* Use distances on all valid paths rather than just shortest distance.
* Optimise BondPaths.
* Optimise BondPaths.
* Hash coded for the bond paths.
* Faster find all paths.
* Build in gcc working.
* Comment.
* Remove debugging code.
* Update GettingStartedInPython.rst.
* Now need to split the clique and keep the largest fragment.
Lots of warnings about how slow this is.
Split out long tests.
* Back out a lot of changes. Remove the distance check with singleLargestFrag when building modular product.
* Tidy code.
Update docstrings.
Add explanation to GettingStartedInPython.rst.
* Fix single fragment test.
* Response to review.
---------
Co-authored-by: David Cosgrove <david@cozchemix.co.uk>
* Attempt at completeRingsOnly in mces
* changed option name and added a test
* code review
* check aromaticity and bond type matches before checking ring equivalencies
* update if statement
* typo
* Initial results sort the wrong way round on number of atoms and bonds.
* Improve sort for singleLargestFrag.
* Response to review - don't sort the fragment sets twice when opts.singleLargestFrag is true.
---------
Co-authored-by: David Cosgrove <david@cozchemix.co.uk>
* Fixes bug in output SMARTS when ringMatchesRingOnly causes an extra &R.
* Punctuation.
* Run clang-format.
* Don't use recursive SMARTS.
---------
Co-authored-by: David Cosgrove <david@cozchemix.co.uk>
Co-authored-by: Greg Landrum <greg.landrum@gmail.com>
* Add option to specify minimum clique size directly.
* Make the minCliqueSize uint and default to 0.
* Brain-fade.
* Send timeout and 'too many bonds' message to BOOST_LOG rather than std::cout, std::cerr respectively.
---------
Co-authored-by: David Cosgrove <david@cozchemix.co.uk>
* Fix atom ordering in bond label.
* Response to review.
---------
Co-authored-by: David Cosgrove <david@cozchemix.co.uk>
Co-authored-by: Greg Landrum <greg.landrum@gmail.com>
* Allow fragments of aromatic rings to match.
* Use existing code for checking bond is in ring.
---------
Co-authored-by: David Cosgrove <david@cozchemix.co.uk>
* 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>
* New option - exactAtomTypeMatch.
* Python wrapper.
* REQUIRE(res.size()) not CHECK. If it fails, you get seg fault on subsequent tests otherwise.
* Change option name.
* C++ implementation of equivalent atoms via SMARTS.
* Python wrapper.
* Tidy.
* Check for too many classes.
* Better handling of spaces in split.
* Pass string by reference. Doh.
* Add ignoreBondOrders option.
* Fix bug where different atom orders gave different MCES sizes.
* Update function description.
---------
Co-authored-by: David Cosgrove <david@cozchemix.co.uk>
* enable Werror on Mac and Linux
* do not fail on boost multiprecision pessimizing move
* fix eigen array_bounds warning
* Fix unused arg in Rascal MCS
* fix range-loop-construct warning in Rascal MCES
* fix sign mismatched comparison
* drop unused lambda capture
* allow FMCS timeout test more time under Debug (not a warning!)
* fix fwd declaration of struct RascalClusterOptions
* fix deallocator mismatch
* fix two minor leaks
* fix a real leak
* more minor leaks
* fix another real leak, plus some potential ones
* fix std::move preventing copy ellision
* allow longer run time for debug builds
* make maxBondMatchPairs and getLargestFragSize unsigned int
* make snake case camel case
* update to current master, fix new warnings
* update again and more fixes
* add #include <optional>
* fix char array deallocation
* update and fixes in Marvin writer
* unsigned int
* more copy ellision fixes
* more copy ellision fixes, and typos
* and some more
