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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 {
namespace ChemDraw {
void ReactionStepInfo::set_reaction_data(
std::string type, std::string prop, const std::vector<int> &frag_ids,
const std::map<unsigned int, size_t> &fragments,
std::map<unsigned int, std::vector<int>> &grouped_fragments,
const std::vector<std::unique_ptr<RWMol>> &mols) const {
unsigned int reagent_idx = 0;
for (auto idx : frag_ids) {
auto iter = grouped_fragments.find(idx);
if (iter == grouped_fragments.end()) {
BOOST_LOG(rdWarningLog) << "CDXMLParser: Schema " << scheme_id << " step "
<< step_id << " " << type << " reaction fragment "
<< idx << " not found in document." << std::endl;
continue;
}
for (auto reaction_fragment_id : iter->second) {
auto fragment = fragments.find(reaction_fragment_id);
if (fragment == fragments.end()) {
BOOST_LOG(rdWarningLog)
<< "CDXMLParser: Schema " << scheme_id << " step " << step_id << " "
<< type << " fragment " << idx << " not found in document."
<< std::endl;
continue;
}
auto &mol = mols[fragment->second];
mol->setProp(CDX_SCHEME_ID, scheme_id);
mol->setProp(CDX_STEP_ID, step_id);
mol->setProp(prop, reagent_idx);
}
reagent_idx += 1;
}
}
void ReactionStepInfo::set_reaction_step(
size_t scheme_id, std::map<unsigned int, Atom *> &atoms,
const std::map<unsigned int, size_t> &fragments,
std::map<unsigned int, std::vector<int>> &grouped_fragments,
const std::vector<std::unique_ptr<RWMol>> &mols) const {
// Set the molecule properties
set_reaction_data("ReactionStepReactants", CDX_REAGENT_ID,
ReactionStepReactants, fragments, grouped_fragments, mols);
set_reaction_data("ReactionStepProducts", CDX_PRODUCT_ID,
ReactionStepProducts, fragments, grouped_fragments, mols);
auto agents = ReactionStepObjectsAboveArrow;
agents.insert(agents.end(), ReactionStepObjectsBelowArrow.begin(),
ReactionStepObjectsBelowArrow.end());
set_reaction_data("ReactionStepAgents", CDX_AGENT_ID, agents, fragments,
grouped_fragments, mols);
// Set the Atom Maps
int atommap = 0;
for (auto mapping : ReactionStepAtomMap) {
++atommap;
unsigned int idx1 = mapping.first;
unsigned int idx2 = mapping.second;
if (atoms.find(idx1) != atoms.end()) {
atoms[idx1]->setAtomMapNum(atommap);
} else {
BOOST_LOG(rdWarningLog)
<< "CDXMLParser: Schema " << scheme_id << " step " << step_id
<< " ReactionStepAtomMap cannot find atom with node id " << idx1
<< "skipping schema..." << std::endl;
}
if (atoms.find(idx2) != atoms.end()) {
atoms[idx2]->setAtomMapNum(atommap);
} else {
// XXX log error
BOOST_LOG(rdWarningLog)
<< "CDXMLParser: Schema " << scheme_id << " step " << step_id
<< " ReactionStepAtomMap cannot find atom with node id " << idx2
<< " skipping schema..." << std::endl;
}
}
}
ReactionInfo::ReactionInfo(CDXReactionScheme &scheme)
: scheme_id(static_cast<unsigned int>(scheme.GetObjectID())) {
for (auto &rxnNode : scheme.ContainedObjects()) {
CDXDatumID type_id = (CDXDatumID)rxnNode.second->GetTag();
if (type_id == kCDXObj_ReactionStep) {
CDXReactionStep &step = (CDXReactionStep &)(*rxnNode.second);
auto step_id = step.GetObjectID();
steps.emplace_back(ReactionStepInfo());
ReactionStepInfo &scheme = steps.back();
scheme.scheme_id = scheme_id;
scheme.step_id = step_id;
scheme.ReactionStepProducts = step.m_products;
scheme.ReactionStepReactants = step.m_reactants;
scheme.ReactionStepObjectsBelowArrow = step.m_objectsBelowArrow;
scheme.ReactionStepAtomMap = step.m_aamap;
steps.push_back(scheme);
}
}
}
void ReactionInfo::set_reaction_steps(
std::map<unsigned int, std::vector<int>> &grouped_fragments,
const std::vector<std::unique_ptr<RWMol>> &mols) const {
if (steps.size()) {
std::map<unsigned int, size_t> fragments;
std::map<unsigned int, size_t> agents;
std::map<unsigned int, size_t> products;
std::map<unsigned int, Atom *> atoms;
size_t mol_idx = 0;
for (auto &mol : mols) {
auto idx = mol->getProp<unsigned int>(CDX_FRAG_ID);
fragments[idx] = mol_idx++;
for (auto &atom : mol->atoms()) {
unsigned int idx = atom->getProp<unsigned int>(CDX_ATOM_ID);
atoms[idx] = atom;
}
}
for (auto &step : steps) {
step.set_reaction_step(scheme_id, atoms, fragments, grouped_fragments,
mols);
}
}
}
}
} // namespace RDKit
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