* Allow the same core to match more than once in a molecule.
* Update annotation.
* Changes after review.
---------
Co-authored-by: David Cosgrove <david@cozchemix.co.uk>
* constexpr Point, Point2D, and Point3D
* constexpr Vector
* cleanup
* rollback overzealous constexpring
* dial back the constexpr to get windows builds working
the math stuff isn't constexpr with MSVC++
* add [[nodiscard]]
* 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>
- implement get_v2Kmolblock() in MinimalLib
- add the possibility to specify the MDL version preference as a get_molblock() forceMDLVersion JSON parameter, which is ignored by get_v3Kmolblock() and get_v2Kmolblock()
- changes in response to review
Co-authored-by: ptosco <paolo.tosco@novartis.com>
* Trim spaces from RDProp strings to simulate reading from SDFiles
* Update documentation
* Use the correct doc strings
---------
Co-authored-by: Brian Kelley <bkelley@glysade.com>
* patch RapidJSON to make sure it builds on all platforms
* remove unnecessary sed command from Docker recipe
---------
Co-authored-by: ptosco <paolo.tosco@novartis.com>
* set export.h and test.h to go to the correct places in RDKitUtils
* use cmake_source_dir so cmake files are picked up in list
* use cmake_current_source_dir in MolInterchange
* use rdkit variables to place rapidjson and headers in correct places
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>
* 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>
* Set explicit COST=100 for SQL functions
* Adjust COST to 100 in current databases and up the cartridge version
* Use CREATE OR REPLACE for consistency
* Update the version number in rdkit.control
Fixes github issue #8597.
* UFFGetMoleculeForceField was returning
PyForceField* before the class was registered via rdForceField,
which caused “No Python class registered” errors in Python when
using multiple conformers.
* This patch forces rdForceField to be
imported during rdForceFieldHelpers module init, ensuring the
class is always registered before helper functions are used.
* Add unit test
* Adds missing options docstring
* Always be cleaning
* Fix typos in RGroupDecomposition module
* Update documentation on configuring doxygen
* Was a step that I couldn't find reference to besides in the Makefile
* Undo american spelling of labelling
* British spelling appears more consistent
* Fix style of RGroupDecompositionParameters parameter
* Also fixes a typo
* Remove unintentional use of docstring
* Was assigning documentation about the parameters to the
RGroupDecomposition
* Remove empty string
* Apply suggestions from code review
Co-authored-by: Greg Landrum <greg.landrum@gmail.com>
---------
Co-authored-by: Greg Landrum <greg.landrum@gmail.com>
* backup
builds but no tests
* deprecate old form
* initial basic tests for bond property lists
* Tests pass
Fixes#8777
* add deprecations to release notes
* - avoid computing size of a constant at runtime
- replace multiple instances of a numeric constant with a literal constant
- avoid unnecessary copying of strings in iterations and function calls
---------
Co-authored-by: ptosco <paolo.tosco@novartis.com>
* - avoid code duplication through a templated function
- enable switching off boolean flags via JSON and not just on as before
* ran clang-format
* change in response to review
---------
Co-authored-by: ptosco <paolo.tosco@novartis.com>
