* 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>
* insert stereogroups
* insert Substance Groups
* fix ownership, bond indexes
* add test
* fix comparison signednedss
* update test
* Brian's suggestion
* allow more than one ABS group
* 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>
* 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>
* 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
* added a set of test files for SGroups.
Many thanks to Gerd Blanke for providing these
* Partial version of the wrapper
Definitely needs more work
* add some properties
* basic SGroup property change test
* not working; backup commit
* disable writing for now
* add ClearMolSGroups() function
* review response: add a couple missing methods
* remove spaces from filenames
* update filename in test
* changes in response to review
* add operator== to SGroups
* solve lifetime problems with a vector_indexing_suite
* Implementation of SGroups
* remove sample files test
* update gitignore with test outputs
* fix RevisionModifier
* re-enable tests
* backup commit; things seem to work so far
* some refactoring; obvious s group tests pass now
* more refactoring
* everything now out of the public API
* not sure why this was still in there
* rename functions; all tests now pass
* remove getNextFreeSGroupId; readd comment in copy SGroups
* clang-format
* squash-merge current master
* squash merge master
* Address comments on PR
- Update to current master.
- Move SGroup parse time checks to SGroupChecks namespace.
- Store SGroups in ROMOl as vector<SGroups>.
- SGroup methods return referenes instead of pointers.
- Use atom/bond/sgroup indexes for properties instead of pointers.
- Have SGroups inherit from RDProps; move properties to RDProps.
- Remove trivial/unused methods.
- Add a link to the SD specification atop SGroup.h
