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9c7ffb33e9
* get SynthonSpace.cpp to build also when RDK_USE_BOOST_SERIALIZATION is not defined * test should not fail when RDK_USE_BOOST_SERIALIZATION is not defined * - expose reading/writing PNG metadata to CFFI and MinimalLib - add relevant CFFI and MinimalLib unit tests - add RDK_USE_BOOST_PROGRAM_OPTIONS CMake option - enable using standalone zlib in the absence of boost::iostreams for parsing PNG files - enable linking against maeparser in the absence of boost::iostreams also on Windows - enable building RDKit in the absence of boost::program_options * add check for boost::program_options * change size_t into std::uint64_t in SearchResults for consistency with doTheSearch() which uses std::uint64_t * change size_t into std::uint64_t in SearchResults for consistency with SynthonSpaceSearcher::doTheSearch() * set CMake policy to allow YAeHMOP to require a version which is not actually supported * reverted External/YAeHMOP/CMakeLists.txt to master version * check if Windows build will work * fix build * configure zlib install location * build zlib dependency * include zlib header directory * explicitly set PropertyFlags.AllProps so the test does not fail on static builds --------- Co-authored-by: ptosco <paolo.tosco@novartis.com>
123 lines
4.9 KiB
C++
123 lines
4.9 KiB
C++
//
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// Copyright (C) 2024 Novartis Biomedical Research and other RDKit contributors
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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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#define USE_BETTER_ENUMS
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#include "JSONParsers.h"
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#include <GraphMol/MolPickler.h>
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#include <GraphMol/FileParsers/PNGParser.h>
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#include <GraphMol/SmilesParse/SmilesJSONParsers.h>
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#include <RDGeneral/BoostStartInclude.h>
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#include <boost/property_tree/ptree.hpp>
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#include <boost/property_tree/json_parser.hpp>
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#include <RDGeneral/BoostEndInclude.h>
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namespace RDKit {
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namespace MinimalLib {
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void updatePropertyPickleOptionsFromJSON(unsigned int &propFlags,
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const char *details_json) {
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if (details_json && details_json[0]) {
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std::istringstream ss;
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boost::property_tree::ptree pt;
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ss.str(details_json);
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boost::property_tree::read_json(ss, pt);
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const auto nodeIt = pt.find("propertyFlags");
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if (nodeIt != pt.not_found()) {
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auto propertyFlagsFromJson =
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(+PicklerOps::PropertyPickleOptions::NoProps)._to_integral();
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for (const auto *key : PicklerOps::PropertyPickleOptions::_names()) {
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if (nodeIt->second.get(key, false)) {
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propertyFlagsFromJson |=
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PicklerOps::PropertyPickleOptions::_from_string(key)
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._to_integral();
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}
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}
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propFlags = propertyFlagsFromJson;
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}
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}
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}
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void updateSanitizeFlagsFromJSON(unsigned int &sanitizeFlags,
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const char *details_json) {
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if (details_json && details_json[0]) {
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std::istringstream ss;
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boost::property_tree::ptree pt;
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ss.str(details_json);
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boost::property_tree::read_json(ss, pt);
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auto sanitizeFlagsFromJson =
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(+MolOps::SanitizeFlags::SANITIZE_NONE)._to_integral();
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for (const auto *key : MolOps::SanitizeFlags::_names()) {
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if (pt.get(key, false)) {
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sanitizeFlagsFromJson |=
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MolOps::SanitizeFlags::_from_string(key)._to_integral();
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}
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}
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sanitizeFlags = sanitizeFlagsFromJson;
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}
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}
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void updateRemoveHsParametersFromJSON(MolOps::RemoveHsParameters &ps,
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bool &sanitize,
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const char *details_json) {
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if (details_json && details_json[0]) {
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boost::property_tree::ptree pt;
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std::istringstream ss;
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ss.str(details_json);
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boost::property_tree::read_json(ss, pt);
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ps.removeDegreeZero = pt.get("removeDegreeZero", ps.removeDegreeZero);
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ps.removeHigherDegrees =
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pt.get("removeHigherDegrees", ps.removeHigherDegrees);
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ps.removeOnlyHNeighbors =
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pt.get("removeOnlyHNeighbors", ps.removeOnlyHNeighbors);
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ps.removeIsotopes = pt.get("removeIsotopes", ps.removeIsotopes);
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ps.removeAndTrackIsotopes =
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pt.get("removeAndTrackIsotopes", ps.removeAndTrackIsotopes);
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ps.removeDummyNeighbors =
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pt.get("removeDummyNeighbors", ps.removeDummyNeighbors);
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ps.removeDefiningBondStereo =
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pt.get("removeDefiningBondStereo", ps.removeDefiningBondStereo);
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ps.removeWithWedgedBond =
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pt.get("removeWithWedgedBond", ps.removeWithWedgedBond);
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ps.removeWithQuery = pt.get("removeWithQuery", ps.removeWithQuery);
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ps.removeMapped = pt.get("removeMapped", ps.removeMapped);
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ps.removeInSGroups = pt.get("removeInSGroups", ps.removeInSGroups);
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ps.showWarnings = pt.get("showWarnings", ps.showWarnings);
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ps.removeNonimplicit = pt.get("removeNonimplicit", ps.removeNonimplicit);
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ps.updateExplicitCount =
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pt.get("updateExplicitCount", ps.updateExplicitCount);
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ps.removeHydrides = pt.get("removeHydrides", ps.removeHydrides);
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ps.removeNontetrahedralNeighbors = pt.get("removeNontetrahedralNeighbors",
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ps.removeNontetrahedralNeighbors);
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sanitize = pt.get("sanitize", sanitize);
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}
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}
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void updatePNGMetadataParamsFromJSON(PNGMetadataParams ¶ms,
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const char *details_json) {
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if (details_json && strlen(details_json)) {
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boost::property_tree::ptree pt;
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std::istringstream ss;
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ss.str(details_json);
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boost::property_tree::read_json(ss, pt);
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params.includePkl = pt.get("includePkl", params.includePkl);
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params.includeSmiles = pt.get("includeSmiles", params.includeSmiles);
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params.includeMol = pt.get("includeMol", params.includeMol);
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updatePropertyPickleOptionsFromJSON(params.propertyFlags, details_json);
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updateSmilesWriteParamsFromJSON(params.smilesWriteParams, details_json);
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unsigned int restoreBondDirs = params.restoreBondDirs;
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updateCXSmilesFieldsFromJSON(params.cxSmilesFlags, restoreBondDirs,
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details_json);
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params.restoreBondDirs =
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RestoreBondDirOption::_from_integral(restoreBondDirs);
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}
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}
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} // end namespace MinimalLib
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} // end namespace RDKit
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