* add MolOps::expandAttachmentPoints, along with tests
* support expandAttachmentPoints in the mol file parser
* switch the v2 stuff in the guts of the reaction parser
* add collapseAttachmentPoints()
add addAsQueries option to expandAttachmentPoints()
lots of testing
* an edge case and some cleanup
* add python wrapper for those two functions
* Update Code/GraphMol/FileParsers/FileParsers.h
Co-authored-by: Ric <ricrogz@users.noreply.github.com>
* changes in response to review
- support addCoords in expandAttachmentPoints()
- support the new attachment point stuff to/from CXSMILES
- add MolOps::details::addExplicitAttachmentPoint() and MolOps::details::isAttachmentPoint() utility functions
---------
Co-authored-by: Ric <ricrogz@users.noreply.github.com>
* 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)
* 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>
Made the following changes
* removed RDK_USE_BOOST_REGEX cmake option and its references
* removed usage of RDKIT_USE_BOOST_REGEX macro
* removed install instructions related to boost regex
* Fixes for canonicalization, and stereochemistry
* chnages from code review
* test that was omitted for canon correction
* PR review changes
* changes as per PR review
* missed file checkint to make PR tests compile
* PR conflict resolution
* change to fix PR buld errors (hopefully)
* line delete to force re-running of tests
* changes as per PR review
* resolve merge conflicts with master
* some suggestions
* revert chirality modifications when sanitization isn't being done
* addl changes: no stereo percept when no sanitize
* missing test expected files added
---------
Co-authored-by: greg landrum <greg.landrum@gmail.com>
* enable Werror on Mac and Linux
* do not fail on boost multiprecision pessimizing move
* fix eigen array_bounds warning
* Fix unused arg in Rascal MCS
* fix range-loop-construct warning in Rascal MCES
* fix sign mismatched comparison
* drop unused lambda capture
* allow FMCS timeout test more time under Debug (not a warning!)
* fix fwd declaration of struct RascalClusterOptions
* fix deallocator mismatch
* fix two minor leaks
* fix a real leak
* more minor leaks
* fix another real leak, plus some potential ones
* fix std::move preventing copy ellision
* allow longer run time for debug builds
* make maxBondMatchPairs and getLargestFragSize unsigned int
* make snake case camel case
* update to current master, fix new warnings
* update again and more fixes
* add #include <optional>
* fix char array deallocation
* update and fixes in Marvin writer
* unsigned int
* more copy ellision fixes
* more copy ellision fixes, and typos
* and some more
* Fix vulnerabilities found by fuzzer.
* Fix Typo in RWMol.cpp
* Update RWMol.cpp
This is an attempt to double check where the test failure is coming from.
* Update RWMol.cpp
Re-adding changes to test tests.
* Add support for dative bonds in MOL files
Dative bonds cannot be read in mol files V2000.
(really not supposed to be, but some software systems put them in there anyway)
* Add documentation about dative bonds in V2000
* suggestion from review
---------
Co-authored-by: Tad Hurst <tad.hurst@collaborativedrug.com>
Co-authored-by: Greg Landrum <greg.landrum@gmail.com>
* Fixes#6395: Move string index appropriately with molfiles
This code gives a fix to issue #6395, where properties lines in molfiles might not be processed correctly when dealing with pairs of values.
* Update tests to reflect molblock parsing changes
* handle the cases when the flag is set
* add python wrapper
* Fixes#6241
update and finish?
* set the chiral flag to 0 in the mol file parsers
* adjust to the chiral flag always being present
* add note
* initial support for wiggly and wedged bonds in cxsmiles
add CX_ALL_BUT_COORDS convenience option to CXSMILES writer
* move ClearSingleBondDirFlags to MolOps
* do a better job of handling the wiggly bonds
* mark 3D conformers from CXSMILES
* remove some extraneous printing
* test wD as well
* remove non-applicable test
* basic tests (not passing) for parsing t/c/ctu
* remove test for unimplemented feature
* changes in response to review
* changes in response to review
check for attempt to set the wedging more than once
testing for invalid w blocks
fix a bad comment
* slow steps towards a string_view experiment
* Move first set of file-handling code to use string_view
This is about 12% faster on my machine
* oops, yaehmop had not been updated to C++17
* start moving v3000 over
* disable storing string_views in Dicts.
* a bit more optimization
* get windows builds working
* fix a couple leaks in the test code
* changes in response to review
* changes suggested in review
+ more refactoring
* fix an oversight
* remove another one
* remove debugging numbers
* Improved regex whitespace handling
Change was made in the parseEnhancedStereo function
* Files for Github #5165 test case
Both files use enhanced stereochemistry, but differ in whitespace content
* Test case for Github Issue #5165
Catches whitespace parsing error
* Improves test case check
Makes test case more specific, less prone to potential invalid access to container
Co-authored-by: Greg Landrum <greg.landrum@gmail.com>
* Improves test case check
Makes test case more specific, less prone to potential invalid access to container
Co-authored-by: Greg Landrum <greg.landrum@gmail.com>
* Update test case "Github #5165"
Add 'require(mol)' to confirm valid molecule before additional testing
* Cleans up test for Issue #5165
* Cleans up test for Issue #5165
Co-authored-by: Greg Landrum <greg.landrum@gmail.com>
* - adds normalizeDepiction() and Python wrappers
- adds straightenDepiction() and Python wrappers
- adds an early check for R-labels to be in the accepted range to avoid throwing an exception later on
- adds a kekulize flag to process_details() to enable depicting molecules which fail to kekulize from JavaScript
- adds JavaScript functions to get fingerprints as Uint8Array
- adds JavaScript function to generate pickled molecule as Uint8Array
- adds JavaScript function to restore molecule from Uint8Array pickled
- adds has_coords() JavaScript function
- adds set_new_coords() to set JSMol coordinates in-place
- adds get_mol_copy() to obtain a JSMol copy
* fix build failures
* changes in response to review
Co-authored-by: Tosco, Paolo <paolo.tosco@novartis.com>
* 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
* stop removing substance groups with replaceAtom()
change default for keepSGroups argument to replaceBond()
* enable logging output for the fileparserscatch
* basics of parsing SMARTSQ SubstanceGroups
* Fixes#4476
test coming in the next commit
* handle multi-atom SMARTS as recursive
more testing
Test #4476
* a bit of cleanup
* get the tests working
* additional testing
* Update Code/GraphMol/FileParsers/MolFileParser.cpp
Co-authored-by: Ric <ricrogz@users.noreply.github.com>
Co-authored-by: Ric <ricrogz@users.noreply.github.com>
* make sure atom and bond bookmarks survive replaceAtom/Bond
* fixes oss-fuzz #30572
* fix possible memory-access error in error reporting
* more defensive deserialization
* switch that recursive smarts error handling to not use an exception
* - eliminate some documentation ambiguity about the role of the strictParsing flag
- fix some inconsistencies between SGroup parsing function prototype declarations and implementations
- add a workaround for accepting malformed V2000 'M SAP' entries affecting older version of MarvinJS (only if strictParsing is set to false)
- if strictParsing is set to false, malformed V2000/V3000 SGroups are ignored rather than causing the parsing to fail
- fix a couple typos in warnings
* changes in response to review
