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//
// 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::shared_ptr<RWMol> m1( SmilesToMol(smi1) );
RWMOL_SPTR m = "C1=CC=CC=C1"_smiles;
RWMOL_SPTR res(cleanup(*m, 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;
RWMOL_SPTR m = "CCC(=O)O[Na]"_smiles;
TEST_ASSERT(m);
md.disconnect(*m);
TEST_ASSERT(MolToSmiles(*m) == "CCC(=O)[O-].[Na+]");
BOOST_LOG(rdInfoLog) << "Finished" << std::endl;
}
void testValidate() {
BOOST_LOG(rdInfoLog) << "-----------------------\n test validate"
<< std::endl;
// testing RDKitDefault
{
RDKitValidation vm;
std::string smi = "CO(C)C";
RWMOL_SPTR m(SmilesToMol(smi, 0, false));
std::vector<ValidationErrorInfo> errout = vm.validate(*m, true);
for (auto &query : errout) {
std::string msg = query.what();
TEST_ASSERT(
msg ==
"INFO: [ValenceValidation] Explicit valence for atom # 1 O, 3, "
"is greater than permitted");
}
}
//**************************
{
MolVSValidation vm;
std::string smi = "O=C([O-])c1ccccc1";
RWMOL_SPTR m(SmilesToMol(smi, 0, false));
std::vector<ValidationErrorInfo> errout = vm.validate(*m, true);
for (auto &query : errout) {
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 vm(atomList);
RWMOL_SPTR m = "CC(=O)CF"_smiles;
std::vector<ValidationErrorInfo> errout = vm.validate(*m, true);
for (auto &query : errout) {
std::string msg = query.what();
TEST_ASSERT(
msg ==
"INFO: [AllowedAtomsValidation] Atom F is not in allowedAtoms list");
}
}
//********************************
{
std::vector<unsigned int> atoms = {9, 17, 35};
std::vector<std::shared_ptr<Atom>> atomList;
for (auto &atom : atoms) {
std::shared_ptr<Atom> a(new Atom(atom));
atomList.push_back(a);
}
DisallowedAtomsValidation vm(atomList);
RWMOL_SPTR m = "CC(=O)CF"_smiles;
std::vector<ValidationErrorInfo> errout = vm.validate(*m, true);
for (auto &query : errout) {
std::string msg = query.what();
TEST_ASSERT(msg ==
"INFO: [DisallowedAtomsValidation] Atom F is in "
"disallowedAtoms list");
}
}
//********************************
// testing MolVSValidation fragmentValidation
// FragmentValidation should identify 1,2-dichloroethane.
{
MolVSValidation vm;
std::string smi = "ClCCCl.c1ccccc1O";
RWMOL_SPTR m(SmilesToMol(smi, 0, false));
std::vector<ValidationErrorInfo> errout = vm.validate(*m, true);
for (auto &query : errout) {
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.
{
RWMOL_SPTR m = "[Na].[Cl]"_smiles;
ROMOL_SPTR reionized(reionizer.reionize(*m));
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.
{
RWMOL_SPTR m = "C(C(=O)[O-])(Cc1n[n-]nn1)(C[NH3+])(C[N+](=O)[O-])"_smiles;
RWMOL_SPTR res(MolStandardize::chargeParent(*m, params));
TEST_ASSERT(MolToSmiles(*res) == "NCC(Cc1nn[nH]n1)(C[N+](=O)[O-])C(=O)O");
}
//**********************************
// Testing MolStandardize::reionize
{
RWMOL_SPTR m = "C1=C(C=CC(=C1)[S]([O-])=O)[S](O)(=O)=O"_smiles;
RWMOL_SPTR res(MolStandardize::reionize(m.get(), params));
TEST_ASSERT(MolToSmiles(*res) == "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.
{
RWMOL_SPTR m = "CS(C)=O"_smiles;
ROMOL_SPTR normalized(normalizer.normalize(*m));
TEST_ASSERT(MolToSmiles(*normalized) == "C[S+](C)[O-]");
}
// normalize sulfone.
{
RWMOL_SPTR m = "C[S+2]([O-])([O-])C"_smiles;
ROMOL_SPTR normalized(normalizer.normalize(*m));
TEST_ASSERT(MolToSmiles(*normalized) == "CS(C)(=O)=O");
BOOST_LOG(rdInfoLog) << "Finished" << std::endl;
}
}
int main() {
test1(); // cleanup test
testMetal();
testValidate();
testCharge(); // TODO
testNormalize();
return 0;
}
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