* 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
* 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
* Nonchiral atoms should be removed from StereoGroups
This fixes a bug where atoms which have no chirality were left in StereoGroups
In order to make this work, ROMol::setStereoGroups() needed to be made public.
That shouldn't be a problem since it doesn't change connectivity.
* support CXSmiles extensions in the hashes
* initial tests for that
* some cleanup
* copyright header cleanup
* minor refactoring
* call out the changes in the release notes
* extension and more testing
* add python wrappers
* Nonchiral atoms should be removed from StereoGroups
This fixes a bug where atoms which have no chirality were left in StereoGroups
In order to make this work, ROMol::setStereoGroups() needed to be made public.
That shouldn't be a problem since it doesn't change connectivity.
* fix some broken old tests
* update cartridge tests
* RWMol: replace atom in stereo groups
Fix https://bugs.chromium.org/p/oss-fuzz/issues/detail?id=36998, a
use-after-free in initFromOther.
* Fix out-of-bounds write in iterateCIPRanks
If the rank has not changed in the current iteration, the cipEntries
vectors might not have increased in size. Accessing `numIts + 1`
resulted in an out-of-bounds write. This commit skip the cipEntries
update when the rank is unchanged.
Fix https://bugs.chromium.org/p/oss-fuzz/issues/detail?id=28660
* Fix use of uninitialized values in MolSGroupParsing
`stream >> count` may silently fail without an exception. In that case,
`count` was uninitialized but used. This commit initalizes `count` to 0,
as well as other variables that may be read without being initialized.
Fix https://bugs.chromium.org/p/oss-fuzz/issues/detail?id=25220
Fix https://bugs.chromium.org/p/oss-fuzz/issues/detail?id=25225
* Fix vector size cast in streamReadVec
In 32-bit systems, the implicit conversions from 64-bit to a 32-bit
size_t could lead to an underallocation of the vector. This would follow
by a out-of-bounds write while trying to populate the vector. Now, the
code throws an exception in case of a cast that would change the size.
Fix https://bugs.chromium.org/p/oss-fuzz/issues/detail?id=28034
* RWMol: improve atom replacement in stereo groups
This code is cleaner and more efficient.
* Add test for replaceAtom and stereo groups
* test getIdOfEntryWithBitId()
* remove unused functions
* improve bv tests in python wrapper
* more UniformGrid tests
* improve deprotect coverage
* improve abbreviations coverage
* add operator!= to DeprotectData
* more testing for adjustQueryProperties
* fix a copy-paste bug
* copy-paste bug
* more testing
* more testing
* more testing
* fix an edge case bug in getValenceContrib
* more bond tests
* add operator!= to StereoInfo
tests StereoInfo::operator==
* make some internal functions testable
* more testing
* minor code cleanup
* fix some bad caching behavior in getDistanceMat() and get3DDistanceMat()
testing
* test FixeMolSizeMolBundle() copy ctor
* deprecate BalabanJ
* more testing
* testing
* mods to get things working for windows DLL builds
(don't bother running some of the tests there)
* fix a typo
* prefer to not wedge bonds to double bonds
* addWavyBondsForStereoAny() works
* add option to clear bond stereo
* support wavy bonds in prepareMolForDrawing()
get rid of MolDraw2D/catch_main.cpp
* add a drawing example
* name the bug correctly
* add that new functionality to the python wrapper
* remove some debugging cruft
* 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
