* add AtomValenceException
* refactor a bit and add KekulizeException
* add copy ctor and copy() method
* add detectChemistryProblems
* add getType() method
want to be able to get the type of the exception without requiring doing a bunch of dynamic casts
* first pass at exception inheritance/translation
needs some cleanup and expansion, but this does pass all tests.
* cleanup and finish the python wrappers for the new exceptions
* make sure things are truly polymorphic
* wrap shared_ptrs of the new exception types
* expose DetectChemistryProblems()
* get the java wrappers building again
* transfer those changes to the c# wrapper
* add detectChemistryProblems()
and deal with the fun fun exception inheritance things that ensue
* response to review
* 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
* 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
* add a couple test files
* backup
* first pass at some theory documentatin
* it's a draft
* Update enhanced stereochemistry documentation
Adds initial target use case and caveats about the tentative
nature of the current implementation.
* Support read/write of molfile enhanced stereochemistry
This includes reading and writing of enhanced stereochemistry
from v3000 molfiles (sdf). Enhanced stereochemistry encodes
the relative configuration of stereocenters, allowing
representation of racemic mixtures and compounds with
unknown absolute stereochemistry.
It does not include:
* Python wrapping
* invalidation of the enhanced stereochemistry
* use of enhanced stereochemistry in search
* depiction of enhanced stereochemistry.
* Update to reflect changes from #1971
* change names of enum elements to allow compilation in VS2017
I think it's also clearer to do things this way
* Addressed most review comments.
* Run missed test "testEnhancedStereoChemistry"
* In tests, added size checks to group equality checks
* Updated copyright statements
* Deleted mol created for a test
* Use perfect forwarding in RWMol::setStereoGroups()
* use references for stereo groups that are checked in write and pickle
* Updated stereogroup.h in hopes of fixing compilation on Windows.
* clang-format
* try allowing a switch to boost regex and requiring it for g++-4.8
* do a better job of that
* typo
* Code review comments. Updated Copyright notice.
* When an atom is deleted, delete stereo groups containing it.
Also updates StereoGroup toUse accessors instead of
constant member attributes. This allows move of StereoGroups.
* RDKit style guide
* Add header required on Windows.
* get the SWIG wrappers to build
* this is a rough first pass, needs to be finished and is a strong argument for changing the names of some of the #defines that are currently used
* rationalize the rest of the #defines
add something to the release notes about this
* Fixes csharp build for 64 bit systems
* Need to support make and make install stages
* switch to an alternate strategy and get it working for the java wrappers too
this now builds for me on 64bit win10 with MSVC14
* add missing files from that last commit
* Hopefully fixes unix and osx builds while maintaining msvc builds
* Fixes mono builds, removes python check
* Adds RDAny (smaller generic holder) Updates all used dictionaries
This is an API compliant version of the current rdany system,
but uses a lot less memory in practice.
* Removes code duplication
* Converts CHECK_INVARIANT to TEST_ASSERT
* Fixes DoubleTag issue
* Adds Bool to DoubleMagic implementation
* Removes reference to property pickler
