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#
# Copyright (C) 2024 Tad Hurst
# 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 os
import sys
import unittest
from rdkit import Chem
from rdkit.Chem import RDConfig
class TestCase(unittest.TestCase):
def setUp(self):
pass
def testSCSR(self):
"""Test the SCSR system"""
ofile = os.path.join(RDConfig.RDBaseDir, 'Code', 'GraphMol', 'FileParsers', 'test_data',
'macromols', 'Triplet.mol')
with open(ofile) as inf:
scsrBlock = inf.read()
molFromSCSRParams = Chem.MolFromSCSRParams()
molFromSCSRParams.includeLeavingGroups = True
molFromSCSRParams.scsrTemplateNames = Chem.SCSRTemplateNames.AsEntered
molFromSCSRParams.scsrBaseHbondOptions = Chem.SCSRBaseHbondOptions.Ignore
for mol in (Chem.MolFromSCSRBlock(scsrBlock, False, False, molFromSCSRParams),
Chem.MolFromSCSRFile(ofile, False, False, molFromSCSRParams)):
self.assertTrue(mol.GetNumAtoms() == 30)
sgs = Chem.GetMolSubstanceGroups(mol)
self.assertEqual(len(sgs), 6)
# check defaults:
for mol in (Chem.MolFromSCSRBlock(scsrBlock), Chem.MolFromSCSRFile(ofile)):
self.assertTrue(mol.GetNumAtoms() == 30)
sgs = Chem.GetMolSubstanceGroups(mol)
self.assertEqual(len(sgs), 6)
def testSCSRRna(self):
"""Test the SCSR system with and RNA double strand"""
ofile = os.path.join(RDConfig.RDBaseDir, 'Code', 'GraphMol', 'FileParsers', 'test_data',
'macromols', 'DnaTest.mol')
with open(ofile) as inf:
scsrBlock = inf.read()
molFromSCSRParams = Chem.MolFromSCSRParams()
molFromSCSRParams.includeLeavingGroups = True
molFromSCSRParams.scsrTemplateNames = Chem.SCSRTemplateNames.AsEntered
molFromSCSRParams.scsrBaseHbondOptions = Chem.SCSRBaseHbondOptions.Auto
mol = Chem.MolFromSCSRBlock(scsrBlock, False, False, molFromSCSRParams)
self.assertTrue(mol.GetNumAtoms() == 254)
self.assertTrue(mol.GetNumBonds() == 300)
sgs = Chem.GetMolSubstanceGroups(mol)
self.assertTrue(len(sgs) == 38)
molFromSCSRParams.scsrBaseHbondOptions = Chem.SCSRBaseHbondOptions.Ignore
mol = Chem.MolFromSCSRBlock(scsrBlock, False, False, molFromSCSRParams)
self.assertTrue(mol.GetNumAtoms() == 254)
self.assertTrue(mol.GetNumBonds() == 282)
sgs = Chem.GetMolSubstanceGroups(mol)
self.assertTrue(len(sgs) == 38)
def testThreeLetterCodes(self):
"""Test the SCSR system with three letter codes"""
ofile = os.path.join(RDConfig.RDBaseDir, 'Code', 'GraphMol', 'FileParsers', 'test_data',
'macromols', 'PepTla.mol')
with open(ofile) as inf:
scsrBlock = inf.read()
molFromSCSRParams = Chem.MolFromSCSRParams()
molFromSCSRParams.includeLeavingGroups = True
molFromSCSRParams.scsrTemplateNames = Chem.SCSRTemplateNames.AsEntered
mol = Chem.MolFromSCSRBlock(scsrBlock, False, False, molFromSCSRParams)
self.assertEqual(mol.GetNumAtoms(), 26)
self.assertEqual(mol.GetNumBonds(), 25)
sgs = Chem.GetMolSubstanceGroups(mol)
self.assertTrue(len(sgs) == 7)
sgs[0].GetProp('LABEL')
self.assertEqual(sgs[0].GetProp('LABEL'), 'Ala_4')
molFromSCSRParams.scsrTemplateNames = Chem.SCSRTemplateNames.UseFirstName
mol = Chem.MolFromSCSRBlock(scsrBlock, False, False, molFromSCSRParams)
self.assertEqual(mol.GetNumAtoms(), 26)
sgs = Chem.GetMolSubstanceGroups(mol)
self.assertEqual(len(sgs), 7)
self.assertEqual(sgs[0].GetProp('LABEL'), 'Ala_4')
molFromSCSRParams.scsrTemplateNames = Chem.SCSRTemplateNames.UseSecondName
mol = Chem.MolFromSCSRBlock(scsrBlock, False, False, molFromSCSRParams)
self.assertEqual(mol.GetNumAtoms(), 26)
sgs = Chem.GetMolSubstanceGroups(mol)
self.assertEqual(len(sgs), 7)
self.assertEqual(sgs[0].GetProp('LABEL'), 'A_4')
if __name__ == '__main__':
unittest.main()
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