mirror of
https://github.com/rdkit/rdkit.git
synced 2026-06-06 22:39:55 +08:00
bbac292b4c
* First pass at splitting molecule. * Interim commit. Reading libraries from file in original format. * Basic search seems to be working. * Pattern fingerprint screening. * Connector region heuristic. * Fixed triazole (aromatic/non-aromatic connectors). * Fix search with non-split parent query, where query is substructure of a single reagent. * Remove duplicate hits by reaction/reagents used. * Implement largest fragment heuristic. * Extra test files. * Read/write binary file. Program for conversion from text format to binary format. * Remove empty reagent sets on reading, probably due to synthon number counting from 1 rather than 0. * Tidy SSSearch functions. * Stash pending major surgery for triazole bug. * Revert to using unique_ptr. Correct use of reagent order. * Function to summarise Hyperspace. * Delay building hits till end and put cutoff on number. * Earlier bale-out in getHitReagents. * Streamline checkConnectorRegions. * Remove free functions for search. * Correct name of Python test. * First stage of Python wrappers. * Rename namespace. * Parameters object. * Mysterious windows export thing. * Fix bug - not matching number of connectors in fragment and synthon. * Back like it was. The connector count wasn't the problem. * Put the substructure results into their own class. * gcc 14 didn't like my use of std::reduce. Update expected test results. * Remove write statement. * Tidy. * Tidy. * Enable random sample of hits. * Test that complex SMARTS works. Update Python wrappers. * Rename Hyperspace to SynthonSpace. * More renaming. Python test. * Enable Python test. Remove write. * Plug memory leak. * Response to Greg's initial look. * More response to Greg's initial look. * get the windows DLL builds working * Do away with mutable. Purge a few more uses of reagent in favour of synthon. Remove the c++ exe for converting text to binary databases. * Better Synthon c'tor. * More feedback from Greg. * Tidy the Python wrapper. * Remove tags from catch tests. * Don't allow copying of SubstructureResults. * Revert to allow copying of SubstructureResults. The Python wrapper needs it. * Refinements based on CLion/clangd suggestions. * Allow for map numbers in connectors in space file. * Refactor to make the searcher a separate class from the space. * Transfer Greg's review suggestions from Hyperspace merge. * First cut of fingerprint searcher. * Python wrapper. Some tidying. * Better random selection. * Fix bug in preparing frags for fingerprints. Re-factor. * Minor-refactor. * Sort hits by similarity if available. * Option for a few different fingerprint types. Pending a better solution. * Write fingerprints to binary file. * Use any fingerprint generator for similarity searching. No Python wrapper yet. * Python wrapper. * Change random selection to use distribution weighted by number of hits in each reaction. * Lots of suggestions from CLion/clang. * Use boost discrete_distribution for cross-platform consistency. * Tidy test up. * Try boost rng as well. * uniform_int_distribution to boost also. * Small tidy. * Method to write enumerated library. * Windows export thing. * Windows export thing. * Allow for commas in tab-separated fields. * win64 dll builds now work * More aliphatic synthon, aromatic product joy. * Force ring finding if it hasn't been done. * Fingerprint hits not being sorted if maxHits reached. * Remove debugging write. Doh! * Response to review of SynthonSpace2. * Missed one. * Add test file. * Hand merge Greg's #8050. * Discard nodiscard. * Move include of export.h inside include guards. * Response to review. * Fix memory leaks. --------- Co-authored-by: David Cosgrove <david@cozchemix.co.uk> Co-authored-by: Greg Landrum <greg.landrum@gmail.com>