* 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>
* move mol weight and formula calculators to MolOps and refactor them a bit.
The descriptors are still there and should remain.
* remove other unnecessary dependencies on Descriptors
* Update adapter.cpp
Co-authored-by: Paolo Tosco <paolo.tosco.mail@gmail.com>
---------
Co-authored-by: Paolo Tosco <paolo.tosco.mail@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>
* move detectBondStereoChemistry() into MolOps
* switch more code over to using the new function
* add an addStereoChemistryFrom3D() function. Needs testing still.
* add some tests
* cleanups and rename
* StructChecker changes. Initial commit. First implementation. Added some tests.
* StructChecker: add GoodAtoms and AcidicAtoms. new updates
* StructChecker: add new tests
* StructChecker: added TransformAugmentedAtoms()
* StructCheck: add structCheck to GraphMol. Fix compilation errors.
* StructChecker: add stereo verification and some utilities.
* StructChecker: function FixDubious3DMolecule was added
* StructChecker: checkStereo added. done with stereo.
* StructChecker: add StripSmallFragments()
* StructChecker: add AtomClash() function. Some cosmetic + tests
* StructChecker: checkAtoms() was started
* StructChecker: checkAtoms is ready
* StructChecker: user RingInfo from RDkit. Start regarge
* StructChecker: ReCharge molecule method prototype
* StructChecker: updates for ReCharge. Almost finished
* StructChecker: all ReCharge is done except external data tables loading
* StructChecker: add path tables into API. ReCharge completed
* Adds augmented atom data
Signed-off-by: Brian Kelley <brian.kelley@novartis.com>
* Removes extra files
Signed-off-by: Brian Kelley <brian.kelley@novartis.com>
* Adds path to test data via RDBASE environment
Signed-off-by: Brian Kelley <brian.kelley@novartis.com>
* Revert "Struct checker apr15"
* StructChecker: add missing tautomer tests
* Updates test to use RDBASE
* Adds initialization of data from data section
* Adds Python API and tests
* Fixes namespace for enum
* StructChecker: update/imporve strip small fragments
* StructChecker: fix acidic atoms (but logic does not work)
* StructChecker: fix match issue for CheckAtoms
* Adds macro guards
* Adds loading API and proper constructor
* Fixes tests, adds stereo test
* Fixes crash bug, matches[0] was being accessed from an empty match vector
* Reverts crash fix - conflicts with previous
* Adds the rest of the structure checker options
* StructChecker: fix atom matching for aromatic rings
* StructChecker: add tautomers checks. Update some tests
* StructChecker: stereo fixes. Add some tests
* StructChecker: fix check atoms. Start ligand symbol list
* StructChecker: fix some check atoms validation. Add Tranform to query lists. Start correct loading augmented atoms
* update
* another set of fixes
* StructChecker: fix loadDefaultAugmentedAtoms. Some changes in CheckAtom + tests + debug conditional breakpoints (TEMP operators)
* StructChecker: rewrited RecMatch() to sequential. Changed bond matching algorithm. small bug fixes
* Adds better logging of mismatched atoms
* Removes duplicated negative charge
* Fixes charges
* Adds nitro group test
* StructChecker: add better logging
* remove double logging
* Reformats code using RDKit's clang-format style
* StructChecker: Fix charge reformat using RDKit format.
* StructChecker: compilation restore after merge
* restore bond matching
* Removes the same fragments that strucheck does in case of ties
* Don't resanitize - this adds aromaticity which mucks things up
* Adds empty molecule checks
* Fixes atom clashes.
* Removes debug printing
* Removes debug logging info
* First pass at stereo fixes
* Fixes off by one error for dubious stereo fix
* Fixes more off by one errors
* Fixes more off by one errors
* More off by one fixes.
* Another off by one
* Fixes chiral flag set in molfile check
* Copies chiral flag over to largest fragment if necessary
* Poor man’s parity check.
* Find unspecified chiral centers ala Avalon.
* StructChecker: fix recursive match. Fix transformations
* StructChecker: fix transformation for atom list (using query atoms)
* Fixes checks && to &
* StructChecker: fix carboxylic acids tranform issue. Atom list is changed only if different
* StructChecker: documentation was updated
* Fixes snprintf and silences some warnings
* Adds Get/Set StructCheckerOptions
* Adds default AugmentedAtomTransforms
