mirror of
https://github.com/rdkit/rdkit.git
synced 2026-06-04 21:54:27 +08:00
2957ab4576
* switch to catch2 v3 Fixes #6894 * fix a couple of problems noticed in the CI builds * more warning cleanup * changes in response to review
216 lines
7.3 KiB
C++
216 lines
7.3 KiB
C++
//
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// Copyright (C) 2023 Greg Landrum 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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#include <catch2/catch_all.hpp>
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#include <algorithm>
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#include <limits>
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#include <fstream>
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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/SmilesParse.h>
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#include <GraphMol/SmilesParse/SmilesWrite.h>
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using namespace RDKit;
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TEST_CASE("Github #6312: space overhead of serializing properties") {
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SECTION("Bonds v2000") {
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auto mol = R"CTAB(
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Mrv1810 02111915042D
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4 3 0 0 0 0 999 V2000
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-1.5625 1.6071 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
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-0.8480 2.0196 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
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-2.2770 2.0196 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
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-1.5625 0.7821 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
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1 3 1 0 0 0 0
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1 2 6 0 0 0 0
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1 4 1 1 0 0 0
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M END)CTAB"_ctab;
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REQUIRE(mol);
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CHECK(mol->getBondWithIdx(1)->getProp<unsigned int>(
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common_properties::_MolFileBondType) == 6);
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CHECK(mol->getBondWithIdx(2)->getProp<unsigned int>(
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common_properties::_MolFileBondType) == 1);
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CHECK(mol->getBondWithIdx(2)->getProp<unsigned int>(
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common_properties::_MolFileBondStereo) == 1);
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std::string basepkl;
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MolPickler::pickleMol(*mol, basepkl);
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std::string pkl;
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MolPickler::pickleMol(*mol, pkl,
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PicklerOps::PropertyPickleOptions::BondProps |
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PicklerOps::PropertyPickleOptions::PrivateProps);
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// std::cerr << "!!!! " << pkl.size() << " " << basepkl.size() << std::endl;
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RWMol mol2(pkl);
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CHECK(mol2.getBondWithIdx(1)->getProp<unsigned int>(
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common_properties::_MolFileBondType) == 6);
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CHECK(mol2.getBondWithIdx(2)->getProp<unsigned int>(
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common_properties::_MolFileBondType) == 1);
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CHECK(mol2.getBondWithIdx(2)->getProp<unsigned int>(
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common_properties::_MolFileBondStereo) == 1);
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}
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SECTION("bonds-v3k") {
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auto mol = R"CTAB(
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Mrv1810 02111915102D
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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 4 3 0 0 0
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M V30 BEGIN ATOM
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M V30 1 C -2.9167 3 0 0
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M V30 2 C -1.583 3.77 0 0
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M V30 3 C -4.2503 3.77 0 0
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M V30 4 C -2.9167 1.46 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 3
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M V30 2 6 1 2
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M V30 3 1 1 4 CFG=1
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M V30 END BOND
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M V30 END CTAB
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M END)CTAB"_ctab;
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REQUIRE(mol);
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CHECK(mol->getBondWithIdx(1)->getProp<unsigned int>(
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common_properties::_MolFileBondType) == 6);
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CHECK(mol->getBondWithIdx(2)->getProp<unsigned int>(
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common_properties::_MolFileBondType) == 1);
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CHECK(mol->getBondWithIdx(2)->getProp<unsigned int>(
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common_properties::_MolFileBondCfg) == 1);
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std::string basepkl;
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MolPickler::pickleMol(*mol, basepkl);
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std::string pkl;
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MolPickler::pickleMol(*mol, pkl,
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PicklerOps::PropertyPickleOptions::BondProps |
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PicklerOps::PropertyPickleOptions::PrivateProps);
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CHECK(pkl.size() > basepkl.size());
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// make sure the property names aren't in the pickle
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CHECK(pkl.find(common_properties::_MolFileBondType) == std::string::npos);
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CHECK(pkl.find(common_properties::_MolFileBondCfg) == std::string::npos);
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// std::cerr << "!!!! " << pkl.size() << " " << basepkl.size() << std::endl;
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RWMol mol2(pkl);
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CHECK(mol2.getBondWithIdx(1)->getProp<unsigned int>(
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common_properties::_MolFileBondType) == 6);
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CHECK(mol2.getBondWithIdx(2)->getProp<unsigned int>(
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common_properties::_MolFileBondType) == 1);
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CHECK(mol2.getBondWithIdx(2)->getProp<unsigned int>(
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common_properties::_MolFileBondCfg) == 1);
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}
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SECTION("atoms") {
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auto mol = R"CTAB(
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Mrv2211 04272306392D
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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 C -7.375 3.125 0 0 CFG=2
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M V30 2 C -6.0413 3.895 0 0
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M V30 3 O -8.7087 3.895 0 0
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M V30 4 F -7.375 1.585 0 0
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M V30 5 Cl -6.1532 2.1875 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 3
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M V30 2 1 1 4
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M V30 3 1 1 2 CFG=1
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M V30 4 1 1 5 CFG=3
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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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std::string basepkl;
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MolPickler::pickleMol(*mol, basepkl);
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CHECK(mol->getAtomWithIdx(0)->getProp<int>(common_properties::molParity) ==
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2);
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CHECK(mol->getAtomWithIdx(0)->getProp<int>(
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common_properties::_ChiralityPossible) == 1);
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mol->getAtomWithIdx(0)->setProp(common_properties::_CIPCode,
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std::string("S"));
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mol->getAtomWithIdx(1)->setProp(common_properties::molAtomMapNumber, 1);
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mol->getAtomWithIdx(2)->setAtomMapNum(2);
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mol->getAtomWithIdx(3)->setProp(common_properties::dummyLabel,
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std::string("foo"));
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std::string pkl;
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MolPickler::pickleMol(*mol, pkl,
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PicklerOps::PropertyPickleOptions::AtomProps |
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PicklerOps::PropertyPickleOptions::PrivateProps);
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CHECK(pkl.size() > basepkl.size());
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RWMol mol2(pkl);
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CHECK(mol2.getAtomWithIdx(0)->getProp<int>(common_properties::molParity) ==
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2);
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CHECK(mol2.getAtomWithIdx(0)->getProp<int>(
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common_properties::_ChiralityPossible) == 1);
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CHECK(mol2.getAtomWithIdx(0)->getProp<std::string>(
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common_properties::_CIPCode) == "S");
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CHECK(mol2.getAtomWithIdx(1)->getProp<int>(
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common_properties::molAtomMapNumber) == 1);
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CHECK(mol2.getAtomWithIdx(2)->getProp<int>(
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common_properties::molAtomMapNumber) == 2);
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CHECK(mol2.getAtomWithIdx(3)->getProp<std::string>(
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common_properties::dummyLabel) == "foo");
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}
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SECTION("attachment points") {
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auto mol = R"CTAB(
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Mrv2211 09062306242D
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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 3 0 0 0
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M V30 BEGIN ATOM
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M V30 1 C -7.7917 4.0833 0 0
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M V30 2 C -6.458 4.8533 0 0
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M V30 3 C -5.1243 4.0833 0 0
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M V30 4 * -6.458 4.34 0 0
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M V30 5 C -5.303 6.3405 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 2 2 3
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M V30 3 1 4 5 ENDPTS=(3 1 2 3) ATTACH=ANY
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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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CHECK(mol->getBondWithIdx(2)->getProp<std::string>(
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common_properties::_MolFileBondAttach) == "ANY");
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CHECK(mol->getBondWithIdx(2)->getProp<std::string>(
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common_properties::_MolFileBondEndPts) == "(3 1 2 3)");
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std::string pkl;
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MolPickler::pickleMol(*mol, pkl);
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// make sure the property names aren't in the pickle
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CHECK(pkl.find(common_properties::_MolFileBondAttach) == std::string::npos);
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CHECK(pkl.find(common_properties::_MolFileBondEndPts) == std::string::npos);
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// std::cerr << "!!!! " << pkl.size() << " " << basepkl.size() << std::endl;
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RWMol mol2(pkl);
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CHECK(mol2.getBondWithIdx(2)->getProp<std::string>(
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common_properties::_MolFileBondAttach) == "ANY");
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CHECK(mol2.getBondWithIdx(2)->getProp<std::string>(
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common_properties::_MolFileBondEndPts) == "(3 1 2 3)");
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}
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} |