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* backup * update .gitignore * passes tests * all tests now pass * update release notes * cleanup * changes in response to review
767 lines
23 KiB
C++
767 lines
23 KiB
C++
//
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// Copyright (c) 2022 Brian P Kelley
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// All rights reserved.
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//
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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 <RDGeneral/Invariant.h>
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#include <GraphMol/RDKitBase.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/SmartsWrite.h>
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#include <RDGeneral/FileParseException.h>
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#include <boost/algorithm/string.hpp>
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#include <RDGeneral/BadFileException.h>
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using namespace RDKit;
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TEST_CASE("CDXML") {
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std::string cdxmlbase =
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std::string(getenv("RDBASE")) + "/Code/GraphMol/test_data/CDXML/";
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SECTION("SIMPLE") {
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std::string cdxml1 = R"(<?xml version="1.0" encoding="UTF-8" ?>
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<!DOCTYPE CDXML SYSTEM "http://www.cambridgesoft.com/xml/cdxml.dtd" >
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<CDXML
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CreationProgram="ChemDraw JS 2.0.0.9"
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Name="ACS Document 1996"
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BoundingBox="94.75 178.16 154.89 211.17"
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WindowPosition="0 0"
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WindowSize="0 0"
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FractionalWidths="yes"
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InterpretChemically="yes"
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ShowAtomQuery="yes"
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ShowAtomStereo="no"
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ShowAtomEnhancedStereo="yes"
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ShowAtomNumber="no"
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ShowResidueID="no"
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ShowBondQuery="yes"
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ShowBondRxn="yes"
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ShowBondStereo="no"
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ShowTerminalCarbonLabels="no"
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ShowNonTerminalCarbonLabels="no"
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HideImplicitHydrogens="no"
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Magnification="666"
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LabelFont="24"
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LabelSize="10"
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LabelFace="96"
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CaptionFont="24"
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CaptionSize="10"
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HashSpacing="2.50"
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MarginWidth="1.60"
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LineWidth="0.60"
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BoldWidth="2"
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BondLength="14.40"
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BondSpacing="18"
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ChainAngle="120"
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LabelJustification="Auto"
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CaptionJustification="Left"
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AminoAcidTermini="HOH"
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ShowSequenceTermini="yes"
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ShowSequenceBonds="yes"
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ShowSequenceUnlinkedBranches="no"
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ResidueWrapCount="40"
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ResidueBlockCount="10"
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ResidueZigZag="yes"
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NumberResidueBlocks="no"
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PrintMargins="36 36 36 36"
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MacPrintInfo="0003000001200120000000000B6608A0FF84FF880BE309180367052703FC0002000001200120000000000B6608A0000100000064000000010001010100000001270F000100010000000000000000000000000002001901900000000000400000000000000000000100000000000000000000000000000000"
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ChemPropName=""
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ChemPropFormula="Chemical Formula: "
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ChemPropExactMass="Exact Mass: "
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ChemPropMolWt="Molecular Weight: "
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ChemPropMOverZ="m/z: "
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ChemPropAnalysis="Elemental Analysis: "
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ChemPropBoilingPt="Boiling Point: "
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ChemPropMeltingPt="Melting Point: "
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ChemPropCritTemp="Critical Temp: "
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ChemPropCritPres="Critical Pres: "
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ChemPropCritVol="Critical Vol: "
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ChemPropGibbs="Gibbs Energy: "
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ChemPropLogP="Log P: "
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ChemPropMR="MR: "
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ChemPropHenry="Henry's Law: "
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ChemPropEForm="Heat of Form: "
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ChemProptPSA="tPSA: "
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ChemPropID=""
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ChemPropFragmentLabel=""
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color="0"
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bgcolor="1"
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RxnAutonumberStart="1"
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RxnAutonumberConditions="no"
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RxnAutonumberStyle="Roman"
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><colortable>
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<color r="1" g="1" b="1"/>
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<color r="0" g="0" b="0"/>
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<color r="1" g="0" b="0"/>
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<color r="1" g="1" b="0"/>
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<color r="0" g="1" b="0"/>
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<color r="0" g="1" b="1"/>
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<color r="0" g="0" b="1"/>
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<color r="1" g="0" b="1"/>
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</colortable><fonttable>
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<font id="24" charset="utf-8" name="Arial"/>
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</fonttable><page
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id="32"
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BoundingBox="0 0 542 354"
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Width="542"
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Height="354"
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HeaderPosition="36"
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FooterPosition="36"
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PageOverlap="0"
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PrintTrimMarks="yes"
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HeightPages="1"
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WidthPages="1"
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DrawingSpace="poster"
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><fragment
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id="10"
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BoundingBox="94.75 178.16 154.89 211.17"
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Z="4"
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><n
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id="7"
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p="95.05 187.47"
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Z="1"
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AS="N"
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/><n
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id="9"
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p="95.05 201.87"
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Z="3"
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AS="N"
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/><n
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id="11"
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p="106.31 210.84"
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Z="5"
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AS="N"
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/><n
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id="13"
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p="120.35 207.64"
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Z="7"
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AS="N"
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/><n
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id="15"
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p="126.59 194.67"
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Z="9"
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AS="N"
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/><n
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id="17"
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p="120.35 181.69"
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Z="11"
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AS="N"
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/><n
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id="19"
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p="106.31 178.49"
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Z="13"
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AS="N"
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/><n
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id="28"
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p="140.99 194.67"
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Z="22"
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NodeType="Nickname"
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NeedsClean="yes"
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AS="N"
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><fragment
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id="33"
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><n
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id="34"
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p="148.17 207.09"
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Element="8"
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NumHydrogens="0"
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/><n
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id="35"
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p="162.52 207.09"
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/><n
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id="36"
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p="176.87 207.09"
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/><n
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id="37"
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p="169.69 194.67"
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/><n
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id="38"
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p="169.69 219.52"
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/><n
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id="39"
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p="140.99 194.67"
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/><n
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id="40"
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p="148.17 182.24"
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Element="8"
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NumHydrogens="0"
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/><n
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id="41"
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p="126.64 194.67"
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NodeType="ExternalConnectionPoint"
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/><b
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id="42"
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B="39"
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E="40"
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Order="2"
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/><b
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id="43"
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B="35"
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E="38"
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/><b
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id="44"
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B="35"
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E="36"
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/><b
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id="45"
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B="35"
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E="37"
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/><b
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id="46"
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B="34"
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E="35"
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/><b
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id="47"
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B="34"
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E="39"
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/><b
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id="48"
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B="41"
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E="39"
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/></fragment><t
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p="137.66 198.28"
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BoundingBox="137.66 189.64 154.89 198.28"
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LabelJustification="Left"
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LabelAlignment="Left"
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><s font="24" size="9.95" color="0" face="96">Boc</s></t></n><b
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id="21"
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Z="15"
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B="7"
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E="9"
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BS="N"
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/><b
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id="22"
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Z="16"
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B="9"
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E="11"
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BS="N"
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/><b
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id="23"
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Z="17"
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B="11"
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E="13"
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BS="N"
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/><b
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id="24"
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Z="18"
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B="13"
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E="15"
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BS="N"
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/><b
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id="25"
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Z="19"
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B="15"
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E="17"
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BS="N"
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/><b
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id="26"
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Z="20"
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B="17"
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E="19"
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BS="N"
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/><b
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id="27"
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Z="21"
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B="19"
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E="7"
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BS="N"
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/><b
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id="29"
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Z="23"
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B="15"
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E="28"
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BS="N"
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/></fragment></page></CDXML>)";
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std::stringstream iss(cdxml1);
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auto mols = CDXMLDataStreamToMols(iss);
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for (auto &mol : mols) {
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CHECK(MolToSmiles(*mol) == "CC(C)(C)OC(=O)C1CCCCCC1");
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}
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}
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SECTION("REACTION") {
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std::string fname = cdxmlbase + "reaction-with-boc.cdxml";
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std::vector<std::string> expected = {"CC(C)(C)OC(=O)C1CCCCCC1[*:1]",
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"c1ccc([*:1])cc1", "C1CC1", "C1CCC1"};
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auto mols = CDXMLFileToMols(fname);
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CHECK(mols.size() == expected.size());
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int i = 0;
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for (auto &mol : mols) {
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CHECK(MolToSmiles(*mol) == expected[i++]);
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}
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}
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SECTION("RING CHIRALITY") {
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std::string fname = cdxmlbase + "ring-stereo1.cdxml";
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std::vector<std::string> expected = {"C1CC[C@H]2CCCC[C@H]2C1"};
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auto mols = CDXMLFileToMols(fname);
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CHECK(mols.size() == expected.size());
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int i = 0;
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for (auto &mol : mols) {
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CHECK(MolToSmiles(*mol) == expected[i++]);
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}
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}
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SECTION("SIMPLE CHIRAL") {
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std::string fname = cdxmlbase + "chirality1.cdxml";
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std::vector<std::string> expected = {"C[C@H](N)C[C@H](C)N"};
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auto mols = CDXMLFileToMols(fname);
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CHECK(mols.size() == expected.size());
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int i = 0;
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for (auto &mol : mols) {
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CHECK(MolToSmiles(*mol) == expected[i++]);
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}
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}
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SECTION("CDXML-CISTRANS") {
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auto fname = cdxmlbase + "cistrans1.cdxml";
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std::vector<std::string> expected = {"F/C(I)=C(\\Cl)Br"};
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auto mols = CDXMLFileToMols(fname);
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CHECK(mols.size() == expected.size());
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int i = 0;
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for (auto &mol : mols) {
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CHECK(MolToSmiles(*mol) == expected[i++]);
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}
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}
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SECTION("REACTION") {
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auto fname = cdxmlbase + "rxn1.cdxml";
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std::vector<std::string> expected = {
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"Cl[c:1]1[cH:4][cH:3][cH:2][cH:6][cH:5]1",
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"OC(O)B[c:7]1[cH:8][cH:9][cH:10][cH:11][cH:12]1",
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"[cH:1]1[cH:4][cH:3][cH:2][c:6](-[c:7]2[cH:8][cH:9][cH:10][cH:11][cH:12]2)[cH:5]1"};
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auto mols = CDXMLFileToMols(fname);
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int i = 0;
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for (auto &mol : mols) {
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CHECK(mol->getProp<unsigned int>("CDX_SCHEME_ID") == 397);
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CHECK(mol->getProp<unsigned int>("CDX_STEP_ID") == 398);
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if (i == 0) {
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CHECK(mol->getProp<unsigned int>("CDX_REAGENT_ID") == 0);
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} else if (i == 1) {
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CHECK(mol->getProp<unsigned int>("CDX_REAGENT_ID") == 1);
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} else if (i == 2) {
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CHECK(mol->getProp<unsigned int>("CDX_PRODUCT_ID") == 0);
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}
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CHECK(MolToSmiles(*mol) == expected[i++]);
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}
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}
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SECTION("DEUTERIUM") {
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auto fname = cdxmlbase + "deuterium.cdxml";
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{
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std::vector<std::string> expected = {
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"[2H]c1c([2H])c([2H])c([2H])c([2H])c1[2H]"};
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auto mols = CDXMLFileToMols(fname);
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CHECK(mols.size() == expected.size());
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int i = 0;
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for (auto &mol : mols) {
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CHECK(MolToSmiles(*mol) == expected[i++]);
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}
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}
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{
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std::vector<std::string> expected = {
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"[2H]C1=C([2H])C([2H])=C([2H])C([2H])=C1[2H]"};
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auto mols = CDXMLFileToMols(fname, false, false);
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CHECK(mols.size() == expected.size());
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int i = 0;
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for (auto &mol : mols) {
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CHECK(MolToSmiles(*mol) == expected[i++]);
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}
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}
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{
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std::vector<std::string> expected = {
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"[2H]C1=C([2H])C([2H])=C([2H])C([2H])=C1[2H]"};
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auto mols = CDXMLFileToMols(fname, false, true);
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CHECK(mols.size() == expected.size());
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int i = 0;
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for (auto &mol : mols) {
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CHECK(MolToSmiles(*mol) == expected[i++]);
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}
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}
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}
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SECTION("Queries") {
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auto fname = cdxmlbase + "query-atoms.cdxml";
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std::vector<std::string> expected = {"*c1ccccc1", "*c1ccccc1", "*c1ccccc1"};
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std::vector<std::string> expected_smarts = {
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"[#6]1:[#6]:[#6]:[#6]:[#6]:[#6]:1-*",
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"[#6]1:[#6]:[#6]:[#6]:[#6]:[#6]:1-[!#1]",
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"[#6]1:[#6]:[#6]:[#6]:[#6]:[#6]:1-[!#6&!#1]"};
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auto mols = CDXMLFileToMols(fname);
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CHECK(mols.size() == expected.size());
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int i = 0;
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for (auto &mol : mols) {
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CHECK(MolToSmarts(*mol) == expected_smarts[i]);
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CHECK(MolToSmiles(*mol) == expected[i++]);
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}
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}
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SECTION("ElementList") {
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auto fname = cdxmlbase + "element-list.cdxml";
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std::vector<std::string> expected = {"[C]CC"};
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std::vector<std::string> expected_smarts = {"[#6]-[#6]-[#6,#7,#8,#16]"};
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auto mols = CDXMLFileToMols(fname);
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CHECK(mols.size() == expected.size());
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int i = 0;
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for (auto &mol : mols) {
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CHECK(MolToSmarts(*mol) == expected_smarts[i]);
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CHECK(MolToSmiles(*mol) == expected[i++]);
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}
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}
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SECTION("Enhanced Stereo") {
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auto fname = cdxmlbase + "beta-cypermethrin.cdxml";
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std::vector<std::string> expected = {
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"CC1(C)[C@H](C=C(Cl)Cl)[C@@H]1C(=O)O[C@H](C#N)c1cccc(Oc2ccccc2)c1"};
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std::vector<std::string> expected_cx = {
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"CC1(C)[C@H](C=C(Cl)Cl)[C@@H]1C(=O)O[C@H](C#N)c1cccc(Oc2ccccc2)c1 |&1:3,&2:8,12|"};
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auto mols = CDXMLFileToMols(fname);
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CHECK(mols.size() == expected.size());
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int i = 0;
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for (auto &mol : mols) {
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mol.get()->clearConformers();
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CHECK(MolToSmiles(*mol) == expected[i]);
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CHECK(MolToCXSmiles(*mol) == expected_cx[i++]);
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}
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}
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SECTION("Enhanced Stereo 2") {
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auto fname = cdxmlbase + "beta-cypermethrin-or-abs.cdxml";
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std::vector<std::string> expected = {
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"CC1(C)[C@H](C=C(Cl)Cl)[C@@H]1C(=O)O[C@H](C#N)c1cccc(Oc2ccccc2)c1"};
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std::vector<std::string> expected_cx = {
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"CC1(C)[C@H](C=C(Cl)Cl)[C@@H]1C(=O)O[C@H](C#N)c1cccc(Oc2ccccc2)c1 |o1:8,12|"};
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auto mols = CDXMLFileToMols(fname);
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CHECK(mols.size() == expected.size());
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int i = 0;
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for (auto &mol : mols) {
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mol.get()->clearConformers();
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CHECK(MolToSmiles(*mol) == expected[i]);
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CHECK(MolToCXSmiles(*mol) == expected_cx[i++]);
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}
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}
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SECTION("Bad CDXML") {
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auto fname = cdxmlbase + "bad-cdxml.cdxml";
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// Only one passes sanitization
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{
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std::vector<std::string> expected = {"*c1ccccc1"};
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std::vector<std::string> expected_smarts = {
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"[#6]1:[#6]:[#6]:[#6]:[#6]:[#6]:1-*",
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};
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auto mols = CDXMLFileToMols(fname);
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CHECK(mols.size() == expected.size());
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int i = 0;
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for (auto &mol : mols) {
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CHECK(MolToSmarts(*mol) == expected_smarts[i]);
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CHECK(MolToSmiles(*mol) == expected[i++]);
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}
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}
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// setting sanitization to false, we get both
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std::vector<std::string> expected = {"*C1=C([H])C([H])=C([H])C([H])=C1[H]",
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"*C1=C([H])N([H])=C([H])C([H])=C1[H]"};
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std::vector<std::string> expected_smarts = {
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"[#6]1(=[#6](-[#6](=[#6](-[#6](=[#6]-1-*)-[H])-[H])-[H])-[H])-[H]",
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"[#6]1(=[#6](-[#6](=[#7](-[#6](=[#6]-1-[!#1])-[H])-[H])-[H])-[H])-[H]",
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};
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auto mols = CDXMLFileToMols(fname, false);
|
|
CHECK(mols.size() == expected.size());
|
|
int i = 0;
|
|
for (auto &mol : mols) {
|
|
CHECK(MolToSmarts(*mol) == expected_smarts[i]);
|
|
CHECK(MolToSmiles(*mol) == expected[i++]);
|
|
}
|
|
}
|
|
|
|
SECTION("Fusion with chirality") {
|
|
auto fname = cdxmlbase + "fusion-chiral.cdxml";
|
|
auto mols = CDXMLFileToMols(fname);
|
|
std::vector<std::string> expected = {"C[C@@H](O)[C@@H](C)O"};
|
|
CHECK(mols.size() == expected.size());
|
|
int i = 0;
|
|
for (auto &mol : mols) {
|
|
CHECK(MolToSmiles(*mol) == expected[i++]);
|
|
}
|
|
}
|
|
|
|
SECTION("ChemDraw Template from the synthesis-workshop") {
|
|
// this was hella fun to validate the stereo-chemistry...
|
|
auto fname = cdxmlbase + "chemdraw_template1.cdxml";
|
|
auto mols = CDXMLFileToMols(fname);
|
|
std::vector<std::string> expected = {
|
|
"CCC/C=C/C=C/C(=O)O[C@H]1/C(=C/C(=O)OC)C[C@H]2C[C@H]([C@@H](C)O)OC(=O)C[C@H](O)C[C@@H]3C[C@H](OC(C)=O)C(C)(C)[C@](O)(C[C@@H]4C/C(=C/C(=O)OC)C[C@H](/C=C/C(C)(C)[C@]1(O)O2)O4)O3",
|
|
"[B]",
|
|
"*",
|
|
"[C]",
|
|
"Cc1ccc2n1[C@@H]1[C@@H]3O[C@]([C@H](C)O)(C=C2)[C@H]1c1ccc(C)n1[C@@H]3C",
|
|
"Cc1ccc2n1[C@H](C)C(=O)[C@@H]1[C@H]2C(=O)C=Cc2ccc(C)n21",
|
|
"Cc1ccc2ccc(=O)ccn12",
|
|
"Cc1cccn1[C@H](C)C=O",
|
|
"Cc1ccc2ccc([O-])cc[n+]1-2",
|
|
"Cc1ccc2ccc(=O)ccn12",
|
|
"Cc1cccn1[C@H](C)C(C#N)O[Si](C)(C)C",
|
|
"CC1CCC2(O)C3(OC4(O)C[C@]2(C)C2(O)[C@H](OC(=O)c5ccc[nH]5)C(O)(C(C)C)C4(C)C32O)C1O",
|
|
"C=C(C)[C@H]1CC(=O)CC2=C(C1)[C@H]1C(=O)O[C@H]3C[C@@](C)(O)[C@@H](C2=O)[C@@H]13"};
|
|
CHECK(mols.size() == expected.size());
|
|
int i = 0;
|
|
for (auto &mol : mols) {
|
|
CHECK(MolToSmiles(*mol) == expected[i++]);
|
|
}
|
|
}
|
|
|
|
SECTION("deuterium atom") {
|
|
auto fname = cdxmlbase + "deuterium-atom.cdxml";
|
|
auto mols = CDXMLFileToMols(fname, false, false);
|
|
std::vector<std::string> expected = {"[2H]"};
|
|
CHECK(mols.size() == expected.size());
|
|
int i = 0;
|
|
for (auto &mol : mols) {
|
|
CHECK(MolToSmiles(*mol) == expected[i++]);
|
|
}
|
|
}
|
|
SECTION("ChemDraw Template 2 from the synthesis-workshop") {
|
|
// this was another hella fun to validate the stereo-chemistry...
|
|
// there were so many stereo warnings in chemdraw, I'm just going to
|
|
// assume
|
|
// the rdkit is correct here...
|
|
auto fname = cdxmlbase + "chemdraw_template2.cdxml";
|
|
auto mols = CDXMLFileToMols(fname);
|
|
std::vector<std::string> expected = {
|
|
"CCN1CC2(COC)CCC(OC)C34C5CC6C(OC)CC(O)(C(CC23)C14)C5C6O",
|
|
"*",
|
|
"C",
|
|
"[F]",
|
|
"[B]",
|
|
"[C]",
|
|
"[2H]",
|
|
"CCN1CC2(COC)CCC(OC)C34C5CC6C(OC)CC(O)(C(CC23)C14)C5C6O",
|
|
"*",
|
|
"C",
|
|
"[F]",
|
|
"[B]",
|
|
"[C]",
|
|
"[2H]",
|
|
"CCN1CC2(COC)CCC(OC)C34C5CC6C(OC)CC(O)(C(CC23)C14)C5C6O",
|
|
"*",
|
|
"C",
|
|
"[F]",
|
|
"[B]",
|
|
"[C]",
|
|
"[2H]",
|
|
"CCN1CC2(COC)CCC(OC)C34C5CC6C(OC)CC(O)(C(CC23)C14)C5C6O",
|
|
"*",
|
|
"C",
|
|
"[F]",
|
|
"[B]",
|
|
"[C]",
|
|
"[2H]",
|
|
"CCN1CC2(COC)CCC(OC)C34C5CC6C(OC)CC(O)(C(CC23)C14)C5C6O",
|
|
"CCN1CC2(COC)CCC(OC)C34C5CC6C(OC)CC(O)(C(CC23)C14)C5C6O",
|
|
"*",
|
|
"[B]",
|
|
"[C]",
|
|
"[2H]",
|
|
"C",
|
|
"[F]",
|
|
"*",
|
|
"C",
|
|
"[F]",
|
|
"[B]",
|
|
"[C]",
|
|
"[2H]",
|
|
"CCN1CC2(COC)CCC(OC)C34C5CC6C(OC)CC(O)(C(CC23)C14)C5C6O",
|
|
"*",
|
|
"C",
|
|
"[F]",
|
|
"[B]",
|
|
"[C]",
|
|
"[2H]",
|
|
"CCN1CC2(COC)CCC(OC)C34C5CC6C(OC)CC(O)(C(CC23)C14)C5C6O",
|
|
"*",
|
|
"C",
|
|
"[F]",
|
|
"[B]",
|
|
"[C]",
|
|
"[2H]",
|
|
"CC1CCC2(O)C3(OC4(O)C[C@]2(C)C2(O)[C@H](O)C(O)(C(C)C)C4(C)C32O)C1O",
|
|
"CC1=C(C(C)C)[C@@H](O)C2(O)C1(O)C13OC(=O)C[C@@]2(C)C1(O)CCC(C)C3O",
|
|
"CC1=CC23OC(=O)C[C@@](C)(C2(O)CC1)C1(O)[C@H](O)C2(C(C)C)OC2(C)C31O",
|
|
"*",
|
|
"[B]",
|
|
"[C]",
|
|
"CC1CCC2C3(C1)OC1C[C@]2(C)C2CC(C(C)C)C1(C)C23",
|
|
"[2H]",
|
|
"*",
|
|
"[B]",
|
|
"[C]",
|
|
"C",
|
|
"CC1CCC2(O)C3(OC4(O)C[C@]2(C)C2(O)[C@H](O)C(O)(C(C)C)C4(C)C32O)C1O",
|
|
"[2H]"};
|
|
CHECK(mols.size() == expected.size());
|
|
int i = 0;
|
|
for (auto &mol : mols) {
|
|
CHECK(MolToSmiles(*mol) == expected[i++]);
|
|
}
|
|
}
|
|
SECTION("ChemDraw Template 3 from the synthesis-workshop") {
|
|
// this was another hella fun to validate the stereo-chemistry...
|
|
// there were so many stereo warnings in chemdraw, I'm just going to
|
|
// assume
|
|
// the rdkit is correct here...
|
|
auto fname = cdxmlbase + "chemdraw_template3.cdxml";
|
|
auto mols = CDXMLFileToMols(fname);
|
|
std::vector<std::string> expected = {
|
|
"CCC/C=C/C=C/C(=O)O[C@H]1/C(=C/C(=O)OC)C[C@H]2C[C@H]([C@@H](C)O)OC(=O)C[C@H](O)C[C@@H]3C[C@H](OC(C)=O)C(C)(C)[C@](O)(C[C@@H]4C/C(=C/C(=O)OC)C[C@H](/C=C/C(C)(C)[C@]1(O)O2)O4)O3",
|
|
"[B]",
|
|
"*",
|
|
"[C]",
|
|
"CCC/C=C/C=C/C(=O)O[C@H]1/C(=C/C(=O)OC)C[C@H]2C[C@H]([C@@H](C)O)OC(=O)C[C@H](O)C[C@@H]3C[C@H](OC(C)=O)C(C)(C)[C@](O)(C[C@@H]4C/C(=C/C(=O)OC)C[C@H](/C=C/C(C)(C)[C@]1(O)O2)O4)O3",
|
|
"[B]",
|
|
"*",
|
|
"[C]",
|
|
"CCC/C=C/C=C/C(=O)O[C@H]1/C(=C/C(=O)OC)C[C@@H](C[C@@H](O)[C@@H](C)O)O[C@@]1(O)C(C)(C)/C=C/C=O",
|
|
"*",
|
|
"[C]",
|
|
"C=C(C[C@H]([O])C[C@]1(O)O[C@H](C[C@@H](O)CC(=O)O)C[C@H](OC(C)=O)C1(C)C)C[Si](C)(C)C",
|
|
"*.CC[Si](CC)CC",
|
|
"CC[Si](C)(CC)CC",
|
|
"CC[Si](C)(CC)CC",
|
|
"CC",
|
|
"CC",
|
|
"*",
|
|
"C=C(C[C@H]([O])C[C@]1(O)O[C@H](C[C@@H](O)CC(=O)O)C[C@H](OC(C)=O)C1(C)C)C[Si](C)(C)C",
|
|
"*.CC[Si](CC)CC",
|
|
"CCC/C=C/C=C/C(=O)O[C@H]1/C(=C/C(=O)OC)C[C@@H](C[C@@H](O)[C@@H](C)O)O[C@@]1(O)C(C)(C)/C=C/C=O",
|
|
"[C]"};
|
|
int i = 0;
|
|
for (auto &mol : mols) {
|
|
CHECK(MolToSmiles(*mol) == expected[i++]);
|
|
}
|
|
}
|
|
SECTION("protecting group") {
|
|
auto fname = cdxmlbase + "protecting-groups.cdxml";
|
|
auto mols = CDXMLFileToMols(fname);
|
|
std::vector<std::string> expected = {"CC[Si](C)(CC)CC", "CC"};
|
|
CHECK(mols.size() == expected.size());
|
|
int i = 0;
|
|
for (auto &mol : mols) {
|
|
CHECK(MolToSmiles(*mol) == expected[i++]);
|
|
}
|
|
}
|
|
SECTION("protecting group 2") {
|
|
auto fname = cdxmlbase + "protecting-groups2.cdxml";
|
|
auto mols = CDXMLFileToMols(fname);
|
|
std::vector<std::string> expected = {"CC[Si](C)(CC)CC", "CC"};
|
|
CHECK(mols.size() == expected.size());
|
|
int i = 0;
|
|
for (auto &mol : mols) {
|
|
CHECK(MolToSmiles(*mol) == expected[i++]);
|
|
}
|
|
}
|
|
|
|
SECTION("floating protecting group") {
|
|
auto fname = cdxmlbase + "floating-protecting-group.cdxml";
|
|
// This is a weird one, chemdraw simply ignores the error that causes the
|
|
// bond issue, we should probably drop the floating fragment here if
|
|
// we are sanitizing
|
|
auto mols = CDXMLFileToMols(fname);
|
|
std::vector<std::string> expected = {
|
|
"*",
|
|
"C=C(C[C@H]([O])C[C@]1(O)O[C@H](C[C@@H](O)CC(=O)O)C[C@H](OC(C)=O)C1(C)C)C[Si](C)(C)C",
|
|
"*.CC[Si](CC)CC"};
|
|
CHECK(mols.size() == expected.size());
|
|
int i = 0;
|
|
for (auto &mol : mols) {
|
|
CHECK(MolToSmiles(*mol) == expected[i++]);
|
|
}
|
|
}
|
|
|
|
SECTION("Missing File Name") {
|
|
try {
|
|
auto mols = CDXMLFileToMols("missing file");
|
|
CHECK(0); // Bad file exception not caught
|
|
} catch (RDKit::BadFileException &) {
|
|
}
|
|
}
|
|
|
|
SECTION("Aromatic ring (bondorder==4") {
|
|
auto fname = cdxmlbase + "aromatic.cdxml";
|
|
auto mols = CDXMLFileToMols(fname);
|
|
std::vector<std::string> expected = {"c1ccccc1"};
|
|
CHECK(mols.size() == expected.size());
|
|
int i = 0;
|
|
for (auto &mol : mols) {
|
|
CHECK(MolToSmiles(*mol) == expected[i++]);
|
|
}
|
|
}
|
|
SECTION("Malformed") {
|
|
auto fname = cdxmlbase + "malformed.cdxml";
|
|
try {
|
|
auto mols = CDXMLFileToMols(fname);
|
|
CHECK(0);
|
|
} catch (FileParseException &e) {
|
|
CHECK(std::string(e.what()) == "expected > at line: 373");
|
|
}
|
|
}
|
|
SECTION("Lots of stereo") {
|
|
{
|
|
auto fname = cdxmlbase + "stereo.cdxml";
|
|
std::vector<std::string> expected = {
|
|
"C[C@@H](Cl)[C@H](N)O.C[C@@H](F)[C@H](N)O.C[C@H](Br)[C@@H](N)O.C[C@H](I)[C@@H](N)O"};
|
|
auto mols = CDXMLFileToMols(fname);
|
|
CHECK(mols.size() == expected.size());
|
|
int i = 0;
|
|
for (auto &mol : mols) {
|
|
CHECK(MolToSmiles(*mol) == expected[i++]);
|
|
}
|
|
}
|
|
{
|
|
auto fname = cdxmlbase + "wavy.cdxml";
|
|
std::vector<std::string> expected = {"Cc1cccc(C)c1NC(=O)N=C1CCCN1C",
|
|
"Cc1cccc(C)c1NC(=O)/N=C1\\CCCN1C"};
|
|
auto mols = CDXMLFileToMols(fname);
|
|
CHECK(mols.size() == expected.size());
|
|
int i = 0;
|
|
for (auto &mol : mols) {
|
|
if (i == 0) {
|
|
CHECK(mol->getBondWithIdx(11)->getStereo() ==
|
|
Bond::BondStereo::STEREOANY);
|
|
}
|
|
CHECK(MolToSmiles(*mol) == expected[i++]);
|
|
}
|
|
}
|
|
{
|
|
auto fname = cdxmlbase + "wavy-single.cdxml";
|
|
std::vector<std::string> expected = {"CCCC"};
|
|
auto mols = CDXMLFileToMols(fname);
|
|
CHECK(mols.size() == expected.size());
|
|
int i = 0;
|
|
for (auto &mol : mols) {
|
|
CHECK(mol->getBondWithIdx(0)->getBondDir() == Bond::BondDir::NONE);
|
|
CHECK(mol->getBondWithIdx(1)->getBondDir() == Bond::BondDir::NONE);
|
|
CHECK(mol->getBondWithIdx(2)->getBondDir() == Bond::BondDir::NONE);
|
|
CHECK(MolToSmiles(*mol) == expected[i++]);
|
|
}
|
|
}
|
|
}
|
|
SECTION("Lots of bad stereo") {
|
|
{
|
|
auto fname = cdxmlbase + "bad-id.cdxml";
|
|
auto mols = CDXMLFileToMols(fname);
|
|
CHECK(mols.size() == 0);
|
|
}
|
|
{
|
|
auto fname = cdxmlbase + "bad-coords.cdxml";
|
|
auto mols = CDXMLFileToMols(fname);
|
|
CHECK(mols.size() == 0);
|
|
}
|
|
{
|
|
auto fname = cdxmlbase + "bad-bondorder.cdxml";
|
|
auto mols = CDXMLFileToMols(fname);
|
|
CHECK(mols.size() == 0);
|
|
}
|
|
{
|
|
auto fname = cdxmlbase + "bad-bondorder2.cdxml";
|
|
auto mols = CDXMLFileToMols(fname);
|
|
CHECK(mols.size() == 0);
|
|
}
|
|
}
|
|
}
|