Commit Graph

5 Commits

Author SHA1 Message Date
Ricardo Rodriguez
e3f2e4651e Refactor iostreams includes (#8846)
* refactor iostreams includes

* restore ostream to MonomerInfo.cpp
2025-10-31 13:42:16 +01:00
Brian Kelley
553424d6b6 Revert "Create a function to extract some specified atoms from a ROMol as a new ROMol by creating new graph (#8742) (#8743)" (#8814)
This reverts commit 040bdb61c7.

During testing of using this as a replacement for portions of
getTheFrags in getMolFrags, several issues came up regarding
how copies should actually work in practice.  These are being
corrected in a new pr:  https://github.com/rdkit/rdkit/pull/8811

Co-authored-by: Brian Kelley <bkelley@glysade.com>
2025-09-25 10:54:36 +02:00
Hussein Faara
040bdb61c7 Create a function to extract some specified atoms from a ROMol as a new ROMol by creating new graph (#8742) (#8743)
* 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

* review comments

* fix build failure

---------

Co-authored-by: Your Name <you@example.com>
2025-09-24 06:39:52 +02:00
Greg Landrum
2957ab4576 switch to catch2 v3 (#6898)
* switch to catch2 v3
Fixes #6894

* fix a couple of problems noticed in the CI builds

* more warning cleanup

* changes in response to review
2023-11-15 06:45:42 +01:00
Greg Landrum
cb6caa161b Add option to only include shortest paths for topological torsion fingerprints (#6090)
* get findAllPaths versions working

* add that to the python wrapper

* add overlooked test file

* update test

* change in response to review
2023-02-20 11:13:53 +01:00