David Cosgrove 9f551aedbe Multi conf gaussian shape (#9265) ...

* First import of GaussianShape.

* Tidying.

* Custom features.

* Optimise.

* Optimise.

* Return 3 scores rather than 2 including combo score.

* Rename useFeatures to useColors.

* Python wrappers.

* Python tests.

* Take out big test.

* Add new start mode, as PubChem does it.

* Doh!

* Fix MolTransforms eigenvalue return.

* Two cycle optimisation, mostly working.

* Take out bestSoFar score from SCA.

* Take out DTYPE.

* Tidy out redundant variables.

* Optimisation in 2 parts.

* More fiddling in pursuit of speed.

* Update Python wrapper.

* Tweak.

* Atom subsets and different radii.

* Fix test.

* Revert pubchem_shape's test.cpp.

* Serialize ShapeInput.

* Trigger build

* Remove pointers to std::arrays in ShapeInput.

* ShapeInput virtual d'tor.

* Precondition - ShapeInput needs a molecule with at least 1 conformer.

* Rename ShapeInput::d_centroid to ShapeInput::d_canonTrans.

* Fix normalization bugs.

* Select start mode using moments of inertia rather than eigenvalues of canonical transformation.

* Include color features in moments of inertia.

* Smidge faster.

* Tversky similarity.

* Tidy tests.

* Tests working on Linux.

* Revert force of right handed axes in MolTransforms::computePrincipalAxesAndMomentsFromGyrationMatrix replacing with a comment in the code.

* Response to review.

* Sneaky allCarbon bug.

* add multithreaded test

* Response to review.

* Doh! Don't recalculate normalization after every transformation.

* Re-instate d_normalizationOK.

* Re-name functions for fetching canonical transformations.

* Separate alpha from coords.

* MultiConf works with single conf extraction.

* Extract all conformations.
Max and best similarities.

* Renames d_currConformer to d_activeShape.

* Update shapeToMol.

* Update shapeToMol.

* Changes from synthon shape searching.

* Fix normalization of multiple confs.

* Update Python wrappers.

* Fix shape merge.

* Improve bestSimilarity.

* Fix python wrapper.

* Pull in changes from SynthonShapeSearch:
make pruneShapes public.
function to negate Alpha values.

* clang-tidy suggestions.

* clang-tidy suggestions.

* Bug in quaternion gradients - we now have only 3 coordinates.

* Tidy tests.

* Mac result slightly different.

* Multi conformer molecule alignment.

* Optionally return raw overlap volumes in score functions.

* Python wrappers for raw overlap volumes.

* Update Python wrapper ShapeInputOptions.

* Tidy for PR.

* Extra include file.

* Extra library

* Tidy forward declarations.

* Don't prune if threshold < 0.0.

* Windows exporty thing.

* Check SMILES on merge of ShapeInputs.

* PRECONDITION of SMILES on merge of ShapeInputs.

* Response to review - rename some functions.

* change how overlapVols is passed
add a test for it

* API suggestions

* Response to review.

* Remove debugging writes.

* Fix Python wrappers.

---------

Co-authored-by: David Cosgrove <david@cozchemix.co.uk>
Co-authored-by: greg landrum <greg.landrum@gmail.com>

2026-06-03 06:09:09 +02:00

..

CMakeLists.txt

Gaussian shape overlays (#9095)

2026-03-26 21:53:54 +01:00

rdGaussianShape.cpp

Multi conf gaussian shape (#9265)

2026-06-03 06:09:09 +02:00

test_rdgaussian_shape.py

Multi conf gaussian shape (#9265)

2026-06-03 06:09:09 +02:00