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* Create a function to extract some specified atoms from a ROMol as a new ROMol by creating new graph (#8742) This adds a new api, `RDKit::MolOps::ExtractMolFragment`, to allow efficient extractions of mol fragments from large mols. Compared to the approach where we delete "unwanted" atoms/bonds from the input mol, this api is faster for small mols (about 2x faster) and at least 3x faster for big mols (was 10x faster for "CCC"*1000). * clang-format * review comments * cleanup * Consolidate copying subsets of molecules * Readd missing tests * Update comment to restart build * Remove missing test * Remove debugging comment, fix warnings * Fix warnings on gcc11 * Add docs * Make vector<bool> dynamic_bitset<> * Update copyright * Add swig wrappers * Use new designated constructor API * Fix windows builds * Change enum values from unsigned int to integer * Fix unsigned int variable * Update Code/GraphMol/Wrap/test_subset.py Co-authored-by: Greg Landrum <greg.landrum@gmail.com> * Update Code/GraphMol/Subset.cpp Co-authored-by: Greg Landrum <greg.landrum@gmail.com> * Update Code/JavaWrappers/gmwrapper/src-test/org/RDKit/ChemTransformsTests.java Co-authored-by: Greg Landrum <greg.landrum@gmail.com> * Reponse to review * Fix documentation * Remove comments * Remove unnecessary comments * Fix one liners * Change assertion to be clearer (and not one-liners) * Run clang-format --------- Co-authored-by: Your Name <you@example.com> Co-authored-by: Hussein Faara <hussein.faara@schrodinger.com> Co-authored-by: Brian Kelley <bkelley@glysade.com> Co-authored-by: Greg Landrum <greg.landrum@gmail.com>
76 lines
2.4 KiB
Python
76 lines
2.4 KiB
Python
#
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# Copyright (C) 2025 Hussein Faara, Brian Kelley and other RDKit contributors
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# All Rights Reserved
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#
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import doctest
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import gc
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import gzip
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import logging
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import os
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import sys
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import tempfile
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import unittest
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from io import StringIO
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from rdkit import Chem
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def check(info, selection):
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for i,v in enumerate(selection):
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assert (v and i in info) or (i not in info)
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class TestCase(unittest.TestCase):
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def test_subset(self):
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smi = "c1ccccc1CCN"
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m = Chem.MolFromSmiles(smi)
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N = list(range(6))
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sub = Chem.CopyMolSubset(m, N)
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self.assertEqual(Chem.MolToSmiles(sub), "c1ccccc1")
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info = Chem.SubsetInfo()
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sub = Chem.CopyMolSubset(m, N, info)
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check(info.atomMapping, [True]*6 + [False]*3)
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check(info.bondMapping,
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[True, True, True, True, True, False, False, False, True])
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atoms = [(0,0),(1,1),(2,2),(3,3),(4,4),(5,5)]
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bonds = [(0,0),(1,1),(2,2),(3,3),(4,4),(8,5)]
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for src,dst in atoms:
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self.assertEqual(info.atomMapping[src], dst)
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for src,dst in bonds:
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self.assertEqual(info.bondMapping[src], dst)
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opts = Chem.SubsetOptions()
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opts.method = Chem.SubsetMethod.BONDS;
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sub = Chem.CopyMolSubset(m, N, opts)
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self.assertEqual(Chem.MolToSmiles(sub), "ccccccC")
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sub = Chem.CopyMolSubset(m, N, info, opts)
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check(info.atomMapping, [True]*7 + [False]*2)
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check(info.bondMapping, [True]*6 + [False]*3)
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for i in N:
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self.assertEqual(info.atomMapping[i], i)
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self.assertEqual(info.bondMapping[i], i)
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N = list(range(6,11))
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sub = Chem.CopyMolSubset(m, N)
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self.assertEqual(Chem.MolToSmiles(sub), "CCN")
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info = Chem.SubsetInfo()
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sub = Chem.CopyMolSubset(m, N, info)
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self.assertEqual(Chem.MolToSmiles(sub), "CCN")
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check(info.atomMapping, [False]*6 + [True]*3)
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check(info.bondMapping, [False]*6+ [True]*2 + [False])
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sub = Chem.CopyMolSubset(m, N, info, opts)
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self.assertEqual(Chem.MolToSmiles(sub), "CCN.cc")
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check(info.atomMapping, [True, False, False, False, False, True, True, True, True])
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check(info.bondMapping, [False, False, False, False, False, False, True, True, True])
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m.SetProp("foo", "bar", computed=True)
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sub = Chem.CopyMolSubset(m, N)
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self.assertTrue(sub.HasProp("foo"))
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opts.clearComputedProps = True
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sub = Chem.CopyMolSubset(m, N, opts)
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self.assertFalse(sub.HasProp("foo"))
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