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