1 Commits

Author	SHA1	Message	Date
Susan Leung	956fdf268c	Dev/GSOC2018_MolVS_Integration (#2002) ... * 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	2018-09-28 11:24:25 +02:00