* Fixes a bug with chirality perception of T-shaped centers in very large rings
* remove those files from the chemdraw tests
should be added later once we figure out and fix what the problem on the chemdraw side is (it is not directly connected to this PR)
* be more systematic about the tolerance values
carry the same tolerances over into the bond wedging code
* re-enable those chemdraw tests
* typo
* throw if close to zero
* fix moldraw2DTestCatch
* Fix testRGroupDecomp
* fix one test in distGeomHelpersCatch
* fix tests in distGeomHelpersCatch
* retry finding a dir vector when adding Hs
* push UFF fixes to calculateCosY
* fix the setTerminalAtomCoords deg 4 patch
* add a test
* reduce zero tolerance
* 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
* test changes
* 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
* Merge branch 'master' into pr/specialQueries
* changes from previous PR
* Iclude false chiral
* rigorous enhnced stereo canoncalization
* Added more tests and clenup
* removed commented out code
* corrected init of SmilesWriteParams
* added MolFileStereoChem.h to the header files
* Renamed Rxn parser to MrvBlockToChemicalReaction
* To make catch2 work, and match the checksum
* Fixed Structchecker errors
* fix CI for DetermineBonds catch test
* error in catch_test for CI
* Allow custom smileWriteParams in GetMolLayers
* misnamed entry point
* ReactionFromMrvString change name
* remove adding writeParams to GetMolLayers
* make rigorous enhanced stereo the default, and fix tests
* only one abs group no longer needs Rigorous Enhanced treatment
* changed string_view to string in catch test
* Canonicalize Enhnaced Stereo only resturne unique smiles
* Now allows or and and groups together
* internal routines inside detail scope
* fix test error
* changed string back to string_view and fixed a CHECK
* Fixes for PR review tests
* Fix RDKit_Book.rst failure on build test
* fix xqm sql test
* updated expected files for cxsmiles_test
* Fixed removal of atom attrs
* Fixed tests after merge of master
* More efficient version of Stereo Groups Canonicalization
* Fixes for ctests
* removed debug code
* readded cipLabel test
* fix generalizedSubstruct/catch_tests.cpp error
* hueristics to improve speed
* Rationaized control of abs groups
* removed unused routine
* added rigorous stereo group treatment to test
* some suggested changes
* Changes per PR review and removed some changes to smiles
* Fixed CI errors
* changes per PR review
* more PR review vhanges and cleanup
* Fixed PSql PKL change
* changes as per PR review
* Restored error type for bad mols for canonicalizeStereoGroups and added a test
* Merge master and fix test in MolDraw2D
* Fix for randomize test error and other PR review comments
* Removed unsued variable to fix mac CI
* do not force aromatization in canonicalizeStereoGroups
* changes as per PR review
---------
Co-authored-by: greg landrum <greg.landrum@gmail.com>
* removed string_view in favor of string for catch test
* add parsing and generation of atropisomers when coords not present
* changed string_view to string in catch test
* more docs
* reformulation of the docs
* make an error message a little bit more useful
* small optimization
clang-format
* add `BondWedgingParameters` to new function
* changes for CIP test errors
* Updated internal doc to match what it does
* changes per PR review
* removed cout statements in tests
---------
Co-authored-by: Greg Landrum <greg.landrum@gmail.com>
* Allow reapplyMolBlockWedging to restore the original wedging regardless the bond type
* update python wrapper for Chirality::reapplyMolBlockWedging
* changes in response to review
* update the API documentation
* removed string_view in favor of string for catch test
* add parsing and generation of atropisomers when coords not present
* changed string_view to string in catch test
* more docs
* reformulation of the docs
* make an error message a little bit more useful
* small optimization
clang-format
* add `BondWedgingParameters` to new function
---------
Co-authored-by: Greg Landrum <greg.landrum@gmail.com>
* 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>
* fixes#6816
* cover the case where `CFG=0` is specified, which was missing
* roundtripping a CTAB should not change a cis/trans double bond into a crossed bond after calling reapplyMolBlockWedging(), no matter if the molecule is sanitized or not
---------
Co-authored-by: ptosco <paolo.tosco@novartis.com>
* ci updates
* forgotten update
* inch by inch
* remove unused variable
* try a gcc bump
* get rid of a bunch of unused-but-set errors in clang16
* be more selective
* disable a test in an obsolete module which is mysteriously failing
* Revert "Revert "Removed some code duplication between Depictor.cpp and common.h (#6368)" (#6797)"
This reverts commit 824616c5b9.
* security blanket: add back tests of the current usage pattern
* - fixed bug in get_sss_json() (#6806)
- added unit test for the above
Co-authored-by: ptosco <paolo.tosco@novartis.com>
---------
Co-authored-by: Paolo Tosco <paolo.tosco.mail@gmail.com>
Co-authored-by: ptosco <paolo.tosco@novartis.com>
* - implemented alignOnly mode into RDDepict::generateDepictionMatching2DStructure()
- the allowRGroups option now also supports potentially missing R groups (i.e., R groups that do not match any atom, such as those connected to generic aromatic atoms)
- added the adjustMolBlockWedging parameter (which defaults to true) to invert/clear molblock wedging information as appropriate
- added unit tests for the above new features
- added RDDepict::generateDepictionMatching2DStructure() overloads taking RDDepict::ConstrainedDepictionParams parameter for convenience
- removed some redundant RDDepict:: namespace specifications
* Fix chirality handling when the chiral atom is the first one in a SMARTS (#6730)
* Set _SmilesStart when parsing SMARTS.
* SmartsWriter should also invert first atoms, like SMILES.
* Update test cases now these SMILES match themselves as SMARTS.
* rerun bison
* cleanup a possible repeated define
* When an atom moves from the first to second position winding should flip in SMARTS (i.e. same as SMILES).
---------
Co-authored-by: greg landrum <greg.landrum@gmail.com>
* Some small cleanups from the UGM Hackathon (#6744)
* move definition of a couple global constants from a .h to a .cpp
* careful removal of some redundant atom PRECONDITIONS
* careful remove of some redundant ROMol PRECONDITIONS
a bit of additional cleanup
* optimization masquerading as modernization
* some more tidying
* a bit more atom cleanup
* change in response to review
* Fixes#6756 (#6780)
* update release notes and cmakelists for beta (#6788)
* move problematic functions to Chirality namespace
* - implemented alignOnly mode into RDDepict::generateDepictionMatching2DStructure()
- the allowRGroups option now also supports potentially missing R groups (i.e., R groups that do not match any atom, such as those connected to generic aromatic atoms)
- added the adjustMolBlockWedging parameter (which defaults to true) to invert/clear molblock wedging information as appropriate
- added unit tests for the above new features
- added RDDepict::generateDepictionMatching2DStructure() overloads taking RDDepict::ConstrainedDepictionParams parameter for convenience
- removed some redundant RDDepict:: namespace specifications
* move problematic functions to Chirality namespace
* added missing dependency
* let's check what is going wrong
* CoordGen tests should not run if CoordGen support is not available in the build
---------
Co-authored-by: Tosco, Paolo <paolo.tosco@novartis.com>
Co-authored-by: John Mayfield <john@nextmovesoftware.com>
Co-authored-by: greg landrum <greg.landrum@gmail.com>
* refactoring: move a bunch of bond-wedging code into WedgeBonds.cpp and
into the Chirality namespace (since it's not just connected to mol files)
* remove a compiler warning
* more cleanup
* backup
* basics work; needs testing and edge cases
* backup
* progress
* better
* make sure the new wedges are also inverted
* docs
* favor lower degree atoms, even if the angle isn't ideal
* fix clang compile problems (hopefully)
