* Fixes#6017
* a bit of cleanup work
* remove unused variable
* change in response to review
switch to using std::max(maxMatches,maxRecursiveMatches)
* test the case where maxSubstructMatches<maxMatches
* backup
* basic tests pass
* add JSON out to substruct match parameters
* serialize the substruct match parameters in reactions
* add that to the python wrapper
* more testing
* backup commit
This is mabye heading in the right direction and at least passes the basic tests which are there.
* some progress
* more tests and refactoring
* additional aliases
add carboaryl
* add CYC and ACY
* add ABC
* add AHC
* CBC and AOX
* add CHC and HAR
* add CXX
* cleanup: remove a bunch of nullptrs
* initial tagging support
* remove atom labels/sgroups after using them
* docs
* start handing writing
NOTE: this does not currently work: the generic code needs to move out of SubstructSearch
* move the generic groups to their own library
Signed-off-by: greg landrum <greg.landrum@gmail.com>
* make sure the generic groups end up in ctabs
* add forgotten CMakeLists.txt
* fix includes
* expose this stuff to Python
* CYC needs to initialize rings
* renaming
* add docs
* change in response to review
* Most tests working
* All tests working
* Fixed tests after merge with master
* Create header and implementations for RCore
* Updated comments
* Removed old code
* DLL export for MolMatchFinalCheckFunctor
* Information line for failing Mac test
* Log replace core behaviour
* Ordering fix for OSX
* Possible fuzzer fix
* Removed debug output
* Fix unmatched user R group bug
* Code review changes
* Bug fix and ChemTransforms test
* hello world works
* more
* more
minimallib needs to be tested
* parse substructure parameters from JSON
* add substruct search and parameters
* add descriptors
* register more descriptors
* fingerprints, first pass
* stop outputting tiny coord vals
* support generating 2d coords
* coordgen testing
* return nulls
* initial 3d support; add/removeHs; cleanup
* Embedding parameters from JSON
* update
* pattern fp, fps as bytes
* use json to configure MFP
* use json to configure rdkit and pattern fps
* aligned 2d coords
* parsing options
* options for writers
* rename remove_hs
* get this working on windows (kind of)
* silence some msvc warnings
* cmake updates
* update python tests
* add the CFFI code to CI builds
* cleanup line ending mess?
* a couple small fixes
* make this work with URF
* support coordMap in the 3D coordinate generation
* updates in response to review
* Test only commit for using enhanced stereo in substructure search
Adds some test cases to demonstrate what I'm planning.
When the test cases fail, the messages look like this:
-------------------------------------------------------------------------------
Enhanced stereochemistry
AND and OR match their enantiomer
-------------------------------------------------------------------------------
/Users/wandschn/Documents/src/rdkit/Code/GraphMol/Substruct/catch_tests.cpp:216
...............................................................................
/Users/wandschn/Documents/src/rdkit/Code/GraphMol/Substruct/catch_tests.cpp:218: FAILED:
CHECK_THAT( *opposite_mol, IsSubstructOf(*mol_and, ps) )
with expansion:
CC[C@@H](F)[C@@H](C)O is not a substructure of CC[C@H](F)[C@H](C)O |&1:2,4|
/Users/wandschn/Documents/src/rdkit/Code/GraphMol/Substruct/catch_tests.cpp:219: FAILED:
CHECK_THAT( *opposite_mol, IsSubstructOf(*mol_or, ps) )
with expansion:
CC[C@@H](F)[C@@H](C)O is not a substructure of CC[C@H](F)[C@H](C)O |o1:2,4|
* rename parameter to include q and m to reduce my confusion
* Don't keep recreating a map
This map is the same in every loop. And actually, the desired
information is slightly different than what was formerly stored
in the map.
* Fix tests after our discussion.
Also adds more exciting tests of disastereomers and structures
with multiple stereo groups.
* Use enhanced stereochemistry in substructure searching
Allows use of enhaced stereochemistry in substructure searching
if `SubstructMatchParameters.useEnhancedStereo` is set.
The matching rules are pretty obnoxious, but a synopsis is:
* An achiral query/substructure matches everything, because it
means "ignore chirality".
* An absolute query matches AND or OR, because they both include
the molecule with an absolute center
* An query with an OR matches either an OR or an AND, because
AND is more molecules.
* add info about matching to the documentation
* expose extended stereo matching option to python
* Some updates/tweaks to the documentation of enhanced stereochemistry
especially about searching.
* Code review comments.
Co-authored-by: greg landrum <greg.landrum@gmail.com>
* backup, does not work
* working on the C++ side
* backup
* fix the API
* document the new functionality
* improve that example
* final bit of cleanup
* switch to std::function
* first pass at adding a SubstructMatchParameter struct
* start moving the rest of the backend to use the parameters
* backend at least mostly moved over
* add aromaticMatchesConjugated
add tests
* switch over the MolBundle too
Add templates to reduce duplicated code
* support older compilers
let's see if it works...
* add SubstructMatchParameters to Python wrapper
* remove some deprecations and warnings
* damn compilers
* parameter support for bundles in python wrapper
* add the parameters to the java wrappers
* response to review
* very basics
* add the version to get all matches
* better exceptions, including tests
* documentation and actually add the test code
* responses to review
- added threading support to the ResonanceMolSupplier-enabled
SubstructMatch() and relevant tests
- modified/removed some code in O3AAlignMolecules.cpp which doesn't
seem necessary anymore
- modified Code/GraphMol/CMakeLists.txt to allow building
on Windows
as conjugated like their oxygen analogs
- fixed an issue with large numbers of resonance structures exceeding
the unsigned int allowance
- implemented the uniquify feature properly
- uniquify now defaults to false when using the ResonanceMolSupplier-
enabled SubstructMatch() version
- the concept of 'laziness' is now clearer
- TODO:
* remove some debugging info
* move classes from .h to .cpp
* SWIG wrappers
* improve resonance structure sorting for degenerate resonance
structures
I will do all of the above ASAP
smarts queries run faster (like vector bindings). Though there is an addition to the smarts parser
exposed here, I do not recommend using it in client code.
