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//
// Copyright (c) 2025 Glysade Inc and other RDkit contributors
// All rights reserved.
//
// Redistribution and use in source and binary forms, with or without
// modification, are permitted provided that the following conditions are
// met:
//
// * Redistributions of source code must retain the above copyright
// notice, this list of conditions and the following disclaimer.
// * Redistributions in binary form must reproduce the above
// copyright notice, this list of conditions and the following
// disclaimer in the documentation and/or other materials provided
// with the distribution.
// * Neither the name of Novartis Institutes for BioMedical Research Inc.
// nor the names of its contributors may be used to endorse or promote
// products derived from this software without specific prior written
// permission.
//
// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS
// "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT
// LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR
// A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT
// OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
// SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT
// LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE,
// DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY
// THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
// (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
// OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
//
#include "chemdraw.h"
#include "chemdrawreaction.h"
#include <catch2/catch_all.hpp>
#include "RDGeneral/test.h"
#include <RDGeneral/Invariant.h>
#include <GraphMol/RDKitBase.h>
#include <GraphMol/ChemReactions/Reaction.h>
#include <GraphMol/ChemReactions/ReactionParser.h>
#include <GraphMol/ChemReactions/SanitizeRxn.h>
#include <GraphMol/SmilesParse/SmilesWrite.h>
#include <filesystem>
using namespace RDKit;
using namespace RDKit::v2;
TEST_CASE("CDXML Parser") {
std::string cdxmlbase =
std::string(getenv("RDBASE")) + "/Code/GraphMol/test_data/CDXML/";
SECTION("CDXML REACTION") {
auto fname = cdxmlbase + "rxn2.cdxml";
std::vector<std::string> expected = {
"Cl[c:1]1[cH:4][cH:3][cH:2][cH:6][cH:5]1",
"OC(O)B[c:7]1[cH:8][cH:9][cH:10][cH:11][cH:12]1",
"[cH:1]1[cH:4][cH:3][cH:2][c:6](-[c:7]2[cH:8][cH:9][cH:10][cH:11][cH:12]2)[cH:5]1"};
auto rxns = ChemDrawFileToChemicalReactions(fname);
CHECK(rxns.size() == 1);
unsigned int i = 0;
int count = 0;
for (auto &mol : rxns[0]->getReactants()) {
CHECK(mol->getProp<unsigned int>("CDX_SCHEME_ID") == 397);
CHECK(mol->getProp<unsigned int>("CDX_STEP_ID") == 398);
CHECK(mol->getProp<unsigned int>("CDX_REAGENT_ID") == i++);
CHECK(MolToSmiles(*mol) == expected[count++]);
}
i = 0;
for (auto &mol : rxns[0]->getProducts()) {
CHECK(mol->getProp<unsigned int>("CDX_SCHEME_ID") == 397);
CHECK(mol->getProp<unsigned int>("CDX_STEP_ID") == 398);
CHECK(mol->getProp<unsigned int>("CDX_PRODUCT_ID") == i++);
CHECK(MolToSmiles(*mol) == expected[count++]);
}
auto smarts = ChemicalReactionToRxnSmarts(*rxns[0]);
CHECK(
smarts ==
"[#6&D2:2]1:[#6&D2:3]:[#6&D2:4]:[#6&D3:1](:[#6&D2:5]:[#6&D2:6]:1)-[#17&D1].[#6&D3](-[#5&D2]-[#6&D3:7]1:[#6&D2:8]:[#6&D2:9]:[#6&D2:10]:[#6&D2:11]:[#6&D2:12]:1)(-[#8&D1])-[#8&D1]>>[#6&D2:1]1:[#6&D2:5]:[#6&D3:6](:[#6&D2:2]:[#6&D2:3]:[#6&D2:4]:1)-[#6&D3:7]1:[#6&D2:8]:[#6&D2:9]:[#6&D2:10]:[#6&D2:11]:[#6&D2:12]:1");
}
SECTION("Github #7528 CDXML Grouped Agents in Reactions") {
// The failing case had fragments grouped with labels, ensure the grouped
// cersion and the ungrouped versions have the same results
auto fname = cdxmlbase + "github7467-grouped-fragments.cdxml";
auto rxns = ChemDrawFileToChemicalReactions(fname);
CHECK(rxns.size() == 1);
fname = cdxmlbase + "github7467-ungrouped-fragments.cdxml";
auto rxns2 = ChemDrawFileToChemicalReactions(fname);
CHECK(ChemicalReactionToRxnSmarts(*rxns[0]) ==
ChemicalReactionToRxnSmarts(*rxns2[0]));
// Check to see if our understanding of grouped reagents in reactions is
// correct
fname = cdxmlbase + "reaction-with-grouped-templates.cdxml";
auto rxns3 = ChemDrawFileToChemicalReactions(fname);
CHECK(rxns3.size() == 1);
std::string rxnb = R"RXN($RXN
Mrv2004 062120241319
2 0
$MOL
Mrv2004 06212413192D
5 5 0 0 0 0 999 V2000
2.6221 -4.6475 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
2.6221 -5.4725 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
3.4070 -5.7274 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
3.8918 -5.0600 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
3.4070 -4.3926 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
1 2 2 0 0 0 0
2 3 1 0 0 0 0
3 4 2 0 0 0 0
4 5 1 0 0 0 0
5 1 1 0 0 0 0
M END
$MOL
Mrv2004 06212413192D
11 11 0 0 0 0 999 V2000
6.9305 -4.5100 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
6.9305 -5.3350 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
7.6450 -5.7475 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
8.3594 -5.3350 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
8.3594 -4.5100 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
7.6450 -4.0975 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
8.6171 -4.4825 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
8.6171 -5.3075 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
9.4020 -5.5624 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
9.8868 -4.8950 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
9.4020 -4.2276 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
1 2 1 0 0 0 0
6 1 1 0 0 0 0
2 3 1 0 0 0 0
3 4 1 0 0 0 0
4 5 1 0 0 0 0
5 6 1 0 0 0 0
7 8 2 0 0 0 0
11 7 1 0 0 0 0
8 9 1 0 0 0 0
9 10 2 0 0 0 0
10 11 1 0 0 0 0
M END
)RXN";
std::unique_ptr<ChemicalReaction> rxn_mb{RxnBlockToChemicalReaction(rxnb)};
// CDXMLToReaction is sanitized by default, this might be a mistake...
unsigned int failed;
RxnOps::sanitizeRxn(
*rxn_mb, failed,
RxnOps::SANITIZE_ADJUST_REACTANTS | RxnOps::SANITIZE_ADJUST_PRODUCTS,
RxnOps::MatchOnlyAtRgroupsAdjustParams());
CHECK(rxns3[0]->getNumReactantTemplates() ==
rxn_mb->getNumReactantTemplates());
CHECK(ChemicalReactionToRxnSmarts(*rxns3[0]) ==
ChemicalReactionToRxnSmarts(*rxn_mb));
}
}
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