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//
// Copyright (c) 2024, Glysade Inc
// 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 "reaction.h"
#include "utils.h"
#include <GraphMol/QueryOps.h>
#include <GraphMol/ChemReactions/SanitizeRxn.h>
#include <GraphMol/ChemReactions/ReactionUtils.h>
#include <GraphMol/ChemTransforms/ChemTransforms.h>
namespace RDKit {
using namespace RDKit::v2;
using namespace RDKit::ChemDraw;
// ChemDraw reaction API
// Convert reaction information to RDKIT reactions
namespace {
void make_query_atoms(RWMol &mol) {
for (auto &atom : mol.atoms()) {
QueryOps::replaceAtomWithQueryAtom(&mol, atom);
}
}
void add_template(const std::string &prop, std::map<int, ROMOL_SPTR> &templates,
std::unique_ptr<RWMol> &mol) {
auto reactant_idx = mol->getProp<int>(prop);
if (templates.find(reactant_idx) != templates.end()) {
templates[reactant_idx] =
ROMOL_SPTR(combineMols(*templates[reactant_idx], *mol));
} else {
templates[reactant_idx] = ROMOL_SPTR(std::move(mol));
}
}
} // namespace
namespace v2 {
//! Parse a text stream with ChemDraw data into a ChemicalReaction
std::vector<std::unique_ptr<ChemicalReaction>>
ChemDrawDataStreamToChemicalReactions(std::istream &inStream, bool sanitize,
bool removeHs) {
ChemDrawParserParams params;
params.sanitize = sanitize;
params.removeHs = removeHs;
auto mols = MolsFromChemDrawDataStream(inStream, params);
std::vector<std::unique_ptr<ChemicalReaction>> result;
std::map<std::pair<unsigned int, unsigned int>, std::vector<unsigned int>>
schemes;
std::set<unsigned int> used;
std::map<int, ROMOL_SPTR> reactant_templates;
std::map<int, ROMOL_SPTR> product_templates;
std::map<int, ROMOL_SPTR> agent_templates;
for (size_t i = 0; i < mols.size(); ++i) {
unsigned int step = 0;
unsigned int scheme = 0;
if (mols[i]->getPropIfPresent(CDX_SCHEME_ID, scheme) &&
mols[i]->getPropIfPresent(CDX_STEP_ID, step)) {
auto schemestep = std::pair<unsigned int, unsigned int>(scheme, step);
schemes[schemestep].push_back(i);
}
}
if (schemes.empty()) {
return result;
}
for (const auto &scheme : schemes) {
// convert atoms to queries:
ChemicalReaction *res = new ChemicalReaction;
result.push_back(std::unique_ptr<ChemicalReaction>(res));
for (auto idx : scheme.second) {
CHECK_INVARIANT(
used.find(idx) == used.end(),
"Fragment used in twice in one or more reactions, this shouldn't happen");
if (mols[idx]->hasProp(CDX_REAGENT_ID)) {
used.insert(idx);
make_query_atoms(*mols[idx]);
add_template(CDX_REAGENT_ID, reactant_templates, mols[idx]);
} else if (mols[idx]->hasProp(CDX_AGENT_ID)) {
used.insert(idx);
make_query_atoms(*mols[idx]);
add_template(CDX_AGENT_ID, agent_templates, mols[idx]);
} else if (mols[idx]->hasProp(CDX_PRODUCT_ID)) {
used.insert(idx);
make_query_atoms(*mols[idx]);
add_template(CDX_PRODUCT_ID, product_templates, mols[idx]);
}
}
for (auto reactant : reactant_templates) {
res->addReactantTemplate(reactant.second);
}
for (auto reactant : agent_templates) {
res->addAgentTemplate(reactant.second);
}
for (auto reactant : product_templates) {
res->addProductTemplate(reactant.second);
}
updateProductsStereochem(res);
// ChemDraw-based reactions do not have implicit properties
res->setImplicitPropertiesFlag(false);
if (!sanitize) { // we still need to fix the reaction for smarts style
// matching
unsigned int failed;
RxnOps::sanitizeRxn(
*res, failed,
RxnOps::SANITIZE_ADJUST_REACTANTS | RxnOps::SANITIZE_ADJUST_PRODUCTS,
RxnOps::MatchOnlyAtRgroupsAdjustParams());
}
}
return result;
}
std::vector<std::unique_ptr<ChemicalReaction>> ChemDrawToChemicalReactions(
const std::string &rxnBlock, bool sanitize, bool removeHs) {
std::istringstream inStream(rxnBlock);
return ChemDrawDataStreamToChemicalReactions(inStream, sanitize, removeHs);
}
std::vector<std::unique_ptr<ChemicalReaction>> ChemDrawFileToChemicalReactions(
const std::string &fName, bool sanitize, bool removeHs) {
std::ifstream inStream(fName.c_str());
std::vector<std::unique_ptr<ChemicalReaction>> res;
;
if (!inStream || inStream.bad()) {
return res;
}
if (!inStream.eof()) {
return ChemDrawDataStreamToChemicalReactions(inStream, sanitize, removeHs);
}
return res;
}
}
} // namespace RDKit
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