mirror of
https://github.com/rdkit/rdkit.git
synced 2026-06-03 21:44:30 +08:00
ca41fa5bfd
* Parsing SCSR * add scsrol to mol * removed bad include file * loosen distGeom test slightly * add wrap test for SCSRMol * Add test for scsr in python * tests added for scsr and strict parsing removed * remove extra stuff * More fully specified use of SCSRMol for PR CI build * Added flags for SCSR expansion to not include any leaving groups * Added MolFromScsrParams to Wrap for python * added SCSRMol destructor * Added two tests for RNA macromols, and fixed a bug they revealed * Added new tests abd expected files * changes as per PR review * SCSR Chnages for leaving groups * fixed testScsr.py * hydrogen bond treatment * in SCSR expand, allow Hbond to be autoatically detected * changes as per code review * Adding new test file * chages for SCSR contructors, destructors for CI build * fixed pyton for SCSR hydrogen bond modes, and added tests * Added new test files * fixed edge case for SCSR * fix checksum for inchi * consistent capitalization of SCSR throughout * switch to enum class * make things shorter * simplify * get rid of the ATTCHORD class * New section for SCSR in RDKit_book * addeed section to RDKit_Book * SCSRMol is no longer exposed in Python * fix leak in MolFromSCSRFile() light refactoring * expose MolFromSCSRFile() to python make the MolFromSCSR functions work with default args a bit more testing * removed C++ access to SCSRMol * CXMsiles now ouputs hbonds, fix to template matching, and a few other things * Addl fix for bad aromaticity in Hbond rings * Test files needed * Test files needed * try to fix a CI build errors * CI error fix * Added missing test file * CMake version - for CI build * remove full file compoarison from macromol test file * accidental change to debug restored to release * Code review changes * As per PR review --------- Co-authored-by: Greg Landrum <greg.landrum@gmail.com>
122 lines
4.0 KiB
Python
122 lines
4.0 KiB
Python
#
|
|
# 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()
|