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9f103a9913
* Fixes #2383 (tests coming in the next commit) Minor typo fix Fixes a "bug" in one of the default transforms * Adds support for directly providing normalization parameter data instead of requiring the use of a text file. * allow fragment removers to be initialized with string data * remove unicode * allow the reionizer to be initialized from a stream
83 lines
2.2 KiB
C++
83 lines
2.2 KiB
C++
//
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// Copyright (C) 2018 Susan H. Leung
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//
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// @@ All Rights Reserved @@
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// This file is part of the RDKit.
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// The contents are covered by the terms of the BSD license
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// which is included in the file license.txt, found at the root
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// of the RDKit source tree.
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//
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#include "FragmentCatalogParams.h"
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#include "FragmentCatalogUtils.h"
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#include <GraphMol/RDKitBase.h>
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#include <sstream>
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namespace RDKit {
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namespace MolStandardize {
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FragmentCatalogParams::FragmentCatalogParams(const std::string &fgroupFile) {
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d_funcGroups.clear();
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d_funcGroups = readFuncGroups(fgroupFile);
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}
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FragmentCatalogParams::FragmentCatalogParams(std::istream &fgroupStream) {
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d_funcGroups.clear();
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d_funcGroups = readFuncGroups(fgroupStream);
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}
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FragmentCatalogParams::FragmentCatalogParams(
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const FragmentCatalogParams &other) {
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d_typeStr = other.d_typeStr;
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d_funcGroups.clear();
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const std::vector<std::shared_ptr<ROMol>> &ofgrps = other.getFuncGroups();
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for (auto &fgi : ofgrps) {
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std::shared_ptr<ROMol> nmol(new ROMol(*fgi));
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d_funcGroups.push_back(nmol);
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}
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}
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FragmentCatalogParams::~FragmentCatalogParams() {}
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const std::vector<std::shared_ptr<ROMol>>
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&FragmentCatalogParams::getFuncGroups() const {
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return d_funcGroups;
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}
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const ROMol *FragmentCatalogParams::getFuncGroup(unsigned int fid) const {
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URANGE_CHECK(fid, d_funcGroups.size());
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return d_funcGroups[fid].get();
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}
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void FragmentCatalogParams::toStream(std::ostream &ss) const {
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ss << d_funcGroups.size() << "\n";
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// for (const auto &d_funcGroup : d_funcGroups) {
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// std::string text;
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// d_funcGroup->getProp(common_properties::_Name, text);
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// ss << text;
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// ss << "\t";
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// d_funcGroup->getProp(common_properties::_fragSMARTS, text);
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// ss << text;
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// ss << "\n";
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// }
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}
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std::string FragmentCatalogParams::Serialize() const {
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std::stringstream ss;
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toStream(ss);
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return ss.str();
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}
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void FragmentCatalogParams::initFromStream(std::istream &ss) {
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RDUNUSED_PARAM(ss);
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UNDER_CONSTRUCTION("not implemented");
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}
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void FragmentCatalogParams::initFromString(const std::string &text) {
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RDUNUSED_PARAM(text);
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UNDER_CONSTRUCTION("not implemented");
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}
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} // namespace MolStandardize
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} // namespace RDKit
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