Brian Kelley 70540c2eed Add extract mol fragment api (#8811) ...

* 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>

2025-12-09 15:06:29 +01:00

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