* refactor the code to determine whether or not an atom is in brackets
* move the definition of isMetal to QueryOps
* atoms bound to metals in SMILES should always be in square brackets
Implementation and some test updates
needs confirmation that all of tests run
* basic tests pass
* java tests pass
* update js tests
* doc updates
* Update Code/GraphMol/catch_graphmol.cpp
Co-authored-by: Ricardo Rodriguez <ricrogz@users.noreply.github.com>
* Update Code/GraphMol/SmilesParse/test.cpp
Co-authored-by: Ricardo Rodriguez <ricrogz@users.noreply.github.com>
* finish fixing tests
* bump yaehmop version to allow compilation to work
---------
Co-authored-by: Ricardo Rodriguez <ricrogz@users.noreply.github.com>
* Properly cleanup Dict::Pair when serializing HasPropWithQueryValue
* Make sure pickling doesn't change original molecule
* Fix bad cut and paste
* Add PairHolder utility class for memory management of non Dict Dict::Pairs, fix mem leak in pickler
* Edit comment to force a rebuild
* Ignore PairHolder from Java/Swig builds
* Ignore PairHolder API from swig
* Reponses to review
* Add backward incompatible change
* Make release note a bullet point
* fixes a regression introduced in #7582 which made all SWIG enums become type-unsafe
* fix also PipelineStrage asserts
---------
Co-authored-by: ptosco <paolo.tosco@novartis.com>
* - moved SMILES and RGroupDecomp JSON parsers to their own translation units
- added missing DLL export decorators that had been previously forgotten
- changed the signatures of MolToCXSmiles and updateCXSmilesFieldsFromJSON
to replace enum parameters with the underlying types
- updated ReleaseNotes.md
* make sure cxSmilesFields is only updated if the JSON string contains keys
belonging to the CXSmilesFields enum
* added missing copyright notices
---------
Co-authored-by: ptosco <paolo.tosco@novartis.com>
* Extend RDKit::MolStandardize with a validation and standardization Pipeline
* suggested changes
* apply clang-format
* apply yapf
* MolStandardize::FeaturesValidation optionally disallow dative bonds
* add allowDativeBondType to MolStandardize::PipelineOptions
* apply clang-format
* make the API of other validation classes more consistent with MolStandardize::FeaturesValidation
* apply clang-format
* PipelineStage to enum class
remove virtual functions from Pipeline class
be explicit about enums
* light refactoring to avoid what I think is an unnecessary call to `parse`
* a bit of modernization
* make the pipeline configurable
* make parse and serialize configurable too
* switch to storing pipeline stages using uints
* add a simple test for providing a pipeline
* update pointer alignment for clang-format
* test modifying the parser and serializer
* update swig requirement
* changes in response to review
* changes in response to review
* rename PipelineResult's *MolBlock members to *MolData
* upgrade swig to 4.2 in the CI environments
* add a few missing export directives
---------
Co-authored-by: greg landrum <greg.landrum@gmail.com>
* change valence model to use isolobal analogy
Remove support for five-coordinate C+ and, by analogy, five-coordinate N+2
Removes support for charge states that take atoms past the end of the periodic table
i.e. [Lv-4] is no longer supported
* update the tests for that
* remove valence state of 6 for Al
* fix representation of phosphate in the mol2 parser
this is a correction of what was done during #5973
* cleanup the exceptions for P, S, As, and Se
* drop valence states:
Si 6, P 7, As 7
* a couple of additional changes from #7397
* update java tests
* fix an inconsistency: Rb now supports valence -1
* documentation
* - replace operator[] with at() for bounds check
- extract some code into a function to avoid duplication
- use TAB as separator throughout in the periodic table data for consistency
* removing the .at() usage
We know that these vectors aren't empty, so there's no need for the bounds check.
---------
Co-authored-by: ptosco <paolo.tosco@novartis.com>
* Query atom information in swig
* Atom query swig wrapping working
* SWIG wrapper for queries
* Add match to QueryAtom and QueryBond
* CShart test
* Added Java test
* Replace var with type for Java test
* Apply suggestions from code review
Co-authored-by: Paolo Tosco <paolo.tosco.mail@gmail.com>
* Update Code/JavaWrappers/Queries.i
Co-authored-by: Paolo Tosco <paolo.tosco.mail@gmail.com>
* Apply suggestions from code review
Co-authored-by: Paolo Tosco <paolo.tosco.mail@gmail.com>
* Get SWIG build working again
* Remove trailing whitespace from Queries.i
* Update Queries.i to use shared_ptr
* small simplification
* remove boost::make_iterator from ROMol.i
* further simplification
---------
Co-authored-by: Paolo Tosco <paolo.tosco.mail@gmail.com>
Co-authored-by: ptosco <paolo.tosco@novartis.com>
* Add mono build back into C# build
* Add mono build back into C# build
* Add mono build back into C# build
* Don't do mono build on Linux if dotnet is used
* CSharp dotnet build always on windows. Enable dotnet testing in vs_build_swit
* Fix typos
* Dotnet core build and test for RDKit
* Cmake dot net build and ctest working on windows
* Remove old Linux mono build
* Update to net8 and create RDK_BUILD_DOTNET_CSHARP_TESTS flag
* backup
* backup
* backup
* new testing file
* reorder things in the SMILES and SMARTS parser
parameters to allow easier struct initialization
* add v2 of SmilesMolSupplier
v1 is not yet there
* add TDTMolSupplier
add some very basic tests for v1 suppliers
* more progress
* all tests passing
I think all the suppliers are now moved over
* check for maeparser before building the tests
* get SWIG builds working
* changes in response to review
* basic approach to v2api
* does not work, backup commit
* well, that now compiles
* cleaner
* more cleanup and testing
* get the SWIG wrappers to build
* swig wrappers now build
* switch back to using references to default values
* adjust to new catch version
* move the implementation to v2 and call it from v1
* update the parameter object too
* move debugParse down
* a couple of review changes
* make v2 naming consistent with Python
* first pass at v2 for the ctab parsers
* move a the writing functionality to a different header
this is just an organizational thing at the moment; we still import the writers header in the parsers header so as to not break code
* do v2 of the tpl parser
* fix missing dependency
* Mol2 parser
* move over the XYZ parser
* switch over the PDB parsers too
* get mac and java builds working (hopefully)
* basic approach to v2api
* does not work, backup commit
* well, that now compiles
* cleaner
* more cleanup and testing
* get the SWIG wrappers to build
* swig wrappers now build
* switch back to using references to default values
* adjust to new catch version
* move the implementation to v2 and call it from v1
* update the parameter object too
* move debugParse down
* a couple of review changes
* make v2 naming consistent with Python
* 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>
* Added fingerprints to GeneralizedSubstruct search
* Small change to fire tests
* Edits from code review
* Updated swig - newobject not required for GeneralizedSubstruct fingerprint methods
* GeneralizedSubstruct only supports unique_ptr in SWIG4.1
* 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
* support generalized substructure search in the SubstructLibrary
* simplify namespaces
* support the new functionality in the swig wrappers
* update mac swig version in CI
* ensure swig4
* switch mac_java ci builds to conda-forge
* change in response to review
* add copy ctor to extendedquerymol
* Back to the way it was
* Add support for Marvin files
* And MRV lib to the Java wrapper
* And MRV lib to the Java wrapper
* Removed use of void * in MarvinParser.cpp and MarvinParser.h
* Changes as per code review from Greg
* Changes for PR review - many virtual methods
* changes as per Jonathan's comments
* some suggested changes
* PR review changes and fixed unit tests
* after merge, changes to make it run
* More PR review changes
* removed unneeded std::move()s · rdkit/rdkit@b4b8b9a · GitHub
* More PR review changes
* fix a compile error
* more defensive programming
* reorder
* final? PR review updates
* Erata
---------
Co-authored-by: Tad Hurst <tad.hurst@collaborativedrug.com>
Co-authored-by: greg landrum <greg.landrum@gmail.com>
Co-authored-by: tadhurst-cdd <112502803+tadhurst-cdd@users.noreply.github.com>
* Support tautomer queries in RGD
* Continuing RGD and tautomer development
* Python and C# tests
* Python and C# tests
* C# test
* Typo fix
* For cire tautomer query update properties instead of full sanitization
* Added query comment
* Code review change
* Support Enumeration of input cores
* Mol enumeration test
* Remove useNormalMatch from RGroupDecomp
* Added comments for handling tautomeric core
* Added comments for handling tautomeric core
* 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
* expose RDLog to SWIG wrappers
* - added a SetTee() overload that takes a filename as parameter to simplify redirecting from wrappers that do not have interface with C++ streams (e.g., Java and C#)
- replaced some duplicate code with ClearTee() calls
- replaced RDLogger std::shared_ptr with boost::shared_ptr to make it more easily available from SWIG wrappers
- exposed the RDLogger methods to SWIG wrappers
- added Java test for RDLogger
* this should fix the segfault
* avoid issues on case-insensitive platforms
* here's a solution keeping std:;shared_ptr
* change in response to review
---------
Co-authored-by: Tosco, Paolo <paolo.tosco@novartis.com>
* wip
* - avoid leaking memory after instantiating UChar_Vect
- fix some indentation
- make it easier to read/write pickles as native byte arrays from Java and C#
- add tests
---------
Co-authored-by: Tosco, Paolo <paolo.tosco@novartis.com>
* - expose [sg]etUseLegacyStereo()
- In MolToSmiles() doIsomericSmiles should default to true as in C++ and Python
- added missing parameters to MolToSmiles() and MolToMolBlock()
- added SmilesWriteParams MolToSmiles() overload
- added and updated Java tests
* - changes in response to review
- exposed the same functionality also in MinimalLib and CFFI and added tests
---------
Co-authored-by: Tosco, Paolo <paolo.tosco@novartis.com>
- remove redundant Point2D_Vect definition (laready defined elsewhere)
- blacklist getPositions() whose return type is not accessible from SWIG
Co-authored-by: Tosco, Paolo <paolo.tosco@novartis.com>
* 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
* Test routine working
* Fix python molzip signature clash
* Update SWIG bindings
* Add C++ and Python documentation
* Add C++ and Python documentation
