* Parsing SCSR
* add scsrol to mol
* removed bad include file
* loosen distGeom test slightly
* add wrap test for SCSRMol
* Add test for scsr in python
* tests added for scsr and strict parsing removed
* remove extra stuff
* More fully specified use of SCSRMol for PR CI build
* Added flags for SCSR expansion to not include any leaving groups
* Added MolFromScsrParams to Wrap for python
* added SCSRMol destructor
* Added two tests for RNA macromols, and fixed a bug they revealed
* Added new tests abd expected files
* changes as per PR review
* SCSR Chnages for leaving groups
* fixed testScsr.py
* hydrogen bond treatment
* in SCSR expand, allow Hbond to be autoatically detected
* changes as per code review
* Adding new test file
* chages for SCSR contructors, destructors for CI build
* fixed pyton for SCSR hydrogen bond modes, and added tests
* Added new test files
* fixed edge case for SCSR
* fix checksum for inchi
* consistent capitalization of SCSR throughout
* switch to enum class
* make things shorter
* simplify
* get rid of the ATTCHORD class
* New section for SCSR in RDKit_book
* addeed section to RDKit_Book
* SCSRMol is no longer exposed in Python
* fix leak in MolFromSCSRFile()
light refactoring
* expose MolFromSCSRFile() to python
make the MolFromSCSR functions work with default args
a bit more testing
* removed C++ access to SCSRMol
* CXMsiles now ouputs hbonds, fix to template matching, and a few other things
* Addl fix for bad aromaticity in Hbond rings
* Test files needed
* Test files needed
* try to fix a CI build errors
* CI error fix
* Added missing test file
* CMake version - for CI build
* remove full file compoarison from macromol test file
* accidental change to debug restored to release
* Code review changes
* As per PR review
---------
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>
* 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
* do not remoge H if it has a special purpose in an SGroup
* flip the removeinSGroup default
* do not remove H from H-only SGroups
* remove atoms/bonds from SGroups
* update existing tests
* add tests
* Apply suggestions from code review
Co-authored-by: Greg Landrum <greg.landrum@gmail.com>
Co-authored-by: Greg Landrum <greg.landrum@gmail.com>
* some initial work...
Still some real questions here about what should be done with dp_mol data members
* add some tests for move semantics of Dict and Props
remove extraneous clear()
* more in-depth testing of the molecule results
* test refactoring
* improve the molecule move test
* fix some leaks found by valgrind
the new tests are now all clean in valgrind
* additional classes
QueryAtom, QueryBond, RingInfo, Conformer
* get swig working again.
Not sure why this is necessary, but SWIG is a mysterious beast
* fixes in response to review
* updates in response to review
* Remove accidentally tracked files and unset x flag
* Ignore ComicNeue
* Unify test tag to `reader`
* Trivial destructors
* Bump CMAKE_CXX_STANDARD to 14 (#4165)
* - 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
* backup
* further progress
* backup
* refactor handling of atom/bond annotations
move to a single annotation list to make it easier to add new annotation
types
* backup, doesn't actually work
* not unhappy with how the bracket rendering now works
still need to do bracket annotations
* backup
* commit first pass at brackets annotations
* add a bit more flexibility to how we handle annotations
Stll needs to be elaborated a bit, but the tests currently pass
* cleanup
* support comic mode with brackets
moves the handdrawnLine code to MolDraw2D_detail, which is a better place for it
* updates in response to review
* Progress on #3168
* Fixes#3167
* Fixes#3169
* deal with CBONDS too
* test PATOMS
* Fixes#3175
* a bit of code simplification and test updates
still needs more testing
* more testing
* handle s-group hierarchy
also a couple of other changes in response to the review
* add forgotten test file
* changes in response to review
* first steps towards StructureGroups being editable in Python
* typo fix
* Add initial features to allow editing SGroups from Python.
* update test
* typo
* Fixes#2450
adds `hasOwningMol()` to the public API for Bond and Atom
* add to other classes;
add to python wrappers
* get the smiles generation partially working
* changes in response to review
