* add the _CIPNeighborRanks property
* store CIP-ranked chiral neighbors
* store CIP-ranked SP2 bond and atropisomer anchors
* add a test
* boost headers in test
* add Atom::NOATOM
* add NOATOM test
* amend and clarify implicit H in Tetrahedral
* rename property
* rename property to _CIPNeighborOrder
* deprecate Chirality::StereoInfo::NOATOM
* add test
* potential fix
* whops\!
* support disabling ring stereo in rankMolAtoms
* pass atom ranks into the ring-stereo detection code
* all tests pass
* forgot a file
---------
Co-authored-by: Ric R. <ricrogz@gmail.com>
* 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: = <=>
* add option to use chiral presence in atom ranking
* add findMesoCenters
* add includeChiralPresence to python wrapper
* add python wrapper for that
* backup, not working
* backup
* all tests pass
* add tests for partial coverage of stereo groups
all tests pass
* backout the cleanup operations for the initial merge
* track the meso atoms with atom properties.
this is an optimization for later.
* changes in response to review
* 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
* 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 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>
* add test
* fix the issue
* make imines w/ implicit H unspecified, but allow unknown
* improve test in 6527
* do not mark double bonds as EITHERDOUBLE if no neighbors
* 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
* basic tests (not passing) for parsing t/c/ctu
* backup
* parsing works
* Fixes#5585
* cleanup, use the constant instead of hardcoding
* write ctu block
* document new cxsmiles additions
* more stereo info in the docs
* changes in response to review
* this passes all tests
Need to still think a bit about whether the "basic writing" test results are actually correct
* happier with those results
* 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
* basic tests (not passing) for parsing t/c/ctu
* backup
* parsing works
* Fixes#5585
* cleanup, use the constant instead of hardcoding
* write ctu block
* document new cxsmiles additions
* more stereo info in the docs
* changes in response to review
* bring over some new functionality
* adjust your expectations
* more tests
* additional cleanup and testing
* implement fix from #5407
* more testing
* a bit of optimization
* add the new func to the python wrappers
* cleanup
* findPossible working in the new code
NOTE: the combination of findPossible and cleanIt does not work and needs to be disallowed
* do some cleanup
* better handling of UNKNOWN (not unspecified) atoms and bonds
* update
* backup... we're close
* catch_chirality tests all pass
* all tests pass
* cleanup
* docs and a bit of optimization
* "optimization" which makes things slower... maybe revert this
* we don't need cleanExistingStereo() anymore... get rid of it
* cleanup
* changes in response to review
* very basics: actually parsing the new atom stereochem features
* add some input verification for the chiral permutations
* fix a typo
add quadruple bond SMILES/SMARTS extension
* add forgotten files
* patch from Roger
* add Roger's parsing examples
* typo
* new tests
* adjusted version of next PR from Roger:
- add SP2D hybridization for square planar (this may change)
- some modernizationof Chirality.cpp
- stop using < HybridizationType in Chirality.cpp (should probably do this elsewhere too)
- improved handling of hybridization assignment for new stereochem
- handle new stereo/hybridization in UFF
- tests for the above
* perception of non-tetrahedral stereo from 3D (from Roger S)
Basic testing of SP and TB based on opensmiles docs
* potential fixes for octahedral assignment
more tests
* docs update
need way more!
* map the TH tags directly to @ tags
* very basics of SMILES writing
this does not work with anything that changes the permutation order
like canonicalization or writing things in rings.
* start to support the getChiralAcross API
* more testing
* consistency
* add hasNonTetrahedralStereo() and getIdealAngleBetweenLigands()
* assignStereochemistry should only remove non-tetrahedral stereo
* re-simplify those tests
* cleanup matrix stream output
* initial pass at supporting nontet stereo in distgeom
* backup
* start on the reference docs
* TBP reference
* first pass at Oh finished
* update SP section
* more doc updates
* fix a typo
* add param to not remove Hs connected to non-tetrahedral atoms
* VERY basic coord generation for square planar
* TBP basics
* basic OH depiction
* start testing missing ligands
allow non-tet stereo in rings (ugly, but correct)
* add new TBP functions from Roger
* update depiction code for new API
* backup, the new tests work so far
* Finish the TB tests
* OH tests pass too
* cleanup
* first pass at getting correct SMILES with reordering
need way more testing than this
* ensure permutation 0 is correctly preserved
* some progress towards adding non-tetrahedral stereo to StereoInfo
* doc update
* add non-tet chiral classes to python wrappers
* make sure removeAllHs also gets neighbors of non-tetrahedral centers
more testing
* a bit of depictor cleanup
* make the assignment from 3D more tolerant
more testing
* improve the bulk testing
* cleanup
* remove a bit of redundant code
* ensure we don't write bogus permutation values to SMILES
* fix some rebase problems
* allow assignStereochemistryFrom3D() to be called without sanitization
* allow disabling the non-tetrahedral stereo when it's not explicit
* get that working on windows too
* Fixes#5196
This fixes the bug as reported, but there's more work to do in order to get the other cases
* cleanup
* fix assignStereochemistry()
* Fixes#5200
* move those functions to the public API
* fix assignStereochemistry
* cleanup
* refactoring in response to review
* backup, definitely does not work
* remove obsolete test
(not even really sure anymore that's a bug)
* remove code from a false path
* at this point the code passes all tests
* backup
* handle isotopes and h counts properly
* remove some compiler warnings
* all tests passing
* Use InChI minimimum ring size for bonds
* Fixes edge-case bug in canonicalization when bond labels are provided
* cleanup, no substance here
* fixes the last set of problems I've seen
* document that this is still experimental
* remove obsolete/testing comments
* stop considering charge and H count in chirality
* 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
