* Fixes#8379
* check in some working tests
* test passes
* test passes
* test passes
* test passes
* test passes
* ensure that the invariants flush the streams on failure
* tests pass
* test passes
* tests pass
* tests pass
* tests pass
* tests pass
* tests pass
* tests pass
* tests pass
* tests pass
* tests pass
* tests pass
* tests pass
* tests pass
* tests pass
* tests pass
* Fixes#8391
* tests pass
* fix a test with legacy
not clear why this was not causing problems before
* make a test work
* Fixes#8396
* gcc builds work
* fingerprint tests pass
* mention backwards incompatible change
* fix a problem with FindMolChiralCenters
* more testing details
* enable the test status output
* Fixes#8432
fix a bug in double-bond stereo handling for template matching
* all depictor tests pass
* use the new-stereo chiral ranks in the depiction code
* always assign new-stereo chiral ranks
* make _ChiralAtomRank a computed property
This is analogous to _CIPRank
* tweak to the way the atom ordering is computed for 2D coordinate generation
* update two expected results
* backup
* response to review
* tests pass
* tests pass
---------
Co-authored-by: = <=>
* fixleak in CIP labels catch test
* fix leak in Murtagh clustering
* do not leak writers in streambuf
* fix leaks in fingerprintgeneratorwrapper
* remove 'minor leak' comments
* 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>
* changed string_view to string in catch test
* fix for ring-stereo atropisomers
* removed debug cout
* removed change to build in debug mode
* change catch arg to a rerference
* changes as per PR review
* removed string_view in favor of string for catch test
* add parsing and generation of atropisomers when coords not present
* changed string_view to string in catch test
* more docs
* reformulation of the docs
* make an error message a little bit more useful
* small optimization
clang-format
* add `BondWedgingParameters` to new function
* changes for CIP test errors
* Updated internal doc to match what it does
* changes per PR review
* removed cout statements in tests
---------
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>
* Fixes#4996
also switches to using the GraphMol version of catch_main.cpp so builds are faster
* Fixes#4998
we should probably discuss this one
* compare with previous results
* add new test (it fails, of course)
* isAtomPotentialTetrahedralCenter() there and tested
tests cases for molecular stereo written (but failing, of course)
create new_chirality.cpp, we will probably want to change this at some point
new StereoInfo structure
* more infrastructure
- isBondPotentialStereoBond()
- two getStereoInfo() functions
- associated unit tests
* backup
* oops
* backup
* switch to always using four atoms for bonds
* backup
* add new test (it fails, of course)
* isAtomPotentialTetrahedralCenter() there and tested
tests cases for molecular stereo written (but failing, of course)
create new_chirality.cpp, we will probably want to change this at some point
new StereoInfo structure
* more infrastructure
- isBondPotentialStereoBond()
- two getStereoInfo() functions
- associated unit tests
* backup
* oops
* backup
* switch to always using four atoms for bonds
* backup
* this now actually works
* doc update
* add a test to demo that ring stereo is not working
* more testing
* add a fun CIP test
* add review note
* debugging
* remove extraneous debugging
turn off tests for ring-double bond stereo
* disable the ring-stereo fix... this breaks a few tests, but we will recover
* works, needs cleanup, chirality code needs re-testing
* nothing works
* Fixes#3322
* Python and C++ tests now pass
* clang-format
* first pass at python wrappers
* improve doctest
* basic optimization...
stop with the copying
* rename
* all tests passing again
* optimization
* fix the sort in the tests
* looks like this might fix the windows-dll build problems
* update tests
* the fun never ends
* comment cleanup
* handle deliberately unspecified atoms/bonds
* add cleanIt option
* add flagPossible
* add option to use the new code to the SMILES parser
* additional testing
* additional testing
* a bit of additional testing never hurts
* changes in response to review
* fixes a bug with potential parastereo not being cleared
other changes in response to review
* update docs
* add port of centres
* Several changes:
- Added a test based on RDKit issue 2984
(default RDKit fails it, this gets it right)
- Use bond directions for bond stereo (label is no longer required)
- Fix bugs in rules 4b and 5new
- Fix some mem errors
- clang-formatted
- some other minor cleanups
* Several changes and some improvements:
- Added LGPL license, as well as a mention in the doc.
- Fix/update/add some comments
- Fix typo/bug in Mancude calculation
- Fix bug in rules 4b, 5New
- Fix Sp2 Bond dir reference
- Re clang-format
- other minor changes suggested by Dan
* Another bunch of changes:
- require integer-order bonds; kekulize when required
- fix fraction comparison
- rename sq Cis/Trans e/z
- replace queues with vectors
- update copyright notices
- revert LGPL changes
- fix Asymmetric typo
* move to separate lib/mod, add python validation test
* Moving away from the original implementation:
- Rename to CIPLabeler
- Remove the abstraction layer
- Remove some stats stuff
- Push some CIPMol functions down to Node
- Use RDKit's isotope info
* Another bundle of changes. The most relevant ones:
- fix parity translation
- use cis trans as bond reference -- breaks #2984 test
- kill a lot of unused code
- use lists for queues
- store nodes and edges in digraph
- add prefixes to class data member names
- update changeRoot() test
- use fastFindRings() for mancude rings
- update docs
- add references to the scientific paper
- Document the Mancude functions
- Fix Mancude atom types and their comments
- remove mol data member from SequenceRule
- replace Fraction with boost::rational
- update comments, docstrings and the doc
* fix building the test
* Changes here include:
- adding bitset overload for the labeling function
- python wrap of the overload
- handling trigonal pyramids with implicit H
- setting bond labels sets stereo atoms, cis/trans
- nix LEFT/RIGHT/TOGETHER/OPPOSITE constants
- don't use GLOB in cmake
- a decent amount of refactoring
* Minor edits to new_CIP_labeling (#6)
* Some changes for clarity
Added some documentation and changed some variable names to match
my understanding. Also a ran clang-tidy to ensure that all blocks
were brace-enclosed.
* Return a reference instead of a copy for performance
This is called many times and showed up after some light
profiling. This change bumped throughput by about 20%
* move out of Graphmol
* move .hpp headers to .h
* update documentation; add label set of atoms test
* Address comments:
- Added references to centres to CIPLabeler.h and Python Wrap.
- Update validation test to skip sanitization.
- Document mancude fractional atomic number calculation.
- Use unittest assertions in python test.
- Update mancude docstrings to 'resonance' instad of 'tautomers'.
- Rename prioritise() to prioritize().
- Add postcondition to check carriers size in Tetrahedral.cpp.
- Use getNeighbors() in Tetrahedral.cpp.
- Move findStereoAtoms to Chirality namespace.
- Move code back into GraphMol.
- Fix typos and reformat doc.
* More comments:
- Mention why we use boost's unordered map rather than the std one.
- Fix include in Python wrapper.
* Addressed second batch of comments:
- fix the bug in rule 4b
- fix docstring for rule 2
- move atomic mass calculation from rule 2 to node
- addressed some build warnings
- simplify sp2bond::label(comp)
- add start/end atoms to Sp2Bond constructor
- update system/local includes
Co-authored-by: Dan N <dan.nealschneider@schrodinger.com>
