* 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
* update some expected results that changed with previous fixes
* Fixes#4386
* try to actually generate an error when the cartridge tests fail
* update azure pipelines cartridge builds
* ensure psql dev env is there
temporarily disable other azure pipelines builds
* psql version
* gather info
* gather info
* gather info
* gather info
* gather info
* more descriptors
* try forcing psql12
* remove the package correctly
* remove the package correctly
* remove the package correctly
* sooo much fun
* sooooo much fun
* seems to be working now, enable the others
* support v3k output in cartridge
* tests do not pass
* docs
* update expected tests
* Start providing an update script for the cartridge
* update readme
* support enhanced stereo in cartridge
* it makes more sense to bump the cartridge version to 4.0
* add MolToJSON to cartridge
* add mol_from_json
* docs update
* changes in response to review
* set all source code files to have native line endings
* normalized all source code line endings
Co-authored-by: Paolo Tosco <paolo.tosco@novartis.com>
* run clang-tidy with modernize-use-default-member-init
* results from modernize-use-emplace
* one uniform initialization per line
otherwise SWIG is unhappy
Co-authored-by: Brian Kelley <fustigator@gmail.com>
* change minimal cmake version to a consistent 3.5
* progress towards a cleanup
* get the basic python deps working
* two more libs
* another round of changes
all tests pass at this point
* next round of changes
all tests pass at this point
* close to done
all tests pass
* very close
* almost done
* shift the RDBoost dependencies around a bit
* remove an extraneous python linkage
this is trying to get the mac builds working again
* Only link to python if it was built shared (#3091)
* change in response to review
Co-Authored-By: Ric <ricrogz@users.noreply.github.com>
* move that suppression of the maybe-uninitialized warning to BoostStartInclude.h
Co-authored-by: Brian Kelley <fustigator@gmail.com>
Co-authored-by: Ric <ricrogz@users.noreply.github.com>
