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//
// Copyright (C) 2018-2021 Susan H. Leung and other RDKit contributors
//
// @@ 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 "TransformCatalogParams.h"
#include "TransformCatalogUtils.h"
#include <GraphMol/RDKitBase.h>
#include <sstream>
namespace RDKit {
namespace MolStandardize {
#include "normalizations.in"
TransformCatalogParams::TransformCatalogParams(
const std::string &transformFile) {
d_transformations.clear();
if (transformFile.empty()) {
d_transformations = readTransformations(defaults::defaultNormalizations);
} else {
d_transformations = readTransformations(transformFile);
}
}
TransformCatalogParams::TransformCatalogParams(std::istream &transformStream) {
d_transformations.clear();
d_transformations = readTransformations(transformStream);
}
TransformCatalogParams::TransformCatalogParams(
const std::vector<std::pair<std::string, std::string>> &data) {
d_transformations.clear();
d_transformations = readTransformations(data);
};
TransformCatalogParams::TransformCatalogParams(
const TransformCatalogParams &other) {
d_typeStr = other.d_typeStr;
d_transformations.clear();
const std::vector<std::shared_ptr<ChemicalReaction>> &otransforms =
other.getTransformations();
for (auto &transi : otransforms) {
std::shared_ptr<ChemicalReaction> transform(new ChemicalReaction(*transi));
d_transformations.push_back(transform);
}
}
TransformCatalogParams::~TransformCatalogParams() {}
const std::vector<std::shared_ptr<ChemicalReaction>> &
TransformCatalogParams::getTransformations() const {
return d_transformations;
}
const ChemicalReaction *TransformCatalogParams::getTransformation(
unsigned int fid) const {
URANGE_CHECK(fid, d_transformations.size());
// return d_transformations[fid];
return d_transformations[fid].get();
}
void TransformCatalogParams::initializeTransforms() const {
for (auto &transform : d_transformations) {
if (!transform || transform->isInitialized()) {
continue;
}
transform->initReactantMatchers();
}
}
void TransformCatalogParams::toStream(std::ostream &ss) const {
ss << d_transformations.size() << "\n";
}
std::string TransformCatalogParams::Serialize() const {
std::stringstream ss;
toStream(ss);
return ss.str();
}
void TransformCatalogParams::initFromStream(std::istream &) {
UNDER_CONSTRUCTION("not implemented");
}
void TransformCatalogParams::initFromString(const std::string &) {
UNDER_CONSTRUCTION("not implemented");
}
} // namespace MolStandardize
} // namespace RDKit
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