* Extend RDKit::MolStandardize with a validation and standardization Pipeline
* suggested changes
* apply clang-format
* apply yapf
* MolStandardize::FeaturesValidation optionally disallow dative bonds
* add allowDativeBondType to MolStandardize::PipelineOptions
* apply clang-format
* make the API of other validation classes more consistent with MolStandardize::FeaturesValidation
* apply clang-format
* PipelineStage to enum class
remove virtual functions from Pipeline class
be explicit about enums
* light refactoring to avoid what I think is an unnecessary call to `parse`
* a bit of modernization
* make the pipeline configurable
* make parse and serialize configurable too
* switch to storing pipeline stages using uints
* add a simple test for providing a pipeline
* update pointer alignment for clang-format
* test modifying the parser and serializer
* update swig requirement
* changes in response to review
* changes in response to review
* rename PipelineResult's *MolBlock members to *MolData
* upgrade swig to 4.2 in the CI environments
* add a few missing export directives
---------
Co-authored-by: greg landrum <greg.landrum@gmail.com>
* refactoring of the Uncharger class
* optionally limit the Uncharger to only change the protonation state
* changes in response to review
* refactor the handling of positively charged atoms
* changes in response to review
* changes in response to review
* Revert "changes in response to review"
This reverts commit d42e1286d5.
* changes in response to review
* Add a 'force' option to MolStandardize::Uncharger
* update comment
* add more test cases exercising MolStandardize::Uncharger
* fix the neutralization of surplus negative charges
* changes in response to review
* Add a test case for MolStandardize::Uncharger
* refactor the neutralization of negative charges in MolStandardize::Uncharger
* reionizer and uncharger and normalizer can now operate in place
* add removeUnmatchedAtoms argument to in-place version of runReactant
When set to false atoms which are not explicitly removed by the reaction are preserved
* Fix a case where transforms were incorrectly updating atomic numbers
* add more inplace operations to MolStandardize
* support those in the Python layer
* support inplace for the rest of the python wrappers
* move a few more functions over to the inplace code
* Swap to using a data structure for default normalization parameters
* bring the default fragment data into the code too
* cleanup
* add reionizer parameters via data
change fragment parse failures to ValueErrorExceptions
* tautomer parameters in the code
* got a little over-enthusiastic in that last cleanup
* use boost::flyweight to cache normalization and charge data params
* a bit more cleanup
* support reading params from JSON
* fragments from JSON
single-call for fragment removal
* add a one-liner for the canonical tautomer
* quick refactor
* Fixes#4115
* complete the parents
* docs
* move the definitions to a namespace and make them const
* see if switching to c++14 fixes the CI compile problems with g++ 5.5
* somewhat uglier way of solving the initalizer list problem
* Make MetalDisconnector more robust against metallorganics
* - fixed misbehavior with radicals
- added tests
- code cleanup
* - fixed MetalDisconnector with dative bonds
- removed pointless test
* - refactoring to remove code duplication
- make sure that inorganic acids are correctly neutralized
* - added note about change in behaviour of Uncharger::uncharge()
* stop neutralizing zwitterionic S+ species
* add a test for that recent change
I also did a bit of modernization to the test case we're using
(because the old style really burns my eyes now)
and disabled the rdApp.info log so as not to fill the console
with useless info while running the test
* improved performance
Co-authored-by: greg landrum <greg.landrum@gmail.com>
* stop returning local memory in exceptions
* remove a couple unnecessary copies in loops
* fix a bug in the way the default MMFF aromatic parameters are constructed
* remove a bunch of loop-variable warnings
* remove a bunch of clang warnings
* disable clang warnings in python wrappers
* remove some warnings when building the python wrappers
* run clang-tidy with readability-braces-around-statements
clang-format the results
clean up all the parts that clang-tidy-8 broke
* fix problem on windows
* a round of cleanups courtesy of PVS studio
* add a test to make sure that a warning is a false alarm
* bug fix
* Fix a UFF bug
* more PVS studio cleanups
* next round of PVS studio cleanups
* completely remove the chances for that bug
* changes in response to review
* add an additional test
+ a bit of reformatting that snuck in
* Fixes#2383 (tests coming in the next commit)
Minor typo fix
Fixes a "bug" in one of the default transforms
* Adds support for directly providing normalization parameter data
instead of requiring the use of a text file.
* allow fragment removers to be initialized with string data
* remove unicode
* allow the reionizer to be initialized from a stream
* modify the uncharger to be use a canonical atom ordering
* add doCanonical cleanup parameter
make canonical ordering the default
document the change
* Add neutralization of additonal negative groups (not just acids).
This may not be the right thing to do.
* expose the new parameter to python
* changes in 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
