* 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>
* Compile time and runtime deprecation warnings
* Used [[deprecated]] attribute to mark deprecation on cpp side
* Used RDLog to escalate deprecation warnings to python
* deprecated non fingerprint generator fingerprint generation functions
* Address build errors
* suppress deprecation warnings in cpps and tests
* experiment with new SWIG versions in the mac azure pipeline
* More deprecation suppression
* revert mac java experiment
* Fix SWIG syntax errors
* Attempt to fix windows unit test
* Remove test because of logging behavior
* Change linux java build to SWIG 4.1
- removes the need for preprocessor interaction
* Change mac java build to SWIG 4.1
* try updating the CI buid
* lock cmake version
needed to find JNI correctly
* update compiler versions
needed for the boost
* Fix typo and unavailable version
* Fix version conflict
* update mac build
* get linux build working?
---------
Co-authored-by: Patrick Penner <patrick@ppenner.com>
* add RDKIT_CFFI_STATIC option
minimallib cmake cleanup
* clean up a lot of boost::iostreams nonsense
* find_package(boost cleanup
* update the swig wrappers
* updates to psql
* get the Qt demo working again
* fix? coordgen
* only use std::regex in moldraw2d test
this is consistent with the other tests
* cleanup the serialization stuff too
* store more bond properties (if present) when pickling
* store the attachpts stuff more efficiently in pickles
* better error reporting in the cartridge
* updated cartridge use cases
* framework for extended query.
serialization works
to/from text doesn't work
* first pass at getting substructure search working
basic tests
improved error handling (try not to take down the server thread!)
* add serialization to MolBundle
* we really need to pickle mol properties
* basic support for molbundle
including substructure search
* tautomer and molbundle queries to JSON
* remove debug msg
* cleanup debug
initial index steps (not tested)
* remove indexing stuff since it wasn't working
will try to come back to that
* add xqm to update script
* add c++ testing for molbundle serialization
* add serialization of molbundles to python interface
* support expanding molbundles to arrays of tautomer queries
* edge cases
Signed-off-by: greg landrum <greg.landrum@gmail.com>
* change in response to review
* a bunch of updates
* make sure the mol props needed for XQMs are being serialized
* update update script
* fix binary string output from ExtendedQueryMols in python
* tautomer queries should serialize properties
* more testing never hurts
* combo of generic groups and generalized queries works
* Update Code/PgSQL/rdkit/adapter.cpp
Co-authored-by: Paolo Tosco <paolo.tosco.mail@gmail.com>
* Update Code/PgSQL/rdkit/adapter.cpp
Co-authored-by: Paolo Tosco <paolo.tosco.mail@gmail.com>
* Update Code/PgSQL/rdkit/adapter.cpp
Co-authored-by: Paolo Tosco <paolo.tosco.mail@gmail.com>
* Fix weird quotes?
---------
Signed-off-by: greg landrum <greg.landrum@gmail.com>
Co-authored-by: Paolo Tosco <paolo.tosco.mail@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>
* make sure we don't try to access an SG which no longer exists
* Fixes#6479
updates a bunch of tests to support this
* test ring stereo too
* update expected results from the tests
* Add optional sortsupport methods to the bfp and mol/qmol indices
* update the postgres version to be removed
* Revert "update the postgres version to be removed"
This reverts commit 59c6eb12dd.
* install the specific version of postgresql-client
* try pinning postgresql-common too
* try something else
* try something else
* try configuring cmake with explicit paths to version 12
* try uninstalling libpq5
* check if it's possible to run the cartridge test build w/ pg14
* Revert "check if it's possible to run the cartridge test build w/ pg14"
This reverts commit f1c2f9f783.
* fix the updated cartridge version number
* do not by default enable the sort_support method for the bfp gist index
* backup
* does not work
* backup
* passes all tests
send more tests!
* backup
* seems to mostly work
needs cleanup still
* more tests + python wrappers
* more testing
* some cleanup
* fix problem with newer boost
* be more expansive about unsaturation
* be symmetric in choosing the starting bond
fix a test error
* passes all tests;
passes ChEMBL regression test
* docs
* update cookbook
* expose the new hash function to the cartridge too
* support v2 hash in the registration hash
* better testing
* alternate, simpler approach for that
* remove vestigial docs
* Add support for generic matching in the PgSQL cartridge
Two new operators (and their inverse) `mol @>> q?mol` and `q?mol @<< mol` where q?mol getGenericGroups::setGenericQueriesFromProperties is applied to convert sgroups to query atoms and enable useGenericMatchers in the substructure matcher.
(q?mol means qmol or mol)
* Only transform the query once
* Revert "Only transform the query once"
This reverts commit 1873268cf6.
* - renamed Code/PgSQL/rdkit/README to Code/PgSQL/rdkit/README.md such that markdown can be used
- updated Code/PgSQL/rdkit/README.md with updated instructions how to build and install the PostgreSQL on all supported OSs
- fixed an issue with the PgSQL install script on Windows where the path to the update_sql directory was incorrect
* changes in response to review
* resolves it; needs more testing and cleanup
* still flailing a bit
* update expected test results
* cleanup
* revert extraneous changes
* revert these to master, will do this in a separate PR
* revert these to master, will do this in a separate PR
* back to master
* add function to canonicalize enhanced stereo representations
* use enhanced stereo in canonicalization
* Fixes#6045
enables the doc tests for EnumerateStereoisomers.py
Re-enables the BRICS tests
* some things work... tests need to be updated
* c++ and python tests pass
* update expected psql results
* run the canonicalization on SMILES generation;
c++ and python tests pass
* cartridge and java tests pass
* update doctests
* Change atom to metal bonds from single to dative if appropriate.
* Pedantic change whilst I was in the area.
* Reinstate all tests, leave in debugging writes to see failing tests.
* Re-did it. Failing tests now pass.
* Move any positive charge from the non-metal to the metal.
Fix expected test results.
* Write dative bond to JSON.
* Bump currentRDKitJSONVersion to 11, but allow parser to still read 10.
* Only move 1 unit of charge at a time from non-metal to metal.
* Greg's hack to not do it for O+ and N+ etc.
Explicitly exclude H, He, F, Ne from dative bonds.
Fix tests.
* Update expected PostGres json version to 11.
* suggestions for PR
* Correct comment.
---------
Co-authored-by: David Cosgrove <david@cozchemix.co.uk>
Co-authored-by: greg landrum <greg.landrum@gmail.com>
* write stereogroups
* Parse stereogroups
* add parameters to python wrappers
* more tests
* write substancegroups
* parse SubstanceGroups
* Fix a crashing bug with null molecules
* more testing
* add some docs
* update expected cffi results
* oh, this is delightful syntax
* adapt minimallib and the cartridge tests
some small cleanups
* stupid padding
* update expected
* changes in response to review
* stop using CIP codes in the atomic canonicalization
this will change results in some cases, so lots of tests need to be updated.
* stop breaking string literals... ARGH
* tests now pass
* update double bond canonicalization
* update a python test
* some cleanup
* update expected results for cartridge
* revert duplicate chunk in release notes
* replace deprecated ifdefs
This one gets rid of USE_BUILTIN_POPCNT and RDK_THREADSAFE_SS
use RDK_OPTIMIZE_POPCNT or RDK_BUILD_THREADSAFE_SSS instead
* get rid of BUILD_COORDGEN_SUPPORT from ROMol.i
* fix a stupid typo
* update release notes
* Fixes#5095
* add some casts to make that a bit less disruptive
* go back to the simpler form for constructing the test table
* fix release notes
* do cleanup step too
* updates in response to review
* Nonchiral atoms should be removed from StereoGroups
This fixes a bug where atoms which have no chirality were left in StereoGroups
In order to make this work, ROMol::setStereoGroups() needed to be made public.
That shouldn't be a problem since it doesn't change connectivity.
* fix some broken old tests
* update cartridge tests
* preliminary
* all tests pass
* cleanup
* more testing!
* we do still want to raise errors for aromatic atoms not in rings
fix one missed change for mol blocks
* update expected results for psql test
* fixes#4787
* additional test
* version bump
* do the same thing with SMILES
* Update Code/PgSQL/rdkit/adapter.cpp
Co-authored-by: Paolo Tosco <paolo.tosco.mail@gmail.com>
Co-authored-by: Paolo Tosco <paolo.tosco.mail@gmail.com>
* refactor cleanupRDKitCache for readability
* fix the indentation
* add comments
* add some comments
* allocate/deallocate the cache holder in the associated memory context
* exit the cache holder memory context callback once done
* more consistent use of the memory context from ValueCache
* refactor the cleanupRDKitCache callback
* minor changes to comments and renaming variables
* fixes#4681
* fixes a few Windows build problems
* added comments to adapter.cpp to explain the changes
* get PostgreSQL to build on Windows with both MSVC and MinGW compilers
Co-authored-by: Tosco, Paolo <paolo.tosco@novartis.com>
* remove deprecated useCountSimulation argument
* remove the mol_from_smarts() function from the cartridge
* remove the balabanj
* a couple final cleanups to the countSimulation thing
* document changes
* Fixes#4442
* add qmol_from_json()
* allow casting from mol->qmol
* avoid repeating ourselves
* add chiral substructure functions and operators
not available with indices yet
* remove the @@> operators
since I can't figure out how to support them in the index
