* Improved handling of SP/TB/OH reording in SMILES/SMARTS.
- add a getMaxNbors(tag) utility function to avoid repeated logic in multiple places
- tweak getChiralPermutation() for handling implicit/missing ligands (uses -1), allow inverse lookup
- use the tweaked chiral ordering in the reading/writing from SMILES
* clang-format run
* Reviewer requested changes.
- curly braces on all if conditions
- null check raw pointers with precondition.
* Correct additional test case introduced in the last year
* 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
* prefer wedging ring bonds for atropisomers
* update expected results
* handle 3D as well
* prefer wedging to larger rings
wedging bonds in 5 rings make later attempts at improving kekulization very difficult
update expected results
* extend those changes to 3D
* update tests for those changes
* avoid wedging atropisomers if possible
response to review
* Fixes#7140
deprecates the old version and creates a new one in Chirality.h
adds it to the python wrappers
* changes in response to review
* backup
* support custom labels with templates
* 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>
* Set squiggle bonds to STEREOANY with stereo atoms
* STEREOANY from squigglebonds is set regardless of sanitization now
* Ensure we have stereo atoms
* Add comment for new behavior
* See if a newer version of cmake works
* rev cmake to a slightly new version
* rev cmake to a slightly older version
* Response to review
* Allow setting of CIS/TRANS in set from squiggle bond
* Fix missing paren
* Add test for the actual enumeration
---------
Co-authored-by: Brian Kelley <bkelley@relaytx.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
* 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
* handle bonds with zero length around chiral centers
* chirality perception fixes
- fix handling of T-shaped chirality
- catch zero-length bonds
- catch opposing bonds with opposite wedging
* another special case
* more quasi-linear handling
* more progress
* backup
* update
* remove some complication with the neighbor order sorting by just doing a sort
🤦
passing all tests again
* oh, isn't this fun?
* no more t-shaped three-coordinate chirality
* still a couple of tests failing
* all tests pass
* overlapping neighbors without wedges remove stereo
* add test for overlapping atoms with wedged bonds
* make warnings consistent to allow easy parsing
* more testing
* docs
* refactoring: move a bunch of bond-wedging code into WedgeBonds.cpp and
into the Chirality namespace (since it's not just connected to mol files)
* remove a compiler warning
* more cleanup
* backup
* basics work; needs testing and edge cases
* backup
* progress
* better
* make sure the new wedges are also inverted
* docs
* favor lower degree atoms, even if the angle isn't ideal
* fix clang compile problems (hopefully)
* 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
* add a global feature flag to control use of the new chirality code
* expose that flag to minimallib
* add getters for allowNontetrahedralChilrality and useLegacyStereoPerception
* switch to using environment variables to store the values
* document that
correct the documentation about nontetrahedral stereo
* yay visual c++
* 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
