* Fist pass at CDX support
* Enable CDX support for reading (also) in the CDXMLParser API
* Add cdxml test files
* Update swig wrappers for CDXMLFormat and Parameters
* Add constructor to ChemDrawParserParams
* Add Java SWIG support for ChemDraw
* Add chemdraw define to rdconfig
* Add missing chemdraw deps
* Remove direct expat link
* Fix Java linkages for ChemDraw
* Remove bad merge code
* Remove bad merge code
* Fix csharp builds
* Add sniffer for the ChemDraw DataStream
* Include filesystem
* Fix test on windows
* Add more CDX tests
* Ensure streams are open in binary mode to support CDX on windows
* Fix text to show that a Block is the text input, not a file
* Fix CSharp test
* Disable CDX tests when not building chemdraw
* Turn back on chemdraw
* Response to review
* Turn off chemdraw support for the limited external test
---------
Co-authored-by: Brian Kelley <bkelley@glysade.com>
* ChemDraw Document and read/write support for the RDKit
* Add missing test file
* Rev chemdraw version
* Rev chemdraw version
* Rev chemdraw version for g++11
* Update CMakeLists.txt
Co-authored-by: Greg Landrum <greg.landrum@gmail.com>
* Build chemdraw from an external CMake file
* Remove unused platform bigendian check
* Revert changes to constants, remove unused ones
* Keep the original constant names
* Remove __main__ section
* Use as much of the ChemDraw CMakeList as possible
* Skip installing expat
* Rev chemdraw version to fix windows issue
* Don't install expat, set the appropriate CHEMDRAW_BUILD definition
* resolve windows builds
* Fix minimal lib builds
* Move ChemDraw document to private header
* Move utility functions to ChemDraw namespace
* Move ChemDraw to v2 unique ptr api namespace
* Make class enum
* Switch to camelCase
* Response to review
* Move ChemDrawToDocument to ChemDraw namespace
* Update External/ChemDraw/Wrap/rdChemDraw.cpp
Co-authored-by: Greg Landrum <greg.landrum@gmail.com>
* Fix typo
* Update External/ChemDraw/Wrap/rdChemDraw.cpp
Co-authored-by: Greg Landrum <greg.landrum@gmail.com>
* Add better documentation
* Rev chemdraw version
---------
Co-authored-by: Brian Kelley <bkelley@glysade.com>
Co-authored-by: Greg Landrum <greg.landrum@gmail.com>
* ChemDraw Document and read/write support for the RDKit
* Add missing test file
* Rev chemdraw version
* Rev chemdraw version
* Rev chemdraw version for g++11
* Update CMakeLists.txt
Co-authored-by: Greg Landrum <greg.landrum@gmail.com>
* Build chemdraw from an external CMake file
* Remove unused platform bigendian check
* Revert changes to constants, remove unused ones
* Keep the original constant names
* Remove __main__ section
* Use as much of the ChemDraw CMakeList as possible
* Skip installing expat
* Rev chemdraw version to fix windows issue
* Don't install expat, set the appropriate CHEMDRAW_BUILD definition
* resolve windows builds
* Fix minimal lib builds
* Move ChemDraw document to private header
* Move utility functions to ChemDraw namespace
* Move ChemDraw to v2 unique ptr api namespace
* Make class enum
* Switch to camelCase
* Response to review
* Move ChemDrawToDocument to ChemDraw namespace
* Update External/ChemDraw/Wrap/rdChemDraw.cpp
Co-authored-by: Greg Landrum <greg.landrum@gmail.com>
* Fix typo
* Update External/ChemDraw/Wrap/rdChemDraw.cpp
Co-authored-by: Greg Landrum <greg.landrum@gmail.com>
* Add better documentation
---------
Co-authored-by: Brian Kelley <bkelley@glysade.com>
Co-authored-by: Greg Landrum <greg.landrum@gmail.com>
* 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>
* 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>
* Allow fragments to be groups in CDXML
* Add support for grouped reactants
* run clang-format
* Change github issue to 7528
* Add documents to the code
* response to review, check grouped reactants in cdxml against rxn file
* Remove unused code
* Add missing file
---------
Co-authored-by: Brian Kelley <bkelley@relaytx.com>
* Allow any bond (smiles ~) recognition in CDXML
* Move anybond.cdxml to the right place
* a bit of simplification
---------
Co-authored-by: Brian Kelley <bkelley@relaytx.com>
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>
* handle bonds with zero length around chiral centers
* chirality perception fixes
- fix handling of T-shaped chirality
- catch zero-length bonds
- catch opposing bonds with opposite wedging
* another special case
* more quasi-linear handling
* more progress
* backup
* update
* remove some complication with the neighbor order sorting by just doing a sort
🤦
passing all tests again
* oh, isn't this fun?
* no more t-shaped three-coordinate chirality
* still a couple of tests failing
* all tests pass
* overlapping neighbors without wedges remove stereo
* add test for overlapping atoms with wedged bonds
* make warnings consistent to allow easy parsing
* more testing
* docs
* 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
* backup
* backup
* passes a lot of tests
* cleanup; still failing some tests
* pay attention to bond starting points... duh
* all tests pass
* invert y coords
* Scale bonds, make the Wedge detection cleaner, add more tests
* Readd comment
* Use document bond length
* Adds roundtrip test through a molblock
* a bit of cleanup
* remove the old code since we aren't using it any more.
* changes in response to review
---------
Co-authored-by: Brian Kelley <bkelley@relaytx.com>
* Scale bonds, make the Wedge detection cleaner, add more tests
* Readd comment
* Use document bond length
* Adds roundtrip test through a molblock
* a bit of cleanup
* change expected results for a bogus structure
add a non-ambiguous version of it
* fixes#6462
* document incompatibility
---------
Co-authored-by: Brian Kelley <bkelley@relaytx.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
