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3aab2653cd
* Fixes #9068 * fix a problem with empty labels in s-group parsing * fix empty column names in smiles suppliers * add the check to setPODVal() --------- Co-authored-by: = <=>
76 lines
2.1 KiB
C++
76 lines
2.1 KiB
C++
//
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// Copyright (C) 2024 Greg Landrum and other RDKit contributors
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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 <string>
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#include "RDGeneral/test.h"
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#include <catch2/catch_all.hpp>
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#include <RDGeneral/Invariant.h>
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#include <GraphMol/RDKitBase.h>
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#include <GraphMol/Chirality.h>
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#include <GraphMol/FileParsers/FileParsers.h>
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#include <GraphMol/FileParsers/MolSupplier.h>
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#include <GraphMol/FileParsers/MolWriters.h>
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#include <GraphMol/SmilesParse/SmilesWrite.h>
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using namespace RDKit;
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using namespace RDKit::v2::FileParsers;
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TEST_CASE("expandAttachmentPoints") {
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SECTION("basics") {
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std::string mb = R"CTAB(
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Mrv2211 02082417032D
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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 2 1 0 0 0
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M V30 BEGIN ATOM
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M V30 1 C -4.7083 3.25 0 0
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M V30 2 O -3.3747 4.02 0 0 ATTCHPT=1
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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 END BOND
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M V30 END CTAB
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M END
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)CTAB";
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auto mol{MolFromMolBlock(mb)};
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REQUIRE(mol);
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CHECK(mol->getNumAtoms() == 2);
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MolFileParserParams ps;
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ps.expandAttachmentPoints = true;
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auto mol2{MolFromMolBlock(mb, ps)};
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REQUIRE(mol2);
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CHECK(mol2->getNumAtoms() == 3);
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SmilesWriteParams sps;
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CHECK(MolToCXSmiles(*mol2, sps,
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SmilesWrite::CXSmilesFields::CX_ALL_BUT_COORDS) ==
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"*OC |$_AP1;;$|");
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// verify coords too
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CHECK(MolToCXSmiles(*mol2) ==
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"*OC |(-2.50869,4.52002,;-3.3747,4.02,;-4.7083,3.25,),$_AP1;;$|");
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}
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}
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TEST_CASE("empty column names in SmilesMolSupplier") {
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std::string rdbase = getenv("RDBASE");
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std::string fName =
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rdbase + "/Code/GraphMol/FileParsers/test_data/s1p_chembldoc89753.txt";
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SmilesMolSupplierParams params;
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params.delimiter = ",";
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params.smilesColumn = 9;
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params.nameColumn = 10;
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v2::FileParsers::SmilesMolSupplier suppl(fName, params);
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auto mol = suppl.next();
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REQUIRE(mol);
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CHECK(mol->hasProp("_Name"));
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CHECK(mol->hasProp("Column_0"));
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} |