mirror of
https://github.com/rdkit/rdkit.git
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ee5176a557
* start refactor query pickling * further query pickling refactoring * bit of modernization * partial implementation of query writing * serialize recursive queries * new tests * support QueryAtom and QueryBond with null queries * more query cleanup * tests pass * switch from std::variant to boost::variant * update clang version for CI * explicit instantiation of templates * get dll builds working on windows * optionally skip h counts on parsing; more query tests * change in response to review * changes in response to review
78 lines
2.3 KiB
C++
78 lines
2.3 KiB
C++
//
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// Copyright (C) 2021 Greg Landrum
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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 <RDGeneral/test.h>
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#include "catch.hpp"
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#include <GraphMol/RDKitBase.h>
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#include <GraphMol/MolPickler.h>
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#include <GraphMol/FileParsers/FileParsers.h>
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#include <GraphMol/SmilesParse/SmilesWrite.h>
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#include <GraphMol/SmilesParse/SmilesParse.h>
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#include <GraphMol/SmilesParse/SmartsWrite.h>
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#include "MolInterchange.h"
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using namespace RDKit;
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TEST_CASE("queries to JSON", "[query]") {
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SECTION("SMARTS 1") {
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auto mol = "C[cH]:[#7+]"_smarts;
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REQUIRE(mol);
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auto json = MolInterchange::MolToJSONData(*mol);
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// no implicit Hs added with queries
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CHECK(json.find("{\"impHs\":3}") == std::string::npos);
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CHECK(json.find("\"descr\":\"AtomHCount\"") != std::string::npos);
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auto nmols = MolInterchange::JSONDataToMols(json);
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CHECK(nmols.size() == 1);
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CHECK(MolToSmarts(*nmols[0]) == MolToSmarts(*mol));
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}
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SECTION("Recursive SMARTS 1") {
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auto mol = "[C;R2]=,#!@[$(CO),r6]"_smarts;
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REQUIRE(mol);
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auto json = MolInterchange::MolToJSONData(*mol);
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CHECK(json.find("\"subquery\":") != std::string::npos);
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auto nmols = MolInterchange::JSONDataToMols(json);
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CHECK(nmols.size() == 1);
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CHECK(MolToSmarts(*nmols[0]) == MolToSmarts(*mol));
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}
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SECTION("mol blocks") {
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auto mol = R"CTAB(
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Mrv2102 04092105442D
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0 0 0 0 0 999 V3000
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M V30 BEGIN CTAB
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M V30 COUNTS 5 4 0 0 0
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M V30 BEGIN ATOM
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M V30 1 Q -1.4583 0.4583 0 0
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M V30 2 C -0.1247 1.2283 0 0
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M V30 3 C 1.209 0.4583 0 0
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M V30 4 C 2.5427 1.2283 0 0
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M V30 5 C 1.209 -1.0817 0 0
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M V30 END ATOM
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M V30 BEGIN BOND
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M V30 1 1 1 2
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M V30 2 1 3 4
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M V30 3 5 2 3
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M V30 4 1 3 5 TOPO=2
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M V30 END BOND
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M V30 END CTAB
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M END
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)CTAB"_ctab;
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REQUIRE(mol);
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auto json = MolInterchange::MolToJSONData(*mol);
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CHECK(json.find("\"type\":\"Q\"") != std::string::npos);
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auto ps = MolInterchange::JSONParseParameters();
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ps.useHCounts = false;
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auto nmols = MolInterchange::JSONDataToMols(json, ps);
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CHECK(nmols.size() == 1);
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auto mb = MolToV3KMolBlock(*nmols[0]);
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CHECK(mb.find(" Q ") != std::string::npos);
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CHECK(mb.find("TOPO=2") != std::string::npos);
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}
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} |