* Remove out_1 and out_2, only need for directed graphs.
* Variable renaming, no other changes.
* Fix a couple things that were forgotten during the rename
* Only one of these counts is updated now.
* Add ifdef to enable/disable VF2Pruning
* Add degree bound check, could be pushed down to the generic VertexCheck predicate.
* The stack knows at each point what was added, by passing these into the Backtrack call the clone allocation can be removed.
* Indent and rename added_node1 to node1.
* Now the clone is removed we can add a member function to handle the recursion cleanly.
* Also make for MatchAll a member function.
* Set lim=0 to mean infinity.
* VF2Plus optimisation, when candidate is in the terminal set select from a mapped neighbours adjacency list.
* Optimisation hint.
* Use a struct for the Pair removing the need for double pointer and heap alloc/delete of the iterators.
* disable pruning by default (it's a bit quicker to not do this)
* update expected test results
The updated VF2 code can return symmetric results in a different order
than we were getting previously. The results are still correct, but they
change some of the downstream things that don't do symmetrization
* update expected java results
* Added rankAtoms to ROMol wrapper and added Java test case
* Added missing argument to rankMolAtoms call in wrapper
* Update ROMol.i
* Update ROMol.i
Removed circular reference to Canon
* Update ROMol.i
* Update ROMol.i
* Update SmilesTests.java
* minor stuff to force the CI builds to run again
* Update the test to match the current code
* updated atomic radii to follow the Blue Obelisk Data Repository
Ubuntu package bodr version 10-1; radii are from file
/usr/share/bodr/elements.xml
* typo
* use 2.0 as default VDW radius instead of 1.7
for elements missing from the Blue Obelisk Data Repository
* Document the atomic_data
* update expected test results
* update java tests
* allow a bit more slop when comparing confs
For cross-platform stability
* Wrapper fixes: Tversky for De Morgan and java byte functions for ExplicitBitVect
* Wrapper fixes: Tversky for De Morgan and java byte functions for ExplicitBitVect
* Move RDBoostStreams to RDStreams
* RDBoostStreams->RDStreams
* RDBoostStreams->RDStreams
* Wrap SWIG (with Java test)
* Fix missing declaration
* Use the file that already exists
* Revert to original version
* Revert to CXSMiles version
* Update boost version
* Remove redundant code
* Add zlib
* check for win32
* FileParsers now builds static on windows
* change to make the SWig builds work on windows
* add the wrapper. Still needs tests
* first rgd java wrapper test, does not pass
* get static builds working on windows
* 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
* short test file for MolVS standardize_sm
* short test file for MolVS fragment
* short test file for MolVS metals
* short test file for MolVS normalize
* short test file for MolVS reionize
* short test file for MolVS tautomer
* short test file for MolVS validate
* long test file for MolVS standardize smiles
* long test file for MolVS fragment
* long test file for MolVS metals
* long test file for MolVS normalize
* long test file for MolVS reionize
* long test file for MolVS tautomer
* long test file for MolVS validate
* Unit tests for MolVS steps
* dropping support for Python2
* molvs/__init__.py
* molvs/charge.py
* molvs/errors.py
* molvs/fragment.py
* molvs/metal.py
* molvs/normalize.py
* molvs/resonance.py
* molvs/standardize.py
* molvs/tautomer.py
* molvs/utils.py
* molvs/validate.py
* molvs/validations.py
* molvs/cli.py
* adapted and renamed molvs/cli.py to work within $RDBASE/Contrib/MolVS/
* setup MolStandardize directories, source with empty cleanup function, header, CMake files
* corrections to empty source, header and test1.cpp
* adding empty functions and initializers to MolStandardize
* empty Metal source, header and added test
* added most of Metal.cpp functionality and made some more tests
* empty functions and initializers to Normalize
* empty functions and initializers to Validate
* added most code for RDKitDefault mode, along with some tests
* restructure for abstract base class ValidateMethod
* written in isNoneValidation for MolVSValidation
* took out isNoneValidation, put in noAtomValidation, neutralValidation, isotopeValidation for MolVSValidation
* added in AllowedAtoms
* added in disallowedAtoms
* corrections to Validate
* added code for FragmentRemover
* extended fragment functionality to include choose largest fragment, added in tests for fragment catalog, fragment remover. Also added fragmentValidation method in MolStandardize
* added another test to testValidate test_fragment
* corrections to fragment
* corrections to Metal
* added code for Normalize
* added normalize member function to MolStandardize and added tests
* added multi fragment functionality to Normalize.cpp and additional tests
* TransformCatalog
* tests for Normalize.cpp
* first bit of cleanup
* added most of Charge functionality and some tests
* some corrections to Charge.cpp and some more tests to testCharge.cpp
* corrections to Charge.cpp
* start of Tautomer Enumerate with some tests
* added BondType option to Tautomer Enumeration
* correcting for some memory leakage
* a few alterations to formatting
* sorting out some memory leaks
* sorting out some memory leaks
* some corrections for PCS test set
* redo tests with updated RDKit
* fixing memory leak
* more fixes after 100kPCS set testing
* using tab as delimiter in CSVs rather than comma
* tutorial for MolStandardize
* still working on Tautomer enumeration
* deleted some empty tests
* starting writing tautomer canonicalize
* rename test_data -> data (the source still needs to be updated)
* automatic source reformatting
* adjust to directory rename
* move the fragment catalog test into the MolStandardize directory
do not create separate library for FragmentCatalog
* stop building separate libraries for the catalogs
* move the CleanupParameters into the MolStandardize namespace
* first pass at python wrapper
* move the py module to the correct dir;
add some python tests;
add standardizeSmiles to python wrapper
* disabling the compareMolVSTest since that requires command line arguments to run
* get this building on windows
* put the python lib in the right place
* further work on python wrapper for rdMolStandardize
* added get and set functions to Metal and wrapped them
* added get and set functions to Metal and wrapped them
* changed construstor of Reionizer class and input args for reionize, wrapped this default
* overload Reionizer constructor so user can input own AcidBaseFile from python
* added Uncharger class to Charge and added test for Uncharger
* wrapped Fragment, fixed some memory leakage, changed some args and return types, added some tests
* wrapped Normalized and changed how Normalizer class is initiated
* changing MolVSValidation structure so user can choose which MolVS submethod they want
* starting to write Wrap for Validate
* now it compiles with Wrap/Validate.cpp
* a couple refactorings around validate
* move the validate code into the rdMolStandardize module
* make sure a valid pointer is returned for standardizeSmiles
* rdMolStandardize.MolVSValidation done and tests added
* half way through AllowedAtomsValidation
* finished AllowedAtomsValidation and DisallowedAtomsValidation
* moved charge, fragment, metal, normalize into the rdMolStandardize module
* changed tutorial to use wrapped code
* added copyrights
* added copyrights
* move the data files
* modify source files to adjust to the move
* added validateSmiles functionality
* removed std::cout
* redid some of the 100k PCS tests
* working on the tutorial
* adding some documentation
* deleting some comment lines
* some changes after pull review
* More changes after pull review
* start of trying to make java wrap
* remove some warnings, add some questions
* additional warning removals, a bit more reporting
* some test cleanups
* enable testing of the java code
* first pass, does not yet actually work
* pass2, same problems
* pass2, same problems
* another test
* new tests; bugfix
* move the code out to a header
* add a double bond example
* enable auto-downloads of the code
* move the function to its own namespace
* first pass at a basic python wrapper
* change coordgen commit used
* try supporting bond stereo; does not currently work
* cis/trans seems to now work.
* first pass at templates; needs testing
* use the fixed flag too
* need mol align
* expand test
* initial pass at python wrapper for template
* simplify tests
* add an option to directly use a substructure match for alignment
* scaling
* add #define
* Define a cache setting for RDK_COORDGEN_LIBS to allow these to be used in other packages
* return the conformer id from addCoords
* Make CoordGen the default when it’s available.
This is a backup commit… the tests don’t even come close to passing.
* add some debugging options for a bit
* add alignment step to testing when using non-fixed coords
* Add global to allow use of CoordGen to be disabled
get the basic depictor tests working
* make coordgen the default when it is available
* make sure things continue to work when coordgen is disabled
* get windows builds working
* mods to get this building on windows.
something is screwy with the fileParsersTest1
* no need to generate coords for the 1K C string
* fix java wrappers
* works on linux
* update the (stupid) way dependencies were handled on windows.
this allows a lot of cleanup of cmake files (still more to do)
the linux build is unlikely to work due to the way _statics aren't handled
* docs
* extend forceRDKit applicability
* switch coordgen version
* try using templates
* try to get the template dir finding reasonably robust w.r.t. conda install
* continuing to iterate on the way the template file is installed
* fix a problem caused by the merge
* remove test that should never have been checked in
* update expected results for cartridge tests
* switch back to using the RDKit as the default coordinate generator
* Added getAlignmentTransform to ROMol.i to expose in Java SWIG wrapper
* Added missing argument
Added missing argument to call to getAlignmentTransform causing build failure
* Added test case for getAlignmentTransform
* Update AlignTests.java
* Update AlignTests.java
* Update AlignTests.java
* initial version; no actual testing yet
* start on tests
* rename seed->randomSeed; add tests
* add support in java wrapper
* add support in python wrapper
* initial version; no actual testing yet
* start on tests
* rename seed->randomSeed; add tests
* add support in java wrapper
* add support in python wrapper
* yapf
* document the parameter object;
introduce pre-defined const objects for ETDG, ETKDG, and KDG
* this is why we write tests
* swig did not like the initialization in the header file
