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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.
//
#include <RDGeneral/test.h>
#include <GraphMol/MolStandardize/FragmentCatalog/FragmentCatalogParams.h>
#include <GraphMol/MolStandardize/FragmentCatalog/FragmentCatalogUtils.h>
#include <GraphMol/MolStandardize/Fragment.h>
#include <RDGeneral/Invariant.h>
#include <GraphMol/RDKitBase.h>
#include <GraphMol/ROMol.h>
#include <GraphMol/SmilesParse/SmilesParse.h>
#include <GraphMol/SmilesParse/SmilesWrite.h>
#include <GraphMol/FileParsers/FileParsers.h>
#include <RDGeneral/FileParseException.h>
#include <GraphMol/FileParsers/MolSupplier.h>
#include <GraphMol/MolStandardize/MolStandardize.h>
#include <iostream>
#include <fstream>
using namespace RDKit;
using namespace MolStandardize;
void test2() {
BOOST_LOG(rdInfoLog) << "-----------------------\n test2" << std::endl;
std::string smi1, smi2, smi3, smi4, smi5, smi6, smi8, smi9, smi10, smi11,
smi12;
// testing parsing of fragment catalog
// std::string rdbase = getenv("RDBASE");
// std::string fgrpFile = rdbase +
// "/Code/GraphMol/MolStandardize/FragmentCatalog/"
// "data/fragmentPatterns.txt";
// auto* fparams = new FragmentCatalogParams(fgrpFile);
// unsigned int numfg = fparams->getNumFuncGroups();
// TEST_ASSERT(fparams->getNumFuncGroups() == 61);
//
// FragmentCatalog fcat(fparams);
FragmentRemover fragremover;
// single salt removal
smi1 = "CN(C)C.Cl";
std::shared_ptr<ROMol> m1(SmilesToMol(smi1));
std::shared_ptr<ROMol> remove(fragremover.remove(*m1));
TEST_ASSERT(MolToSmiles(*remove) == "CN(C)C");
// double salt removal
smi2 = "CN(C)C.Cl.Cl.Br";
std::shared_ptr<ROMol> m2(SmilesToMol(smi2));
std::shared_ptr<ROMol> remove2(fragremover.remove(*m2));
TEST_ASSERT(MolToSmiles(*remove2) == "CN(C)C");
// FragmentPatterns should match entire fragments only,
// matches within larger fragments should be left
smi3 = "CN(Br)Cl";
std::shared_ptr<ROMol> m3(SmilesToMol(smi3));
std::shared_ptr<ROMol> remove3(fragremover.remove(*m3));
TEST_ASSERT(MolToSmiles(*remove3) == "CN(Cl)Br");
// FragmentPatterns should match entire fragments only,
// matches within larger fragments should be left
smi4 = "CN(Br)Cl.Cl";
std::shared_ptr<ROMol> m4(SmilesToMol(smi4));
std::shared_ptr<ROMol> remove4(fragremover.remove(*m4));
TEST_ASSERT(MolToSmiles(*remove4) == "CN(Cl)Br");
// charged salts
smi5 = "C[NH+](C)(C).[Cl-]";
std::shared_ptr<ROMol> m5(SmilesToMol(smi5));
std::shared_ptr<ROMol> remove5(fragremover.remove(*m5));
TEST_ASSERT(MolToSmiles(*remove5) == "C[NH+](C)C");
// Last match should be left.
smi6 = "CC(=O)O.[Na]";
std::shared_ptr<ROMol> m6(SmilesToMol(smi6));
std::shared_ptr<ROMol> remove6(fragremover.remove(*m6));
TEST_ASSERT(MolToSmiles(*remove6) == "CC(=O)O");
// Last match should be removed.
FragmentRemover fr_noleavelast(defaultCleanupParameters.fragmentFile, false);
std::shared_ptr<ROMol> remove7(fr_noleavelast.remove(*m6));
TEST_ASSERT(MolToSmiles(*remove7) == "");
// Multiple identical last fragments should all be left.
smi8 = "Cl.Cl";
std::shared_ptr<ROMol> m8(SmilesToMol(smi8));
std::shared_ptr<ROMol> remove8(fragremover.remove(*m8));
TEST_ASSERT(MolToSmiles(*remove8) == "Cl.Cl");
// Last match should be left.
smi9 = "[Na+].OC(=O)Cc1ccc(CN)cc1.OS(=O)(=O)C(F)(F)F";
std::shared_ptr<ROMol> m9(SmilesToMol(smi9));
std::shared_ptr<ROMol> remove9(fragremover.remove(*m9));
TEST_ASSERT(MolToSmiles(*remove9) == "NCc1ccc(CC(=O)O)cc1");
// 1,4-Dioxane should be removed..
smi10 = "c1ccccc1O.O1CCOCC1";
std::shared_ptr<ROMol> m10(SmilesToMol(smi10));
std::shared_ptr<ROMol> remove10(fragremover.remove(*m10));
TEST_ASSERT(MolToSmiles(*remove10) == "Oc1ccccc1");
// Benzene should be removed.
smi11 = "c1ccccc1.CCCBr";
std::shared_ptr<ROMol> m11(SmilesToMol(smi11));
std::shared_ptr<ROMol> remove11(fragremover.remove(*m11));
TEST_ASSERT(MolToSmiles(*remove11) == "CCCBr");
// Various fragments should be removed.
smi12 = "CC(NC1=CC=C(O)C=C1)=O.CCCCC.O.CCO.CCCO.C1CCCCC1.C1CCCCCC1";
std::shared_ptr<ROMol> m12(SmilesToMol(smi12));
std::shared_ptr<ROMol> remove12(fragremover.remove(*m12));
TEST_ASSERT(MolToSmiles(*remove12) == "CC(=O)Nc1ccc(O)cc1");
BOOST_LOG(rdInfoLog) << "Finished" << std::endl;
}
void test_largest_fragment() {
BOOST_LOG(rdInfoLog) << "-----------------------\n test largest fragment"
<< std::endl;
std::string smi1, smi2, smi3, smi4, smi5, smi6, smi7, smi8, smi9, smi10;
LargestFragmentChooser lfragchooser;
LargestFragmentChooser lfrag_preferOrg(true);
MolStandardize::CleanupParameters params =
MolStandardize::CleanupParameters();
// Multiple organic fragments of different sizes.
smi2 = "O=C(O)c1ccccc1.O=C(O)c1ccccc1.O=C(O)c1ccccc1";
// std::shared_ptr<ROMol> m2( SmilesToMol(smi2) );
// boost::shared_ptr<ROMol> lfrag2 = lfragchooser.choose(*m2);
// std::cout << MolToSmiles(*lfrag2) << std::endl;
// TEST_ASSERT(MolToSmiles(*lfrag2) == "O=C(O)c1ccccc1");
std::shared_ptr<RWMol> m2(SmilesToMol(smi2));
std::shared_ptr<RWMol> res2(MolStandardize::fragmentParent(*m2, params));
TEST_ASSERT(MolToSmiles(*res2) == "O=C(O)c1ccccc1");
// No organic fragments
smi3 = "[N+](=O)([O-])[O-]";
std::shared_ptr<ROMol> m3(SmilesToMol(smi3));
std::shared_ptr<ROMol> lfrag3(lfragchooser.choose(*m3));
TEST_ASSERT(MolToSmiles(*lfrag3) == "O=[N+]([O-])[O-]");
// Larger inorganic should be chosen
smi4 = "[N+](=O)([O-])[O-].[CH3+]";
std::shared_ptr<ROMol> m4(SmilesToMol(smi4));
std::shared_ptr<ROMol> lfrag4(lfragchooser.choose(*m4));
TEST_ASSERT(MolToSmiles(*lfrag4) == "O=[N+]([O-])[O-]");
// Smaller organic fragment should be chosen over larger inorganic fragment.
smi5 = "[N+](=O)([O-])[O-].[CH3+]";
std::shared_ptr<ROMol> m5(SmilesToMol(smi5));
std::shared_ptr<ROMol> lfrag5(lfrag_preferOrg.choose(*m5));
TEST_ASSERT(MolToSmiles(*lfrag5) == "[CH3+]");
// Salt without charges.
smi1 = "[Na].O=C(O)c1ccccc1";
std::shared_ptr<RWMol> m1(SmilesToMol(smi1));
std::shared_ptr<RWMol> res1(MolStandardize::fragmentParent(*m1, params));
// TEST_ASSERT(MolToSmiles(*lfrag) == "CN(C)C");
smi6 = "[Na]OC(=O)c1ccccc1";
std::shared_ptr<RWMol> m6(SmilesToMol(smi6));
// MolStandardize::cleanup(*m6, params);
std::shared_ptr<RWMol> res6(MolStandardize::fragmentParent(*m6, params));
TEST_ASSERT(MolToSmiles(*res6) == "O=C([O-])c1ccccc1");
smi7 = "c1ccccc1C(=O)O[Ca]OC(=O)c1ccccc1";
std::shared_ptr<RWMol> m7(SmilesToMol(smi7));
std::shared_ptr<RWMol> res7(MolStandardize::fragmentParent(*m7, params));
TEST_ASSERT(MolToSmiles(*res7) == "O=C([O-])c1ccccc1");
smi8 = "[Pt](Cl)(Cl)(O)(O)(NC(C)C)NC(C)C";
std::shared_ptr<RWMol> m8(SmilesToMol(smi8));
std::shared_ptr<RWMol> res8(MolStandardize::fragmentParent(*m8, params));
TEST_ASSERT(MolToSmiles(*res8) == "CC(C)[NH-]");
// Mercury containing compound.
smi9 = "CC[Hg]SC1=C(C=CC=C1)C(=O)[O][Na]";
std::shared_ptr<RWMol> m9(SmilesToMol(smi9));
std::shared_ptr<RWMol> res9(MolStandardize::fragmentParent(*m9, params));
TEST_ASSERT(MolToSmiles(*res9) == "CC[Hg]Sc1ccccc1C(=O)[O-]");
// Covalent bond with metal.
smi10 = "[Ag]OC(=O)O[Ag]";
std::shared_ptr<RWMol> m10(SmilesToMol(smi10));
std::shared_ptr<RWMol> res10(MolStandardize::fragmentParent(*m10, params));
TEST_ASSERT(MolToSmiles(*res10) == "O=C([O-])[O-]");
BOOST_LOG(rdInfoLog) << "Finished" << std::endl;
// params->preferOrganic = true;
//
}
void testWhiteSpaceInSmarts() {
BOOST_LOG(rdInfoLog) << "----- Test Whitespace in SMARTS Fragment string."
<< std::endl;
std::vector<std::string> data({
" ", // whitespace only
" \n", // whitespace plus new line
" // initial space plus comment\nfluorine\t[F]\n"
});
std::vector<size_t> reference_sizes({0, 0, 1});
auto reference = reference_sizes.cbegin();
for (const auto& smarts : data) {
std::istringstream input(smarts);
auto groups = readFuncGroups(input);
TEST_ASSERT(groups.size() == *reference);
++reference;
}
BOOST_LOG(rdInfoLog) << "---- Done" << std::endl;
}
void testFragmentWithoutSmarts() {
BOOST_LOG(rdInfoLog) << "----- Test Fragment string without SMARTS."
<< std::endl;
std::vector<std::string> data({
"// Name SMARTS\nnonsense\n",
"// Name SMARTS\nnonsense no new line",
"// Name SMARTS\nnonsense with tab\t\n"
});
for (const auto& smarts : data) {
bool ok = false;
std::istringstream input(smarts);
std::vector<std::shared_ptr<RDKit::ROMol>> groups;
try {
groups = readFuncGroups(input);
} catch (const Invar::Invariant&) {
ok = true;
}
TEST_ASSERT(ok);
TEST_ASSERT(groups.empty());
}
BOOST_LOG(rdInfoLog) << "---- Done" << std::endl;
}
int main() {
// may want to enable this for debugging
// RDLog::InitLogs();
test2();
test_largest_fragment();
testWhiteSpaceInSmarts();
testFragmentWithoutSmarts();
return 0;
}
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