* use std::span for substruct match callbacks
This removes a copy from every evaluation of potential matches
* some cleanup/modernization
* some modernization
* deprecate chiralAtomCompat
* small optimization
* remove naked pointers
* improve new_timings.py script
* changes suggested in review
* response to review
* response to review
* atropisomer handling added
* fixed non-used variables, linking directives
* BOOST LIB start/stop fixes, linking fix
* Fixes for RDKIT CI errors
* minimalLib fix
* changed vector<enum> for java builds
* check for extra chars in CIP labeling
* removed wrong deprecated message
* fix ostrstream output error?
* restored _ChiralAtomRank to lowercase first letter
* changes for merged master
* Fixed catch label for new Catch package
* update expected psql results
* get swig wrappers building
* restore MolFileStereochem to FileParsers
* fix java wrapper for reapplyMolBlockWedging
* some suggestions
* move a couple functions out of Bond
* Merge branch 'master' into pr/atropisomers2
* merged master
* Renamed setStereoanyFromSquiggleBond
* atropisomers in cdxml, rationalize atrop wedging, stereoGroups in drawMol
* fix for CI build
* attempt to fix java build in CI
* attempt to fix java build in CI #2
* New routine to remove non-explicit 3D-geneated chirality
* changed to use pair for atrop atoms and related bonds
* Changes as per PR reviews
* PR review respnses
* PR review reponse - more
* Fix merge from master
* fixing java ci after merge
* Updated the help doc for atripisomers
* update the atropisomer docs
* improve the images
* add the source CXSMILES
---------
Co-authored-by: greg landrum <greg.landrum@gmail.com>
* Add a new parameter to mol_adjust_query_properties for generic query parameters (#46)
Adds a new parameter to mol_adjust_query_properties:"setGenericQueryFromProperties"
that defaults to false (so no change of behavior until used).
This PR also removes the previous way of doing it that involved reprocessing the query molecule for every comparison.
On datasets of 200k molecules the speed-up is between 2 (large complex substructure searches with repeating units) to 5 times (tiny substructures search).
Add support for generic query in PG cartridge
* Add generic groups to the lib
* Move the querying with generic groups out of MolOps to not bloat the library.
* Fix Python calls
* Update doc
* Proof that last 3 commits are mine.
* Fix missing headers
* Fix typo
* Fix call
* Fix calls
* suggested changes
* Update Code/GraphMol/GenericGroups/GenericGroups.h
Co-authored-by: Greg Landrum <greg.landrum@gmail.com>
* Add adjustquery test with default parameters.
---------
Co-authored-by: greg landrum <greg.landrum@gmail.com>
* backup commit
This is mabye heading in the right direction and at least passes the basic tests which are there.
* some progress
* more tests and refactoring
* additional aliases
add carboaryl
* add CYC and ACY
* add ABC
* add AHC
* CBC and AOX
* add CHC and HAR
* add CXX
* cleanup: remove a bunch of nullptrs
* initial tagging support
* remove atom labels/sgroups after using them
* docs
* start handing writing
NOTE: this does not currently work: the generic code needs to move out of SubstructSearch
* move the generic groups to their own library
Signed-off-by: greg landrum <greg.landrum@gmail.com>
* make sure the generic groups end up in ctabs
* add forgotten CMakeLists.txt
* fix includes
* expose this stuff to Python
* CYC needs to initialize rings
* renaming
* add docs
* change in response to review
