir, 'test*.xyz')):
mol = Chem.MolFromXYZFile(fn)
self.assertIsNotNone(mol)
smi = mol.GetProp('_FileComments')
omol = Chem.MolFromSmiles(smi)
self.assertIsNotNone(omol)
rdDetermineBonds.DetermineConnectivity(mol, useHueckel=False)
mol = Chem.RemoveAllHs(mol, sanitize=False)
self.assertEqual(mol.GetNumAtoms(), omol.GetNumAtoms())
self.assertEqual(mol.GetNumBonds(), omol.GetNumBonds())
for aid1 in range(mol.GetNumAtoms()):
for aid2 in range(aid1 + 1, mol.GetNumAtoms()):
if omol.GetBondBetweenAtoms(aid1, aid2):
self.assertIsNotNone(mol.GetBondBetweenAtoms(aid1, aid2))
def testCtDConnectivity(self):
testDir = os.path.join(RDConfig.RDBaseDir, 'Code', 'GraphMol', 'DetermineBonds', 'test_data',
'connectivity')
for fn in glob.glob(os.path.join(testDir, 'test*.xyz')):
mol = Chem.MolFromXYZFile(fn)
self.assertIsNotNone(mol)
smi = mol.GetProp('_FileComments')
omol = Chem.MolFromSmiles(smi)
self.assertIsNotNone(omol)
rdDetermineBonds.DetermineConnectivity(mol, useHueckel=False, useVdw=False)
mol = Chem.RemoveAllHs(mol, sanitize=False)
self.assertEqual(mol.GetNumAtoms(), omol.GetNumAtoms())
self.assertEqual(mol.GetNumBonds(), omol.GetNumBonds())
for aid1 in range(mol.GetNumAtoms()):
for aid2 in range(aid1 + 1, mol.GetNumAtoms()):
if omol.GetBondBetweenAtoms(aid1, aid2):
self.assertIsNotNone(mol.GetBondBetweenAtoms(aid1, aid2))
@unittest.skipUnless(rdDetermineBonds.hueckelEnabled(), "YAeHMOP support not enabled")
def testHueckelConnectivity(self):
testDir = os.path.join(RDConfig.RDBaseDir, 'Code', 'GraphMol', 'DetermineBonds', 'test_data',
'connectivity')
for fn in glob.glob(os.path.join(testDir, 'test*.xyz')):
mol = Chem.MolFromXYZFile(fn)
self.assertIsNotNone(mol)
smi = mol.GetProp('_FileComments')
omol = Chem.MolFromSmiles(smi)
self.assertIsNotNone(omol)
charge = Chem.GetFormalCharge(omol)
rdDetermineBonds.DetermineConnectivity(mol, useHueckel=True, charge=charge)
mol = Chem.RemoveAllHs(mol, sanitize=False)
self.assertEqual(mol.GetNumAtoms(), omol.GetNumAtoms())
self.assertEqual(mol.GetNumBonds(), omol.GetNumBonds())
for aid1 in range(mol.GetNumAtoms()):
for aid2 in range(aid1 + 1, mol.GetNumAtoms()):
if omol.GetBondBetweenAtoms(aid1, aid2):
self.assertIsNotNone(mol.GetBondBetweenAtoms(aid1, aid2))
def testVdWBonds(self):
testDir = os.path.join(RDConfig.RDBaseDir, 'Code', 'GraphMol', 'DetermineBonds', 'test_data',
'connectivity')
for fn in glob.glob(os.path.join(testDir, 'test*.xyz')):
mol = Chem.MolFromXYZFile(fn)
self.assertIsNotNone(mol)
smi = mol.GetProp('_FileComments')
omol = Chem.MolFromSmiles(smi)
self.assertIsNotNone(omol)
charge = Chem.GetFormalCharge(omol)
rdDetermineBonds.DetermineBonds(mol, useHueckel=False, charge=charge)
mol = Chem.RemoveAllHs(mol, sanitize=False)
self.assertEqual(mol.GetNumAtoms(), omol.GetNumAtoms())
self.assertEqual(mol.GetNumBonds(), omol.GetNumBonds())
for aid1 in range(mol.GetNumAtoms()):
for aid2 in range(aid1 + 1, mol.GetNumAtoms()):
if omol.GetBondBetweenAtoms(aid1, aid2):
self.assertIsNotNone(mol.GetBondBetweenAtoms(aid1, aid2))
# FIX: this is problematic...
# def testHueckelBonds(self):
# testDir = os.path.join(RDConfig.RDBaseDir, 'Code', 'GraphMol', 'DetermineBonds', 'test_data',
# 'connectivity')
# for fn in glob.glob(os.path.join(testDir, 'test*.xyz')):
# mol = Chem.MolFromXYZFile(fn)
# self.assertIsNotNone(mol)
# smi = mol.GetProp('_FileComments')
# omol = Chem.MolFromSmiles(smi)
# self.assertIsNotNone(omol)
# charge = Chem.GetFormalCharge(omol)
# try:
# rdDetermineBonds.DetermineBonds(mol, useHueckel=True, charge=charge)
# except ValueError:
# print(fn)
# print(' ', smi)
# print(' ', Chem.MolToSmiles(mol))
# mol = Chem.RemoveAllHs(mol, sanitize=False)
# self.assertEqual(mol.GetNumAtoms(), omol.GetNumAtoms())
# self.assertEqual(mol.GetNumBonds(), omol.GetNumBonds())
# for aid1 in range(mol.GetNumAtoms()):
# for aid2 in range(aid1 + 1, mol.GetNumAtoms()):
# if omol.GetBondBetweenAtoms(aid1, aid2):
# self.assertIsNotNone(mol.GetBondBetweenAtoms(aid1, aid2))
if __name__ == '__main__': # pragma: nocover
unittest.main()
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