rdkit/Code/GraphMol/MolStandardize/test2.cpp

//
//  Copyright (C) 2018 Susan H. Leung
//
//   @@ All Rights Reserved @@
//  This file is part of the RDKit.
//  The contents are covered by the terms of the BSD license
//  which is included in the file license.txt, found at the root
//  of the RDKit source tree.
//
// file used to test memory leakage

#include "MolStandardize.h"
#include "Validate.h"
#include "Metal.h"
#include "Normalize.h"
#include "Charge.h"
#include <GraphMol/RDKitBase.h>
#include <RDGeneral/Invariant.h>
#include <GraphMol/SmilesParse/SmilesParse.h>
#include <GraphMol/SmilesParse/SmilesWrite.h>
#include <GraphMol/ROMol.h>

#include <iostream>

using namespace RDKit;
using namespace MolStandardize;

void test1() {
  BOOST_LOG(rdInfoLog) << "-----------------------\n test1" << std::endl;

  MolStandardize::CleanupParameters params;

  std::string smi1 = "C1=CC=CC=C1";
  //	std::shared_ptr<RWMol> m1( SmilesToMol(smi1) );
  std::unique_ptr<RWMol> m1(SmilesToMol(smi1));
  std::unique_ptr<RWMol> res(cleanup(*m1, params));
  TEST_ASSERT(MolToSmiles(*res) == "c1ccccc1");

  //	std::string smi1 = "CCC(=O)O[Na]";
  ////	std::shared_ptr<RWMol> m1( SmilesToMol(smi1) );
  //	RWMol *m1 = SmilesToMol(smi1);
  //	cleanup(*m1, params);
  //	TEST_ASSERT(MolToSmiles(*m1) == "CCC(=O)[O-].[Na+]");
  BOOST_LOG(rdInfoLog) << "Finished" << std::endl;
}

void testMetal() {
  BOOST_LOG(rdInfoLog) << "-----------------------\n test metal" << std::endl;
  MetalDisconnector md;

  std::string smi1 = "CCC(=O)O[Na]";
  std::unique_ptr<RWMol> m1(SmilesToMol(smi1));
  TEST_ASSERT(m1);
  md.disconnect(*m1);
  TEST_ASSERT(MolToSmiles(*m1) == "CCC(=O)[O-].[Na+]");
  BOOST_LOG(rdInfoLog) << "Finished" << std::endl;
}

void testValidate() {
  BOOST_LOG(rdInfoLog) << "-----------------------\n test validate"
                       << std::endl;
  RDKitValidation vm;

  // testing RDKitDefault
  std::string smi1 = "CO(C)C";
  std::unique_ptr<ROMol> m1(SmilesToMol(smi1, 0, false));
  std::vector<ValidationErrorInfo> errout1 = vm.validate(*m1, true);
  for (auto &query : errout1) {
    std::string msg = query.what();
    TEST_ASSERT(msg ==
                "INFO: [ValenceValidation] Explicit valence for atom # 1 O, 3, "
                "is greater than permitted");
  }
  //**************************
  MolVSValidation vm2;
  std::string smi2 = "O=C([O-])c1ccccc1";
  std::unique_ptr<ROMol> m2(SmilesToMol(smi2, 0, false));
  std::vector<ValidationErrorInfo> errout2 = vm2.validate(*m2, true);
  for (auto &query : errout2) {
    std::string msg = query.what();
    TEST_ASSERT(msg ==
                "INFO: [NeutralValidation] Not an overall neutral system (-1)");
  }
  // ************************
  std::vector<unsigned int> atoms = {6, 7, 8};
  std::vector<std::shared_ptr<Atom>> atomList;

  for (auto &atom : atoms) {
    std::shared_ptr<Atom> a(new Atom(atom));
    atomList.push_back(a);
  }

  AllowedAtomsValidation vm3(atomList);

  std::string smi3 = "CC(=O)CF";
  std::unique_ptr<ROMol> m3(SmilesToMol(smi3));
  std::vector<ValidationErrorInfo> errout3 = vm3.validate(*m3, true);
  for (auto &query : errout3) {
    std::string msg = query.what();
    TEST_ASSERT(
        msg ==
        "INFO: [AllowedAtomsValidation] Atom F is not in allowedAtoms list");
  }
  //********************************
  std::vector<unsigned int> atoms2 = {9, 17, 35};
  std::vector<std::shared_ptr<Atom>> atomList2;

  for (auto &atom : atoms2) {
    std::shared_ptr<Atom> a(new Atom(atom));
    atomList2.push_back(a);
  }

  DisallowedAtomsValidation vm4(atomList2);

  std::string smi4 = "CC(=O)CF";
  std::unique_ptr<ROMol> m4(SmilesToMol(smi4));
  std::vector<ValidationErrorInfo> errout4 = vm4.validate(*m4, true);
  for (auto &query : errout4) {
    std::string msg = query.what();
    TEST_ASSERT(
        msg ==
        "INFO: [DisallowedAtomsValidation] Atom F is in disallowedAtoms list");
  }
  //********************************
  MolVSValidation vm5;

  // testing MolVSValidation fragmentValidation
  // FragmentValidation should identify 1,2-dichloroethane.
  std::string smi5 = "ClCCCl.c1ccccc1O";
  std::unique_ptr<ROMol> m5(SmilesToMol(smi5, 0, false));
  std::vector<ValidationErrorInfo> errout5 = vm5.validate(*m5, true);
  for (auto &query : errout5) {
    std::string msg = query.what();
    TEST_ASSERT(msg ==
                "INFO: [FragmentValidation] 1,2-dichloroethane is present");
  }
  BOOST_LOG(rdInfoLog) << "Finished" << std::endl;
}

void testCharge() {
  BOOST_LOG(rdInfoLog) << "-----------------------\n test charge" << std::endl;

  Reionizer reionizer;

  // Test table salt.
  std::string smi1 = "[Na].[Cl]";
  std::shared_ptr<ROMol> m1(SmilesToMol(smi1));
  ROMOL_SPTR reionized(reionizer.reionize(*m1));
  TEST_ASSERT(MolToSmiles(*reionized) == "[Cl-].[Na+]");
  //*******************************
  MolStandardize::CleanupParameters params;
  // initialize CleanupParameters with preferOrganic=true
  MolStandardize::CleanupParameters params_preferorg;
  params_preferorg.preferOrganic = true;

  // Test neutralization of ionized acids and bases.
  std::string smi2 = "C(C(=O)[O-])(Cc1n[n-]nn1)(C[NH3+])(C[N+](=O)[O-])";
  std::unique_ptr<RWMol> m2(SmilesToMol(smi2));
  std::unique_ptr<RWMol> res2(MolStandardize::chargeParent(*m2, params));
  TEST_ASSERT(MolToSmiles(*res2) == "NCC(Cc1nn[nH]n1)(C[N+](=O)[O-])C(=O)O");
  //**********************************
  // Testing MolStandardize::reionize

  std::string smi3 = "C1=C(C=CC(=C1)[S]([O-])=O)[S](O)(=O)=O";
  std::unique_ptr<RWMol> m3(SmilesToMol(smi3));
  std::unique_ptr<RWMol> res3(MolStandardize::reionize(m3.get(), params));
  TEST_ASSERT(MolToSmiles(*res3) == "O=S(O)c1ccc(S(=O)(=O)[O-])cc1");
  BOOST_LOG(rdInfoLog) << "Finished" << std::endl;
}

void testNormalize() {
  BOOST_LOG(rdInfoLog) << "-----------------------\n test normalize"
                       << std::endl;

  Normalizer normalizer;

  // Test sulfoxide normalization.
  std::string smi1 = "CS(C)=O";
  std::shared_ptr<ROMol> m1(SmilesToMol(smi1));
  ROMOL_SPTR normalized(normalizer.normalize(*m1));
  TEST_ASSERT(MolToSmiles(*normalized) == "C[S+](C)[O-]");

  // normalize sulfone.
  std::string smi2 = "C[S+2]([O-])([O-])C";
  std::shared_ptr<ROMol> m2(SmilesToMol(smi2));
  ROMOL_SPTR normalized2(normalizer.normalize(*m2));
  TEST_ASSERT(MolToSmiles(*normalized2) == "CS(C)(=O)=O");
  BOOST_LOG(rdInfoLog) << "Finished" << std::endl;
}

int main() {
  test1();  // cleanup test
  testMetal();
  testValidate();
  testCharge();  // TODO
  testNormalize();
  return 0;
}