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956fdf268c
* 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
92 lines
3.2 KiB
C++
92 lines
3.2 KiB
C++
//
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// Copyright (C) 2018 Susan H. Leung
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//
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// @@ All Rights Reserved @@
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// This file is part of the RDKit.
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// The contents are covered by the terms of the BSD license
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// which is included in the file license.txt, found at the root
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// of the RDKit source tree.
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//
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#include <GraphMol/MolStandardize/TransformCatalog/TransformCatalogParams.h>
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#include <GraphMol/MolStandardize/TransformCatalog/TransformCatalogUtils.h>
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#include "Normalize.h"
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#include <RDGeneral/Invariant.h>
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#include <GraphMol/RDKitBase.h>
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#include <GraphMol/ROMol.h>
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#include <GraphMol/SmilesParse/SmilesParse.h>
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#include <GraphMol/SmilesParse/SmilesWrite.h>
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#include <GraphMol/FileParsers/FileParsers.h>
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#include <RDGeneral/FileParseException.h>
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#include <GraphMol/FileParsers/MolSupplier.h>
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#include <GraphMol/MolStandardize/MolStandardize.h>
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#include <iostream>
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#include <fstream>
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using namespace RDKit;
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using namespace MolStandardize;
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void test1() {
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BOOST_LOG(rdInfoLog) << "-----------------------\n test1" << std::endl;
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std::string smi1, smi2, smi3, smi4, smi5, smi6, smi7;
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Normalizer normalizer;
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// Test sulfoxide normalization.
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smi1 = "CS(C)=O";
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std::shared_ptr<ROMol> m1(SmilesToMol(smi1));
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ROMOL_SPTR normalized(normalizer.normalize(*m1));
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TEST_ASSERT(MolToSmiles(*normalized) == "C[S+](C)[O-]");
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// Test sulfone
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smi2 = "C[S+2]([O-])([O-])O";
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std::shared_ptr<ROMol> m2(SmilesToMol(smi2));
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ROMOL_SPTR normalized2(normalizer.normalize(*m2));
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TEST_ASSERT(MolToSmiles(*normalized2) == "CS(=O)(=O)O");
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// Test 1,3-separated charges are recombined.
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smi3 = "CC([O-])=[N+](C)C";
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std::shared_ptr<ROMol> m3(SmilesToMol(smi3));
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ROMOL_SPTR normalized3(normalizer.normalize(*m3));
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TEST_ASSERT(MolToSmiles(*normalized3) == "CC(=O)N(C)C");
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// Test 1,3-separated charges are recombined.
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smi4 = "C[n+]1ccccc1[O-]";
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std::shared_ptr<ROMol> m4(SmilesToMol(smi4));
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ROMOL_SPTR normalized4(normalizer.normalize(*m4));
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TEST_ASSERT(MolToSmiles(*normalized4) == "Cn1ccccc1=O");
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// Test a case where 1,3-separated charges should not be recombined.
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smi5 = "CC12CCCCC1(Cl)[N+]([O-])=[N+]2[O-]";
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std::shared_ptr<ROMol> m5(SmilesToMol(smi5));
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ROMOL_SPTR normalized5(normalizer.normalize(*m5));
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TEST_ASSERT(MolToSmiles(*normalized5) ==
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"CC12CCCCC1(Cl)[N+]([O-])=[N+]2[O-]");
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// Test 1,5-separated charges are recombined.
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smi6 = "C[N+](C)=C\C=C\[O-]";
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std::shared_ptr<ROMol> m6(SmilesToMol(smi6));
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ROMOL_SPTR normalized6(normalizer.normalize(*m6));
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TEST_ASSERT(MolToSmiles(*normalized6) == "CN(C)C=CC=O");
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// Test a case where 1,5-separated charges should not be recombined.
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smi7 = "C[N+]1=C2C=[N+]([O-])C=CN2CCC1";
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std::shared_ptr<ROMol> m7(SmilesToMol(smi7));
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ROMOL_SPTR normalized7(normalizer.normalize(*m7));
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TEST_ASSERT(MolToSmiles(*normalized7) == "C[N+]1=C2C=[N+]([O-])C=CN2CCC1");
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// Failed on 1k normalize test sanitizeMol step
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std::string smi8 = "O=c1cc([O-])[n+](C2OC(CO)C(O)C2O)c2sccn12";
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std::shared_ptr<ROMol> m8(SmilesToMol(smi8));
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ROMOL_SPTR normalized8(normalizer.normalize(*m8));
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TEST_ASSERT(MolToSmiles(*normalized8) ==
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"O=c1cc([O-])[n+](C2OC(CO)C(O)C2O)c2sccn12");
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BOOST_LOG(rdInfoLog) << "Finished" << std::endl;
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}
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int main() {
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test1();
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return 0;
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}
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