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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>
74 lines
2.4 KiB
OpenEdge ABL
74 lines
2.4 KiB
OpenEdge ABL
//
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// Copyright (C) 2025 and other RDKit contributors
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//
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// @@ All Rights Reserved @@
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// This file is part of the RDKit.
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// The contents are covered by the terms of the BSD license
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// which is included in the file license.txt, found at the root
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// of the RDKit source tree.
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//
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%{
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#include <GraphMol/Subset.h>
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%}
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%ignore RDKit::copyMolSubset;
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%include <GraphMol/Subset.h>
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%{
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RDKit::ROMol *copyMolSubsetHelper(const RDKit::ROMol& mol,
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const std::vector<unsigned int> &atoms,
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const std::vector<unsigned int> &bonds,
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const RDKit::SubsetOptions &options=RDKit::SubsetOptions()
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)
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{
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return copyMolSubset(mol, atoms, bonds, options).release();
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}
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RDKit::ROMol *copyMolSubsetHelper(const RDKit::ROMol& mol,
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const std::vector<unsigned int> &atoms,
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const std::vector<unsigned int> &bonds,
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RDKit::SubsetInfo &subsetInfo,
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const RDKit::SubsetOptions &options=RDKit::SubsetOptions()
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) {
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return copyMolSubset(mol, atoms, bonds, subsetInfo, options).release();
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}
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RDKit::ROMol *copyMolSubsetHelper(const RDKit::ROMol& mol,
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const std::vector<unsigned int>& path,
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const RDKit::SubsetOptions &options = RDKit::SubsetOptions()) {
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return copyMolSubset(mol, path, options).release();
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}
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RDKit::ROMol *copyMolSubsetHelper(const RDKit::ROMol& mol,
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const std::vector<unsigned int>& path,
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RDKit::SubsetInfo &subsetInfo,
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const RDKit::SubsetOptions &options = RDKit::SubsetOptions()) {
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return copyMolSubset(mol, path, subsetInfo, options).release();
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}
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%}
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%rename("copyMolSubset") copyMolSubsetHelper;
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RDKit::ROMol *copyMolSubsetHelper(const RDKit::ROMol& mol,
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const std::vector<unsigned int> &atoms,
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const std::vector<unsigned int> &bonds,
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const RDKit::SubsetOptions &options=RDKit::SubsetOptions()
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);
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RDKit::ROMol *copyMolSubsetHelper(const RDKit::ROMol& mol,
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const std::vector<unsigned int> &atoms,
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const std::vector<unsigned int> &bonds,
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RDKit::SubsetInfo &subsetInfo,
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const RDKit::SubsetOptions &options=SRDKit::ubsetOptions()
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);
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RDKit::ROMol *copyMolSubsetHelper(const RDKit::ROMol& mol,
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const std::vector<unsigned int>& path,
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const RDKit::SubsetOptions &options = SubsetOptions());
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RDKit::ROMol *copyMolSubsetHelper(const RDKit::ROMol& mol,
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const std::vector<unsigned int>& path,
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RDKit::SubsetInfo &subsetInfo,
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const RDKit::SubsetOptions &options = RDKit::SubsetOptions());
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