* Don't silent ignore missing atoms (and replace them with atom #0) in copymolsubet
* Fail if explicitly set atoms/bonds are not present
* Add tests
* Simplify optimization (copy whole molecule) add test for no bonds
* 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>
* do not remove hydrides by default
* add a minimal test
* add release note about behavior change
* require Hydrides to have degree 1
* also allow hydrides with degree 0 (ionic bond)
* suggested changes
---------
Co-authored-by: greg landrum <greg.landrum@gmail.com>
* allow cleanupOrganometallics to work with carbon
* do not use cleanupOrganometallics with mol2
* fix handling of C atoms in cleanupOrganometallics
* add test for #8312
* Update Code/GraphMol/MolOps.cpp
Co-authored-by: Paolo Tosco <paolo.tosco.mail@gmail.com>
---------
Co-authored-by: Paolo Tosco <paolo.tosco.mail@gmail.com>
* throw if close to zero
* fix moldraw2DTestCatch
* Fix testRGroupDecomp
* fix one test in distGeomHelpersCatch
* fix tests in distGeomHelpersCatch
* retry finding a dir vector when adding Hs
* push UFF fixes to calculateCosY
* fix the setTerminalAtomCoords deg 4 patch
* add a test
* reduce zero tolerance
* move mol weight and formula calculators to MolOps and refactor them a bit.
The descriptors are still there and should remain.
* remove other unnecessary dependencies on Descriptors
* Update adapter.cpp
Co-authored-by: Paolo Tosco <paolo.tosco.mail@gmail.com>
---------
Co-authored-by: Paolo Tosco <paolo.tosco.mail@gmail.com>
