File: file_parsers_catch.cpp

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//
//  Copyright (C) 2020 Greg Landrum
//   @@ All Rights Reserved @@
//  This file is part of the RDKit.
//  The contents are covered by the terms of the BSD license
//  which is included in the file license.txt, found at the root
//  of the RDKit source tree.
//

#include "RDGeneral/test.h"
#include "catch.hpp"

#include <GraphMol/RDKitBase.h>
#include <GraphMol/QueryAtom.h>
#include <GraphMol/MolPickler.h>
#include <GraphMol/FileParsers/FileParsers.h>
#include <GraphMol/SmilesParse/SmilesWrite.h>
#include <GraphMol/SmilesParse/SmilesParse.h>
#include <GraphMol/SmilesParse/SmartsWrite.h>
#include <GraphMol/FileParsers/SequenceParsers.h>
#include <GraphMol/FileParsers/SequenceWriters.h>
#include <GraphMol/FileParsers/PNGParser.h>
#include <RDGeneral/FileParseException.h>
#include <boost/algorithm/string.hpp>

using namespace RDKit;

TEST_CASE("Basic SVG Parsing", "[SVG][reader]") {
  SECTION("basics") {
    std::string svg = R"SVG(<?xml version='1.0' encoding='iso-8859-1'?>
<svg version='1.1' baseProfile='full'
              xmlns='http://www.w3.org/2000/svg'
                      xmlns:rdkit='http://www.rdkit.org/xml'
                      xmlns:xlink='http://www.w3.org/1999/xlink'
                  xml:space='preserve'
width='200px' height='200px' >
<rect style='opacity:1.0;fill:#FFFFFF;stroke:none' width='200' height='200' x='0' y='0'> </rect>
<path d='M 9.09091,89.4974 24.2916,84.7462' style='fill:none;fill-rule:evenodd;stroke:#000000;stroke-width:2px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1' />
<path d='M 24.2916,84.7462 39.4923,79.9949' style='fill:none;fill-rule:evenodd;stroke:#0000FF;stroke-width:2px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1' />
<path d='M 86.2908,106.814 75.1709,93.4683 72.0765,96.8285 86.2908,106.814' style='fill:#000000;fill-rule:evenodd;stroke:#000000;stroke-width:2px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1' />
<path d='M 75.1709,93.4683 57.8622,86.8431 64.051,80.1229 75.1709,93.4683' style='fill:#0000FF;fill-rule:evenodd;stroke:#0000FF;stroke-width:2px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1' />
<path d='M 75.1709,93.4683 72.0765,96.8285 57.8622,86.8431 75.1709,93.4683' style='fill:#0000FF;fill-rule:evenodd;stroke:#0000FF;stroke-width:2px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1' />
<path d='M 86.2908,106.814 82.1459,125.293' style='fill:none;fill-rule:evenodd;stroke:#000000;stroke-width:2px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1' />
<path d='M 82.1459,125.293 78.0009,143.772' style='fill:none;fill-rule:evenodd;stroke:#00CC00;stroke-width:2px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1' />
<path d='M 86.2908,106.814 129.89,93.1862' style='fill:none;fill-rule:evenodd;stroke:#000000;stroke-width:2px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1' />
<path d='M 134.347,94.186 138.492,75.7069' style='fill:none;fill-rule:evenodd;stroke:#000000;stroke-width:2px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1' />
<path d='M 138.492,75.7069 142.637,57.2277' style='fill:none;fill-rule:evenodd;stroke:#FF0000;stroke-width:2px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1' />
<path d='M 125.432,92.1865 129.577,73.7074' style='fill:none;fill-rule:evenodd;stroke:#000000;stroke-width:2px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1' />
<path d='M 129.577,73.7074 133.722,55.2282' style='fill:none;fill-rule:evenodd;stroke:#FF0000;stroke-width:2px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1' />
<path d='M 129.89,93.1862 142.557,104.852' style='fill:none;fill-rule:evenodd;stroke:#000000;stroke-width:2px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1' />
<path d='M 142.557,104.852 155.224,116.517' style='fill:none;fill-rule:evenodd;stroke:#FF0000;stroke-width:2px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1' />
<text x='39.4923' y='83.483' style='font-size:15px;font-style:normal;font-weight:normal;fill-opacity:1;stroke:none;font-family:sans-serif;text-anchor:start;fill:#0000FF' ><tspan>NH</tspan></text>
<text x='67.6656' y='158.998' style='font-size:15px;font-style:normal;font-weight:normal;fill-opacity:1;stroke:none;font-family:sans-serif;text-anchor:start;fill:#00CC00' ><tspan>Cl</tspan></text>
<text x='132.777' y='56.228' style='font-size:15px;font-style:normal;font-weight:normal;fill-opacity:1;stroke:none;font-family:sans-serif;text-anchor:start;fill:#FF0000' ><tspan>O</tspan></text>
<text x='149.782' y='131.743' style='font-size:15px;font-style:normal;font-weight:normal;fill-opacity:1;stroke:none;font-family:sans-serif;text-anchor:start;fill:#FF0000' ><tspan>OH</tspan></text>
<text x='89.9952' y='194' style='font-size:12px;font-style:normal;font-weight:normal;fill-opacity:1;stroke:none;font-family:sans-serif;text-anchor:start;fill:#000000' ><tspan>m1</tspan></text>
<metadata>
<rdkit:mol xmlns:rdkit = "http://www.rdkit.org/xml" version="0.9">
<rdkit:atom idx="1" atom-smiles="[CH3]" drawing-x="9.09091" drawing-y="89.4974" x="-2.78651" y="0.295614" z="0" />
<rdkit:atom idx="2" atom-smiles="[NH]" drawing-x="52.6897" drawing-y="75.8699" x="-1.35482" y="0.743114" z="0" />
<rdkit:atom idx="3" atom-smiles="[C@H]" drawing-x="86.2908" drawing-y="106.814" x="-0.251428" y="-0.273019" z="0" />
<rdkit:atom idx="4" atom-smiles="[Cl]" drawing-x="76.2932" drawing-y="151.385" x="-0.579728" y="-1.73665" z="0" />
<rdkit:atom idx="5" atom-smiles="[C]" drawing-x="129.89" drawing-y="93.1862" x="1.18027" y="0.174481" z="0" />
<rdkit:atom idx="6" atom-smiles="[O]" drawing-x="139.887" drawing-y="48.6148" x="1.50857" y="1.63811" z="0" />
<rdkit:atom idx="7" atom-smiles="[OH]" drawing-x="163.491" drawing-y="124.13" x="2.28366" y="-0.841652" z="0" />
<rdkit:bond idx="1" begin-atom-idx="1" end-atom-idx="2" bond-smiles="-" />
<rdkit:bond idx="2" begin-atom-idx="2" end-atom-idx="3" bond-smiles="-" />
<rdkit:bond idx="3" begin-atom-idx="3" end-atom-idx="4" bond-smiles="-" />
<rdkit:bond idx="4" begin-atom-idx="3" end-atom-idx="5" bond-smiles="-" />
<rdkit:bond idx="5" begin-atom-idx="5" end-atom-idx="6" bond-smiles="=" />
<rdkit:bond idx="6" begin-atom-idx="5" end-atom-idx="7" bond-smiles="-" />
</rdkit:mol></metadata>
</svg>)SVG";

    std::unique_ptr<RWMol> mol(RDKitSVGToMol(svg));
    REQUIRE(mol);
    CHECK(mol->getNumAtoms() == 7);
    CHECK(mol->getNumConformers() == 1);
    CHECK_FALSE(mol->getConformer().is3D());
    auto smiles = MolToSmiles(*mol);
    CHECK(smiles == "CN[C@H](Cl)C(=O)O");
  }
}

TEST_CASE(
    "Github #2040: Failure to parse V3K mol file with bonds to multi-center "
    "linkage points",
    "[bug][reader]") {
  std::string rdbase = getenv("RDBASE");
  SECTION("basics") {
    std::string fName =
        rdbase + "/Code/GraphMol/FileParsers/test_data/github2040_1.mol";
    std::unique_ptr<RWMol> mol(
        MolFileToMol(fName, false));  // don't sanitize yet
    REQUIRE(mol);
    CHECK(mol->getBondWithIdx(0)->getBondType() == Bond::SINGLE);
    CHECK(
        mol->getBondWithIdx(0)->hasProp(common_properties::_MolFileBondEndPts));
    CHECK(mol->getBondWithIdx(0)->getProp<std::string>(
              common_properties::_MolFileBondEndPts) == "(3 5 4 3)");
    CHECK(
        mol->getBondWithIdx(0)->hasProp(common_properties::_MolFileBondAttach));
    CHECK(mol->getBondWithIdx(0)->getProp<std::string>(
              common_properties::_MolFileBondAttach) == "ANY");
    CHECK(mol->getBondWithIdx(1)->getBondType() == Bond::AROMATIC);
  }
}

TEST_CASE("Github #2225: failure round-tripping mol block with Q atoms",
          "[bug][writer]") {
  std::string rdbase = getenv("RDBASE");
  SECTION("basics") {
    std::string fName =
        rdbase + "/Code/GraphMol/FileParsers/test_data/github2225_1.mol";
    std::unique_ptr<RWMol> mol(MolFileToMol(fName));
    REQUIRE(mol);
    REQUIRE(mol->getNumAtoms() == 7);
    REQUIRE(!mol->getAtomWithIdx(0)->hasQuery());
    REQUIRE(mol->getAtomWithIdx(6)->hasQuery());
    auto outBlock = MolToMolBlock(*mol);
    REQUIRE(outBlock.find(" Q ") != std::string::npos);
    REQUIRE(outBlock.find(" ALS ") == std::string::npos);
    std::unique_ptr<RWMol> mol2(MolBlockToMol(outBlock));
    REQUIRE(mol2);
    REQUIRE(mol2->getNumAtoms() == 7);
    REQUIRE(!mol2->getAtomWithIdx(0)->hasQuery());
    REQUIRE(mol2->getAtomWithIdx(6)->hasQuery());
    auto outBlock2 = MolToMolBlock(*mol2);
    REQUIRE(outBlock2.find(" Q ") != std::string::npos);
    REQUIRE(outBlock2.find(" ALS ") == std::string::npos);
  }
  SECTION("check that SMARTS still works") {
    std::unique_ptr<RWMol> mol(SmartsToMol("C[#8,#7]"));
    REQUIRE(mol);
    REQUIRE(mol->getNumAtoms() == 2);
    auto outBlock = MolToMolBlock(*mol);
    REQUIRE(outBlock.find(" Q ") == std::string::npos);
    REQUIRE(outBlock.find(" ALS ") != std::string::npos);
    std::unique_ptr<RWMol> mol2(MolBlockToMol(outBlock));
    REQUIRE(mol2);
    auto smarts = MolToSmarts(*mol2);
    REQUIRE(smarts == "[#6][#8,#7]");
  }
  SECTION("basics with v3K") {
    std::string fName =
        rdbase + "/Code/GraphMol/FileParsers/test_data/github2225_2.mol";
    std::unique_ptr<RWMol> mol(MolFileToMol(fName));
    REQUIRE(mol);
    REQUIRE(mol->getNumAtoms() == 7);
    REQUIRE(!mol->getAtomWithIdx(0)->hasQuery());
    REQUIRE(mol->getAtomWithIdx(6)->hasQuery());

    bool includeStereo = true;
    int confId = -1;
    bool kekulize = true;
    bool forceV3000 = true;
    auto outBlock =
        MolToMolBlock(*mol, includeStereo, confId, kekulize, forceV3000);
    REQUIRE(outBlock.find(" Q ") != std::string::npos);
    REQUIRE(outBlock.find(" ALS ") == std::string::npos);
    std::unique_ptr<RWMol> mol2(MolBlockToMol(outBlock));
    REQUIRE(mol2);
    REQUIRE(mol2->getNumAtoms() == 7);
    REQUIRE(!mol2->getAtomWithIdx(0)->hasQuery());
    REQUIRE(mol2->getAtomWithIdx(6)->hasQuery());
    auto outBlock2 =
        MolToMolBlock(*mol2, includeStereo, confId, kekulize, forceV3000);
    REQUIRE(outBlock2.find(" Q ") != std::string::npos);
    REQUIRE(outBlock2.find(" ALS ") == std::string::npos);
  }
  SECTION("check that SMARTS still works with v3K output") {
    std::unique_ptr<RWMol> mol(SmartsToMol("C[#8,#7]"));
    REQUIRE(mol);
    REQUIRE(mol->getNumAtoms() == 2);
    bool includeStereo = true;
    int confId = -1;
    bool kekulize = true;
    bool forceV3000 = true;
    auto outBlock =
        MolToMolBlock(*mol, includeStereo, confId, kekulize, forceV3000);
    REQUIRE(outBlock.find(" Q ") == std::string::npos);
    REQUIRE(outBlock.find(" [O,N] ") != std::string::npos);
    std::unique_ptr<RWMol> mol2(MolBlockToMol(outBlock));
    REQUIRE(mol2);
    auto smarts = MolToSmarts(*mol2);
    REQUIRE(smarts == "[#6][#8,#7]");
  }
}
TEST_CASE(
    "Github #2229: problem round-tripping mol files with bond topology info",
    "[bug][writer]") {
  std::string rdbase = getenv("RDBASE");
  std::string fName =
      rdbase + "/Code/GraphMol/FileParsers/test_data/github2229_1.mol";
  std::unique_ptr<RWMol> mol(MolFileToMol(fName));
  REQUIRE(mol);
  REQUIRE(mol->getNumBonds() == 9);
  REQUIRE(!mol->getBondWithIdx(0)->hasQuery());
  REQUIRE(mol->getBondWithIdx(7)->hasQuery());
  SECTION("basics") {
    auto outBlock = MolToMolBlock(*mol);
    REQUIRE(outBlock.find(" 7  8  1  0  0  2") != std::string::npos);
    std::unique_ptr<RWMol> mol2(MolBlockToMol(outBlock));
    REQUIRE(mol2);
    REQUIRE(mol2->getNumBonds() == 9);
    REQUIRE(!mol2->getBondWithIdx(0)->hasQuery());
    REQUIRE(mol2->getBondWithIdx(7)->hasQuery());
  }
  SECTION("basics with v3k") {
    bool includeStereo = true;
    int confId = -1;
    bool kekulize = true;
    bool forceV3000 = true;
    auto outBlock =
        MolToMolBlock(*mol, includeStereo, confId, kekulize, forceV3000);
    REQUIRE(outBlock.find("1 7 8 TOPO=2") != std::string::npos);
    std::unique_ptr<RWMol> mol2(MolBlockToMol(outBlock));
    REQUIRE(mol2);
    REQUIRE(mol2->getNumBonds() == 9);
    REQUIRE(!mol2->getBondWithIdx(0)->hasQuery());
    REQUIRE(mol2->getBondWithIdx(7)->hasQuery());
  }
}
TEST_CASE("preserve mol file properties on bonds", "[reader][ctab]") {
  SECTION("basics") {
    std::string molblock = R"CTAB(
  Mrv1810 02111915042D          

  4  3  0  0  0  0            999 V2000
   -1.5625    1.6071    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8480    2.0196    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2770    2.0196    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5625    0.7821    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
  1  3  1  0  0  0  0
  1  2  6  0  0  0  0
  1  4  1  1  0  0  0
M  END
      )CTAB";
    std::unique_ptr<ROMol> mol(MolBlockToMol(molblock));
    REQUIRE(mol);
    CHECK(mol->getBondWithIdx(1)->getProp<unsigned int>(
              common_properties::_MolFileBondType) == 6);
    CHECK(mol->getBondWithIdx(2)->getProp<unsigned int>(
              common_properties::_MolFileBondType) == 1);
    CHECK(mol->getBondWithIdx(2)->getProp<unsigned int>(
              common_properties::_MolFileBondStereo) == 1);
  }
  SECTION("basics-v3k") {
    std::string molblock = R"CTAB(
  Mrv1810 02111915102D          

  0  0  0     0  0            999 V3000
M  V30 BEGIN CTAB
M  V30 COUNTS 4 3 0 0 0
M  V30 BEGIN ATOM
M  V30 1 C -2.9167 3 0 0
M  V30 2 C -1.583 3.77 0 0
M  V30 3 C -4.2503 3.77 0 0
M  V30 4 C -2.9167 1.46 0 0
M  V30 END ATOM
M  V30 BEGIN BOND
M  V30 1 1 1 3
M  V30 2 6 1 2
M  V30 3 1 1 4 CFG=1
M  V30 END BOND
M  V30 END CTAB
M  END
)CTAB";
    std::unique_ptr<ROMol> mol(MolBlockToMol(molblock));
    REQUIRE(mol);
    CHECK(mol->getBondWithIdx(1)->getProp<unsigned int>(
              common_properties::_MolFileBondType) == 6);
    CHECK(mol->getBondWithIdx(2)->getProp<unsigned int>(
              common_properties::_MolFileBondType) == 1);
    CHECK(mol->getBondWithIdx(2)->getProp<unsigned int>(
              common_properties::_MolFileBondCfg) == 1);
  }
}

TEST_CASE("github #2277 : Failure when parsing mol block with M PXA",
          "[reader][ctab]") {
  std::string molblock = R"CTAB(
  Mrv1810 02151911552D          

 13 12  0  0  1  0            999 V2000
   -3.6588  -26.0592    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   -2.9453  -27.2971    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9453  -26.4713    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.6588  -25.2360    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9467  -24.8200    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9467  -23.9968    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2304  -25.2358    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5102  -26.4716    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7989  -25.2306    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7989  -26.0582    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.3730  -26.4732    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2277  -26.0635    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0839  -26.4708    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  1  3  1  0  0  0  0
  3  2  2  0  0  0  0
  1  4  1  1  0  0  0
  4  5  1  0  0  0  0
  5  6  1  0  0  0  0
  5  7  1  0  0  0  0
  8 10  1  0  0  0  0
 10  9  2  0  0  0  0
  3 12  1  0  0  0  0
 12  8  1  0  0  0  0
 11  1  1  0  0  0  0
 10 13  1  0  0  0  0
M  PXA  11   -5.0817  -26.0408    0.0000 H
M  END
)CTAB";
  std::unique_ptr<ROMol> mol(MolBlockToMol(molblock));
  SECTION("basics, make sure we can parse the original data") {
    REQUIRE(mol);
    CHECK(mol->getAtomWithIdx(10)->hasProp("_MolFile_PXA"));
    CHECK(!mol->getAtomWithIdx(11)->hasProp("_MolFile_PXA"));
  }
  SECTION("basics, can we write it?") {
    REQUIRE(mol);
    std::string outmb = MolToMolBlock(*mol);
    CHECK(outmb.find("M  PXA  11") != std::string::npos);
  }
}

TEST_CASE(
    "github #2266: missing stereo in adamantyl-like cages with "
    "exocyclic bonds",
    "[bug]") {
  SECTION("basics") {
    std::string molblock = R"CTAB(
        SciTegic12231509382D

 14 16  0  0  0  0            999 V2000
    1.5584   -5.7422    0.0000 C   0  0
    2.2043   -5.0535    0.0000 C   0  0  2  0  0  0
    2.3688   -5.5155    0.0000 C   0  0  1  0  0  0
    2.9210   -5.3181    0.0000 C   0  0
    3.1270   -5.8206    0.0000 C   0  0
    3.6744   -5.1312    0.0000 C   0  0  2  0  0  0
    2.3619   -4.6609    0.0000 C   0  0
    2.9268   -3.9939    0.0000 C   0  0  2  0  0  0
    2.1999   -4.2522    0.0000 C   0  0
    3.6803   -4.3062    0.0000 C   0  0
    2.9436   -3.1692    0.0000 N   0  0
    4.4569   -5.4095    0.0000 H   0  0
    2.3246   -6.3425    0.0000 H   0  0
    1.4365   -4.7500    0.0000 H   0  0
  1  2  1  0
  1  3  1  0
  2  4  1  0
  3  5  1  0
  4  6  1  0
  5  6  1  0
  7  8  1  0
  3  7  1  0
  2  9  1  0
  6 10  1  0
 10  8  1  0
  8  9  1  0
  8 11  1  1
  6 12  1  6
  3 13  1  1
  2 14  1  6
M  END)CTAB";
    {
      std::unique_ptr<ROMol> mol(MolBlockToMol(molblock));
      REQUIRE(mol);
      CHECK(mol->getNumAtoms() == 11);
      CHECK(mol->getAtomWithIdx(1)->getChiralTag() != Atom::CHI_UNSPECIFIED);
      CHECK(mol->getAtomWithIdx(2)->getChiralTag() != Atom::CHI_UNSPECIFIED);
      CHECK(mol->getAtomWithIdx(5)->getChiralTag() != Atom::CHI_UNSPECIFIED);
    }
    {
      bool sanitize = true;
      bool removeHs = false;
      std::unique_ptr<ROMol> mol(MolBlockToMol(molblock, sanitize, removeHs));
      REQUIRE(mol);
      CHECK(mol->getNumAtoms() == 14);

      CHECK(mol->getAtomWithIdx(1)->getChiralTag() != Atom::CHI_UNSPECIFIED);
      CHECK(mol->getAtomWithIdx(2)->getChiralTag() != Atom::CHI_UNSPECIFIED);
      CHECK(mol->getAtomWithIdx(5)->getChiralTag() != Atom::CHI_UNSPECIFIED);
    }
  }
  SECTION("with F") {
    std::string molblock = R"CTAB(
        SciTegic12231509382D

 14 16  0  0  0  0            999 V2000
    1.5584   -5.7422    0.0000 C   0  0
    2.2043   -5.0535    0.0000 C   0  0  2  0  0  0
    2.3688   -5.5155    0.0000 C   0  0  1  0  0  0
    2.9210   -5.3181    0.0000 C   0  0
    3.1270   -5.8206    0.0000 C   0  0
    3.6744   -5.1312    0.0000 C   0  0  2  0  0  0
    2.3619   -4.6609    0.0000 C   0  0
    2.9268   -3.9939    0.0000 C   0  0  2  0  0  0
    2.1999   -4.2522    0.0000 C   0  0
    3.6803   -4.3062    0.0000 C   0  0
    2.9436   -3.1692    0.0000 N   0  0
    4.4569   -5.4095    0.0000 F   0  0
    2.3246   -6.3425    0.0000 F   0  0
    1.4365   -4.7500    0.0000 F   0  0
  1  2  1  0
  1  3  1  0
  2  4  1  0
  3  5  1  0
  4  6  1  0
  5  6  1  0
  7  8  1  0
  3  7  1  0
  2  9  1  0
  6 10  1  0
 10  8  1  0
  8  9  1  0
  8 11  1  1
  6 12  1  6
  3 13  1  1
  2 14  1  6
M  END)CTAB";
    {
      std::unique_ptr<ROMol> mol(MolBlockToMol(molblock));
      REQUIRE(mol);
      CHECK(mol->getNumAtoms() == 14);
      CHECK(mol->getAtomWithIdx(1)->getChiralTag() != Atom::CHI_UNSPECIFIED);
      CHECK(mol->getAtomWithIdx(2)->getChiralTag() != Atom::CHI_UNSPECIFIED);
      CHECK(mol->getAtomWithIdx(5)->getChiralTag() != Atom::CHI_UNSPECIFIED);
    }
  }
}

TEST_CASE("parsing of SCN lines", "[bug][sgroups]") {
  SECTION("basics") {
    std::string molblock = R"CTAB(
  MJ171200

 76 80  0  0  0  0  0  0  0  0999 V2000
   -6.4802    2.6494    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -6.8927    3.3638    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -7.7177    3.3638    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -8.1302    2.6494    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -7.7177    1.9349    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -6.8927    1.9349    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.2426    1.9349    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.6552    2.6494    0.0000 Cl  0  0  0  0  0  0  0  0  0  0  0  0
   -6.4802    1.2203    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -5.6552    1.2203    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.0051    1.2203    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.4176    1.9349    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.2426    0.5060    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.4176    0.5060    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -6.8927    0.5060    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -6.4802   -0.2085    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.6552   -0.2085    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -8.1302    1.2203    0.0000 Cl  0  0  0  0  0  0  0  0  0  0  0  0
   -6.8927   -0.9230    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -6.4802   -1.6374    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.6552   -1.6374    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.0051   -1.6374    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -5.2426   -2.3519    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -4.4176   -2.3519    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.0051   -3.0663    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1801   -3.0663    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7676   -3.7808    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.4176   -3.7808    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.0051   -4.4953    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1801   -4.4953    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -6.3243   -3.7791    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -6.7368   -3.0648    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -7.5619   -3.0648    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -7.9744   -3.7791    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -7.5619   -4.4936    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -6.7368   -4.4936    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -6.3243   -5.2082    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -7.9744   -5.2082    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -7.5619   -5.9226    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -6.7368   -5.9226    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -7.9744   -2.3503    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -8.7994   -2.3503    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -8.7994   -3.7791    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -9.9487   -5.1497    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
   -6.3243   -6.6371    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.3705   -2.2987    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.9580   -1.5842    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.1329   -1.5842    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2796   -2.2987    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.1329   -3.0132    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.9580   -3.0132    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.1329   -0.1553    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2796   -0.8698    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.3705   -3.7276    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2796   -3.7276    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.1329   -4.4420    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.9580   -4.4420    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.3705   -5.1566    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.8575   -2.2792    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.4450   -1.5648    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.6200   -1.5648    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.2073   -2.2792    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.6200   -2.9937    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.4450   -2.9937    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.3789   -3.8003    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -4.3797   -5.2304    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8445   -5.2489    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.3318   -2.2987    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.2075   -3.7082    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.8195   -3.7288    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    6.3448   -2.2597    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.1706   -0.8729    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.3860   -0.6179    0.0000 O   0  5  0  0  0  0  0  0  0  0  0  0
    3.2997   -0.0580    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1046   -2.2987    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.9675   -0.6233    0.0000 Na  0  3  0  0  0  0  0  0  0  0  0  0
  1  2  2  0  0  0  0
  2  3  1  0  0  0  0
  3  4  2  0  0  0  0
  4  5  1  0  0  0  0
  5  6  2  0  0  0  0
  1  6  1  0  0  0  0
  9 10  1  0  0  0  0
  7 10  1  0  0  0  0
  8  1  1  0  0  0  0
  6  9  1  0  0  0  0
 11 12  1  0  0  0  0
 13 14  1  0  0  0  0
 11 14  2  0  0  0  0
 10 13  2  0  0  0  0
 12  7  2  0  0  0  0
 15 16  2  0  0  0  0
 16 17  1  0  0  0  0
 13 17  1  0  0  0  0
  5 18  1  0  0  0  0
 19 20  1  0  0  0  0
 20 21  1  0  0  0  0
 16 19  1  0  0  0  0
 23 24  1  0  0  0  0
 22 24  2  0  0  0  0
 21 23  1  0  0  0  0
 25 26  1  0  0  0  0
 25 24  1  1  0  0  0
 28 29  1  0  0  0  0
 29 30  1  0  0  0  0
 27 30  1  0  0  0  0
 25 28  1  0  0  0  0
 27 26  1  0  0  0  0
 31 32  1  0  0  0  0
 32 33  1  0  0  0  0
 33 34  1  0  0  0  0
 34 35  1  0  0  0  0
 35 36  1  0  0  0  0
 31 36  1  0  0  0  0
 39 40  2  0  0  0  0
 37 40  1  0  0  0  0
 35 38  1  1  0  0  0
 36 37  1  6  0  0  0
 41 42  1  0  0  0  0
 34 43  1  6  0  0  0
 33 41  1  1  0  0  0
 44 38  1  1  0  0  0
 40 45  1  0  0  0  0
 46 47  1  0  0  0  0
 47 48  1  0  0  0  0
 48 49  1  0  0  0  0
 49 50  1  0  0  0  0
 50 51  1  0  0  0  0
 46 51  1  0  0  0  0
 52 53  1  0  0  0  0
 48 53  1  1  0  0  0
 56 57  2  0  0  0  0
 54 57  1  0  0  0  0
 51 54  1  6  0  0  0
 50 55  1  1  0  0  0
 57 58  1  0  0  0  0
 59 60  1  0  0  0  0
 60 61  1  0  0  0  0
 61 62  1  0  0  0  0
 62 63  1  0  0  0  0
 63 64  1  0  0  0  0
 59 64  1  0  0  0  0
 28 65  1  6  0  0  0
 31 65  1  1  0  0  0
 29 66  1  1  0  0  0
 30 67  1  6  0  0  0
 27 55  1  1  0  0  0
 46 68  1  1  0  0  0
 62 68  1  6  0  0  0
 63 69  1  1  0  0  0
 64 70  1  6  0  0  0
 59 71  1  1  0  0  0
 61 72  1  1  0  0  0
 72 73  1  0  0  0  0
 72 74  2  0  0  0  0
 49 75  1  6  0  0  0
M  STY  3   1 SRU   2 SRU   3 SRU
M  SCN  3   1 HT    2 HT    3 HT
M  SAL   1 15  55  50  51  54  57  58  56  46  68  62  63  69  64  70  61
M  SAL   1 11  72  74  73  60  47  48  53  52  49  75  59
M  SMT   1 b
M  SBL   1  2  71  76
M  SAL   2 15  27  26  25  28  65  31  36  37  40  45  39  35  34  43  33
M  SAL   2 15  41  42  32  29  66  24  22  23  21  20  19  16  17  13  10
M  SAL   2 15   7  12  11   9   6   1   8   2   3   4   5  18  14  15  30
M  SAL   2  2  67  38
M  SMT   2 a
M  SBL   2  2  71  46
M  SAL   3 15  38  35  36  37  40  45  39  31  65  28  25  24  22  23  21
M  SAL   3 15  20  19  16  17  13  10   7  12  11   9   6   1   8   2   3
M  SAL   3 15   4   5  18  14  15  26  27  55  50  51  54  57  58  56  46
M  SAL   3 15  68  62  63  69  64  70  61  72  74  73  60  47  48  53  52
M  SAL   3 13  49  75  30  67  29  66  32  33  41  42  34  43  59
M  SMT   3 n
M  SBL   3  2  46  76
M  END
)CTAB";
    std::unique_ptr<ROMol> mol(MolBlockToMol(molblock));
    REQUIRE(mol);
  }
}

TEST_CASE("A couple more S group problems", "[bug][sgroups]") {
  std::string molblock = R"CTAB(CHEMBL3666739
      SciTegic05171617282D

 35 40  0  0  0  0            999 V2000
   -3.6559    5.8551    0.0000 O   0  0
   -2.6152    5.2576    0.0000 C   0  0
   -2.6120    3.7568    0.0000 N   0  0
   -3.9097    3.0028    0.0000 C   0  0
   -5.2093    3.7519    0.0000 C   0  0
   -6.5078    3.0010    0.0000 C   0  0
   -6.5067    1.5010    0.0000 C   0  0
   -5.2071    0.7519    0.0000 C   0  0
   -3.9086    1.5029    0.0000 C   0  0
   -2.6111    0.7486    0.0000 C   0  0
   -2.6111   -0.7486    0.0000 N   0  0
   -1.2964   -1.4973    0.0000 C   0  0
   -1.2907   -2.9981    0.0000 N   0  0
   -2.5870   -3.7544    0.0000 C   0  0
   -2.5748   -5.2506    0.0000 C   0  0
   -3.8815   -6.0264    0.0000 C   0  0
   -5.1819   -5.2707    0.0000 C   0  0
   -6.6004   -5.7374    0.0000 N   0  0
   -7.4849   -4.5227    0.0000 N   0  0
   -6.6189   -3.3309    0.0000 C   0  0
   -5.1934   -3.7757    0.0000 C   0  0
   -3.9049   -3.0000    0.0000 C   0  0
    0.0000   -0.7486    0.0000 C   0  0
    1.2964   -1.4973    0.0000 C   0  0
    2.5929   -0.7486    0.0000 C   0  0
    2.5929    0.7486    0.0000 C   0  0
    1.2964    1.4973    0.0000 C   0  0
    0.0000    0.7486    0.0000 C   0  0
   -1.2964    1.4973    0.0000 N   0  0
   -1.3175    6.0116    0.0000 C   0  0
   -1.3185    7.5117    0.0000 C   0  0
   -0.0200    8.2626    0.0000 C   0  0
    1.2795    7.5135    0.0000 N   0  0
    1.2806    6.0135    0.0000 C   0  0
   -0.0178    5.2626    0.0000 C   0  0
  1  2  2  0
  2  3  1  0
  3  4  1  0
  4  5  2  0
  5  6  1  0
  6  7  2  0
  7  8  1  0
  8  9  2  0
  4  9  1  0
  9 10  1  0
 10 11  2  0
 11 12  1  0
 12 13  1  0
 13 14  1  0
 14 15  2  0
 15 16  1  0
 16 17  2  0
 17 18  1  0
 18 19  1  0
 19 20  2  0
 20 21  1  0
 17 21  1  0
 21 22  2  0
 14 22  1  0
 12 23  2  0
 23 24  1  0
 24 25  2  0
 25 26  1  0
 26 27  2  0
 27 28  1  0
 23 28  1  0
 28 29  2  0
 10 29  1  0
  2 30  1  0
 30 31  2  0
 31 32  1  0
 32 33  2  0
 33 34  1  0
 34 35  2  0
 30 35  1  0
M  STY  1   1 DAT
M  SLB  1   1   1
M  SAL   1  1  33
M  SDT   1 FAKE_MRV_IMPLICIT_H
M  SDD   1     0.5304   -0.4125    DR    ALL  0       0
M  SED   1 IMPL_H1
M  END
)CTAB";
  SECTION("spaces in count lines") {
    std::unique_ptr<ROMol> mol(MolBlockToMol(molblock));
    REQUIRE(mol);
  }
  SECTION("short SDT lines") {
    std::unique_ptr<ROMol> mol(MolBlockToMol(molblock));
    REQUIRE(mol);
    const auto &sgroups = getSubstanceGroups(*mol);
    CHECK(sgroups.size() == 1);
    CHECK(sgroups[0].hasProp("TYPE"));
    CHECK(sgroups[0].getProp<std::string>("TYPE") == "DAT");
    CHECK(sgroups[0].hasProp("FIELDNAME"));
    CHECK(sgroups[0].getProp<std::string>("FIELDNAME") ==
          "FAKE_MRV_IMPLICIT_H");
  }
}

TEST_CASE("Github #2527: handling of \"R\" in CTABs", "[rgroups]") {
  std::string molblock = R"CTAB(example
  Mrv1902 07031913362D          

  2  1  0  0  0  0            999 V2000
   -1.1418    0.0687    0.0000 N   0  0  0  0  0  0  0  0  0  3  0  0
   -1.9668    0.0687    0.0000 R   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
M  END
)CTAB";
  SECTION("basics") {
    bool sanitize = false;
    std::unique_ptr<ROMol> mol(MolBlockToMol(molblock, sanitize));
    REQUIRE(mol);
    auto *at = static_cast<QueryAtom *>(mol->getAtomWithIdx(1));
    REQUIRE(at->hasQuery());
    CHECK(at->getQuery()->getDescription() == "AtomNull");
  }
}

TEST_CASE("XYZ", "[XYZ][writer]") {
  SECTION("basics") {
    std::unique_ptr<RWMol> mol{new RWMol{}};
    mol->setProp(common_properties::_Name,
                 "methane\nthis part should not be output");

    for (unsigned z : {6, 1, 1, 1, 1}) {
      auto *a = new Atom{z};
      mol->addAtom(a, false, true);
    }

    auto *conf = new Conformer{5};
    conf->setId(0);
    conf->setAtomPos(0, RDGeom::Point3D{0.000, 0.000, 0.000});
    conf->setAtomPos(1, RDGeom::Point3D{-0.635, -0.635, 0.635});
    conf->setAtomPos(2, RDGeom::Point3D{-0.635, 0.635, -0.635});
    conf->setAtomPos(3, RDGeom::Point3D{0.635, -0.635, -0.635});
    conf->setAtomPos(4, RDGeom::Point3D{0.635, 0.635, 0.635});
    mol->addConformer(conf);

    const std::string xyzblock = MolToXYZBlock(*mol);
    std::string xyzblock_expected = R"XYZ(5
methane
C      0.000000    0.000000    0.000000
H     -0.635000   -0.635000    0.635000
H     -0.635000    0.635000   -0.635000
H      0.635000   -0.635000   -0.635000
H      0.635000    0.635000    0.635000
)XYZ";
    CHECK(xyzblock == xyzblock_expected);
  }
}

TEST_CASE("valence writing 1", "[bug][writer]") {
  SECTION("carbon") {
    std::string molblock = R"CTAB(carbon atom


  1  0  0  0  0  0            999 V2000
   -0.3958   -0.0542    0.0000 C   0  0  0  0  0 15
M  END)CTAB";
    bool sanitize = false;
    bool removeHs = false;
    std::unique_ptr<ROMol> mol(MolBlockToMol(molblock, sanitize, removeHs));
    REQUIRE(mol);
    mol->updatePropertyCache();
    CHECK(mol->getAtomWithIdx(0)->getNoImplicit());
    CHECK(mol->getAtomWithIdx(0)->getExplicitValence() == 0);
    CHECK(mol->getAtomWithIdx(0)->getTotalValence() == 0);
    auto outBlock = MolToMolBlock(*mol);
    REQUIRE(outBlock.find("0  0 15") != std::string::npos);
  }
  SECTION("P valences") {
    std::string molblock = R"CTAB(H2PO2


  3  2  0  0  0  0            999 V2000
    0.2667   -0.4167    0.0000 P   0  0  0  0  0  5
    0.2667    1.1083    0.0000 O   0  0
   -1.0958   -1.0042    0.0000 O   0  0
  2  1  2  0
  3  1  1  0
M  END)CTAB";
    bool sanitize = false;
    bool removeHs = false;
    std::unique_ptr<ROMol> mol(MolBlockToMol(molblock, sanitize, removeHs));
    REQUIRE(mol);
    mol->updatePropertyCache();
    CHECK(mol->getAtomWithIdx(0)->getNoImplicit());
    CHECK(mol->getAtomWithIdx(0)->getExplicitValence() == 5);
    CHECK(mol->getAtomWithIdx(0)->getTotalValence() == 5);
    auto outBlock = MolToMolBlock(*mol);
    REQUIRE(outBlock.find("0  0  5") != std::string::npos);
  }
}

TEST_CASE("Github #2695: Error when a squiggle bond is in an aromatic ring",
          "[bug][reader]") {
  SECTION("reported") {
    auto ctab = R"CTAB(
  -ISIS-  -- StrEd -- 

 19 22  0  0  0  0  0  0  0  0999 V2000
   -3.1355   -0.9331    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6355   -1.7990    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6356   -1.7990    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1356   -0.9331    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6356   -0.0671    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6355   -0.0671    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1355    0.7991    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6355    1.6651    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6356    1.6651    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1356    0.7991    0.0000 C   0  0  3  0  0  0  0  0  0  0  0  0
   -0.1354    0.7991    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.4523    1.6080    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.4034    1.2991    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.2693    1.7990    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.1355    1.2991    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.1355    0.2991    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    2.2693   -0.2011    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4034    0.2991    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.4523   -0.0099    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  2  3  2  0  0  0  0
  3  4  1  0  0  0  0
  4  5  2  0  0  0  0
  5  6  1  0  0  0  0
  1  6  1  0  0  0  0
  6  7  2  0  0  0  0
  7  8  1  0  0  0  0
  8  9  2  0  0  0  0
 10  9  1  4  0  0  0
  5 10  1  0  0  0  0
 10 11  2  0  0  0  0
 11 12  1  0  0  0  0
 12 13  2  0  0  0  0
 13 14  1  0  0  0  0
 14 15  2  0  0  0  0
 15 16  1  0  0  0  0
 16 17  2  0  0  0  0
 17 18  1  0  0  0  0
 13 18  1  0  0  0  0
 18 19  2  0  0  0  0
 11 19  1  0  0  0  0
M  END)CTAB";
    std::unique_ptr<ROMol> mol(MolBlockToMol(ctab));
    REQUIRE(mol);
  }
}

TEST_CASE("Github #2917: _ctab _mol2 and _pdb support", "[feature][reader]") {
  SECTION("_ctab") {
    auto mol = R"CTAB(
  Mrv1810 01292008292D          

  4  3  0  0  0  0            999 V2000
   -3.7669    1.1053    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0524    1.5178    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3380    1.1053    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -4.4814    1.5178    0.0000 F   0  0  0  0  0  0  0  0  0  0  0  0
  2  3  1  0  0  0  0
  1  4  1  0  0  0  0
  1  2  2  0  0  0  0
M  END
)CTAB"_ctab;
    REQUIRE(mol);
    CHECK(mol->getNumAtoms() == 4);
  }
  SECTION("_ctab failure") {
    auto mol = R"CTAB(
  Mrv1810 01292008292D          

  4  3  0  0  0  0            999 V2000
   -3.7669    1.1053    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0524    1.5178    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3380    1.1053    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -4.4814    1.5178    0.0000 F   0  0  0  0  0  0  0  0  0  0  0  0
  2  3  1  0  0  0  0
  3  4  1  0  0  0  0
  3  1  1  0  0  0  0
M  END
)CTAB"_ctab;
    REQUIRE(!mol);
  }
  SECTION("_pdb") {
    auto mol = R"DATA(HEADER    2VNF_PROTEIN
COMPND    2VNF_PROTEIN
REMARK    GENERATED BY X-TOOL on Wed Nov 21 18:02:19 2012
ATOM      1  N   ALA A 225      10.250 -13.177   9.152  1.00 19.76           N
ATOM      2  H   ALA A 225      10.605 -14.082   8.782  1.00  0.00           H
ATOM      3  CA  ALA A 225      11.136 -12.000   9.236  1.00 21.97           C
ATOM      4  HA  ALA A 225      11.079 -11.589  10.244  1.00  0.00           H
ATOM      5  C   ALA A 225      10.683 -10.934   8.231  1.00 21.61           C
ATOM      6  O   ALA A 225      10.811  -9.723   8.485  1.00 20.83           O
ATOM      7  CB  ALA A 225      12.572 -12.399   8.956  1.00 22.98           C
ATOM      8  HB1 ALA A 225      12.892 -13.138   9.690  1.00  0.00           H
ATOM      9  HB2 ALA A 225      12.641 -12.825   7.955  1.00  0.00           H
ATOM     10  HB3 ALA A 225      13.212 -11.519   9.022  1.00  0.00           H
TER      11      ALA A 225
HETATM   12  O   HOH    43      12.371  -9.746   8.354  0.50 30.13           O
END
)DATA"_pdb;
    REQUIRE(mol);
    CHECK(mol->getNumAtoms() == 6);
  }
  SECTION("_pdb failure") {
    auto mol_ok = R"DATA(HEADER    TEST
COMPND    ACY
REMARK    invented
HETATM 2779  C   ACY A 404      15.911  -4.912  26.073  1.00 30.04           C  
HETATM 2780  O   ACY A 404      15.855  -4.063  25.124  1.00 24.12           O  
HETATM 2781  OXT ACY A 404      16.514  -4.578  27.173  1.00 34.44           O  
HETATM 2782  CH3 ACY A 404      15.319  -6.258  25.820  1.00 30.60           C  
CONECT 2780 2781
END
)DATA"_pdb;
    REQUIRE(mol_ok);
    CHECK(mol_ok->getNumAtoms() == 4);
    CHECK(mol_ok->getBondBetweenAtoms(1, 2));

    auto mol_fail = R"DATA(HEADER    TEST
COMPND    ACY
REMARK    invented
HETATM 2779  C   ACY A 404      15.911  -4.912  26.073  1.00 30.04           C  
HETATM 2780  O   ACY A 404      15.855  -4.063  25.124  1.00 24.12           O  
HETATM 2781  OXT ACY A 404      16.514  -4.578  27.173  1.00 34.44           O  
HETATM 2782  CH3 ACY A 404      15.319  -6.258  25.820  1.00 30.60           C  
CONECT 2780 2781
CONECT 2780 2779
CONECT 2780 2782
END
)DATA"_pdb;
    REQUIRE(!mol_fail);
  }
  SECTION("_mol2") {
    auto mol = R"DATA(@<TRIPOS>MOLECULE
UNK
6 4 0 0 0
SMALL
GASTEIGER

@<TRIPOS>ATOM
   1   Na        0.0000    0.0000    0.0000 Na    1 UNL  1.0000
   2    C        0.0000    0.0000    0.0000 C.3   1 UNL -0.0305
   3    H        0.0000    0.0000    0.0000 H     1 UNL  0.0265
   4    H        0.0000    0.0000    0.0000 H     1 UNL  0.0265
   5    H        0.0000    0.0000    0.0000 H     1 UNL  0.0265
   6    H        0.0000    0.0000    0.0000 H     1 UNL  0.0265
@<TRIPOS>BOND
    1     2     3  1
    2     2     4  1
    3     2     5  1
    4     2     6  1
)DATA"_mol2;
    REQUIRE(mol);
    CHECK(mol->getNumAtoms() == 2);
  }
  SECTION("_mol2 failure") {
    auto mol = R"DATA(@<TRIPOS>MOLECULE
UNK
6 5 0 0 0
SMALL
GASTEIGER

@<TRIPOS>ATOM
   1   Na        0.0000    0.0000    0.0000 Na    1 UNL  1.0000
   2    C        0.0000    0.0000    0.0000 C.3   1 UNL -0.0305
   3    H        0.0000    0.0000    0.0000 H     1 UNL  0.0265
   4    H        0.0000    0.0000    0.0000 H     1 UNL  0.0265
   5    H        0.0000    0.0000    0.0000 H     1 UNL  0.0265
   6    H        0.0000    0.0000    0.0000 H     1 UNL  0.0265
@<TRIPOS>BOND
    1     2     3  1
    2     2     4  1
    3     2     5  1
    4     2     6  1
    5     2     1  1
)DATA"_mol2;
    REQUIRE(!mol);
  }
}

TEST_CASE("handling STBOX properties from v3k ctabs", "[feature][v3k]") {
  SECTION("atoms and bonds") {
    auto mol = R"CTAB(basic test
  Mrv1810 01292006422D          

  0  0  0     0  0            999 V3000
M  V30 BEGIN CTAB
M  V30 COUNTS 4 3 0 0 0
M  V30 BEGIN ATOM
M  V30 1 C -7.0316 2.0632 0 0 STBOX=1
M  V30 2 C -5.6979 2.8332 0 0 STBOX=1
M  V30 3 O -4.3642 2.0632 0 0
M  V30 4 F -8.3653 2.8332 0 0
M  V30 END ATOM
M  V30 BEGIN BOND
M  V30 1 1 2 3
M  V30 2 1 1 4
M  V30 3 2 1 2 STBOX=1
M  V30 END BOND
M  V30 END CTAB
M  END
)CTAB"_ctab;
    REQUIRE(mol);
    CHECK(mol->getNumAtoms() == 4);
    int val;
    CHECK(mol->getAtomWithIdx(0)->getPropIfPresent(
        common_properties::molStereoCare, val));
    CHECK(val == 1);
    CHECK(mol->getAtomWithIdx(1)->getPropIfPresent(
        common_properties::molStereoCare, val));
    CHECK(val == 1);
    CHECK(!mol->getAtomWithIdx(2)->hasProp(common_properties::molStereoCare));
    REQUIRE(mol->getBondBetweenAtoms(0, 1));
    CHECK(mol->getBondBetweenAtoms(0, 1)->getPropIfPresent(
        common_properties::molStereoCare, val));
    CHECK(val == 1);
  }
  SECTION("bonds set if the atoms are also set 1") {
    auto mol = R"CTAB(basic test
  Mrv1810 01292006422D          

  0  0  0     0  0            999 V3000
M  V30 BEGIN CTAB
M  V30 COUNTS 4 3 0 0 0
M  V30 BEGIN ATOM
M  V30 1 C -7.0316 2.0632 0 0 STBOX=1
M  V30 2 C -5.6979 2.8332 0 0 STBOX=1
M  V30 3 O -4.3642 2.0632 0 0
M  V30 4 F -8.3653 2.8332 0 0
M  V30 END ATOM
M  V30 BEGIN BOND
M  V30 1 1 2 3
M  V30 2 1 1 4
M  V30 3 2 1 2
M  V30 END BOND
M  V30 END CTAB
M  END
)CTAB"_ctab;
    REQUIRE(mol);
    CHECK(mol->getNumAtoms() == 4);
    int val;
    REQUIRE(mol->getBondBetweenAtoms(0, 1));
    CHECK(mol->getBondBetweenAtoms(0, 1)->getPropIfPresent(
        common_properties::molStereoCare, val));
    CHECK(val == 1);
  }
  SECTION("bonds set if the atoms are also set 2") {
    auto mol = R"CTAB(basic test
  Mrv1810 01292006422D          

  0  0  0     0  0            999 V3000
M  V30 BEGIN CTAB
M  V30 COUNTS 4 3 0 0 0
M  V30 BEGIN ATOM
M  V30 1 C -7.0316 2.0632 0 0 STBOX=0
M  V30 2 C -5.6979 2.8332 0 0 STBOX=0
M  V30 3 O -4.3642 2.0632 0 0
M  V30 4 F -8.3653 2.8332 0 0
M  V30 END ATOM
M  V30 BEGIN BOND
M  V30 1 1 2 3
M  V30 2 1 1 4
M  V30 3 2 1 2
M  V30 END BOND
M  V30 END CTAB
M  END
)CTAB"_ctab;
    REQUIRE(mol);
    CHECK(mol->getNumAtoms() == 4);
    REQUIRE(mol->getBondBetweenAtoms(0, 1));
    CHECK(!mol->getBondBetweenAtoms(0, 1)->hasProp(
        common_properties::molStereoCare));
  }
  SECTION("bonds set if the atoms are also set 2") {
    auto mol = R"CTAB(basic test
  Mrv1810 01292006422D          

  0  0  0     0  0            999 V3000
M  V30 BEGIN CTAB
M  V30 COUNTS 4 3 0 0 0
M  V30 BEGIN ATOM
M  V30 1 C -7.0316 2.0632 0 0 STBOX=1
M  V30 2 C -5.6979 2.8332 0 0 STBOX=0
M  V30 3 O -4.3642 2.0632 0 0
M  V30 4 F -8.3653 2.8332 0 0
M  V30 END ATOM
M  V30 BEGIN BOND
M  V30 1 1 2 3
M  V30 2 1 1 4
M  V30 3 2 1 2
M  V30 END BOND
M  V30 END CTAB
M  END
)CTAB"_ctab;
    REQUIRE(mol);
    CHECK(mol->getNumAtoms() == 4);
    REQUIRE(mol->getBondBetweenAtoms(0, 1));
    CHECK(!mol->getBondBetweenAtoms(0, 1)->hasProp(
        common_properties::molStereoCare));
  }
  SECTION("bonds set if the atoms are also set v2k") {
    auto mol = R"CTAB(basic test
  Mrv1810 01292015042D          

  4  3  0  0  0  0            999 V2000
   -3.7669    1.1053    0.0000 C   0  0  0  0  1  0  0  0  0  0  0  0
   -3.0524    1.5178    0.0000 C   0  0  0  0  1  0  0  0  0  0  0  0
   -2.3380    1.1053    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -4.4814    1.5178    0.0000 F   0  0  0  0  0  0  0  0  0  0  0  0
  2  3  1  0  0  0  0
  1  4  1  0  0  0  0
  1  2  2  0  0  0  0
M  END
)CTAB"_ctab;
    REQUIRE(mol);
    CHECK(mol->getNumAtoms() == 4);
    int val;
    REQUIRE(mol->getBondBetweenAtoms(0, 1));
    CHECK(mol->getBondBetweenAtoms(0, 1)->getPropIfPresent(
        common_properties::molStereoCare, val));
    CHECK(val == 1);
  }
}

TEST_CASE("github #2829: support MRV_IMPLICIT_H", "[feature][sgroups]") {
  SECTION("basics v2k") {
    auto mol = R"CTAB(
  Mrv1810 01302015262D          
 
  5  5  0  0  0  0            999 V2000
    1.1387   -1.3654    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.6538   -0.6979    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.1387   -0.0305    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.9233   -0.2854    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.9233   -1.1104    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  4  0  0  0  0
  2  3  4  0  0  0  0
  3  4  4  0  0  0  0
  1  5  4  0  0  0  0
  4  5  4  0  0  0  0
M  STY  1   1 DAT
M  SAL   1  1   3
M  SDT   1 MRV_IMPLICIT_H                                        
M  SDD   1     0.0000    0.0000    DR    ALL  0       0  
M  SED   1 IMPL_H1
M  END
)CTAB"_ctab;
    REQUIRE(mol);
    CHECK(MolToSmiles(*mol) == "c1cc[nH]c1");
  }
  SECTION("basics v3k") {
    auto mol = R"CTAB(
  Mrv1810 01302015452D          
 
  0  0  0     0  0            999 V3000
M  V30 BEGIN CTAB
M  V30 COUNTS 5 5 1 0 0
M  V30 BEGIN ATOM
M  V30 1 C 2.1256 -2.5487 0 0
M  V30 2 C 1.2204 -1.3027 0 0
M  V30 3 N 2.1256 -0.0569 0 0
M  V30 4 C 3.5902 -0.5327 0 0
M  V30 5 C 3.5902 -2.0727 0 0
M  V30 END ATOM
M  V30 BEGIN BOND
M  V30 1 4 1 2
M  V30 2 4 2 3
M  V30 3 4 3 4
M  V30 4 4 1 5
M  V30 5 4 4 5
M  V30 END BOND
M  V30 BEGIN SGROUP
M  V30 1 DAT 0 ATOMS=(1 3) FIELDNAME=MRV_IMPLICIT_H -
M  V30 FIELDDISP="    0.0000    0.0000    DR    ALL  0       0" -
M  V30 FIELDDATA=IMPL_H1
M  V30 END SGROUP
M  V30 END CTAB
M  END
)CTAB"_ctab;
    REQUIRE(mol);
    CHECK(MolToSmiles(*mol) == "c1cc[nH]c1");
    // we removed all the S groups:
    CHECK(getSubstanceGroups(*mol).empty());
  }
  SECTION("v3k two groups") {
    auto mol = R"CTAB(
  Mrv1810 01302016392D          
 
 12 14  0  0  0  0            999 V2000
    1.1387   -1.3654    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.6538   -0.6979    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.1387   -0.0305    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.9233   -0.2854    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.9233   -1.1104    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.6378    0.1271    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.6378   -1.5229    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.3522   -1.1104    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.3522   -0.2854    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.1369   -1.3653    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    4.1369   -0.0305    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.6218   -0.6979    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  4  0  0  0  0
  2  3  4  0  0  0  0
  3  4  4  0  0  0  0
  1  5  4  0  0  0  0
  4  5  4  0  0  0  0
  7  8  1  0  0  0  0
  6  9  1  0  0  0  0
  5  7  1  0  0  0  0
  6  4  1  0  0  0  0
 11 12  4  0  0  0  0
 10 12  4  0  0  0  0
  9 11  4  0  0  0  0
 10  8  4  0  0  0  0
  8  9  4  0  0  0  0
M  STY  2   1 DAT   2 DAT
M  SAL   1  1   3
M  SDT   1 MRV_IMPLICIT_H                                        
M  SDD   1     0.0000    0.0000    DR    ALL  0       0  
M  SED   1 IMPL_H1
M  SAL   2  1  10
M  SDT   2 MRV_IMPLICIT_H                                        
M  SDD   2     0.0000    0.0000    DR    ALL  0       0  
M  SED   2 IMPL_H1
M  END
)CTAB"_ctab;
    REQUIRE(mol);
    CHECK(MolToSmiles(*mol) == "c1cc2c([nH]1)Cc1cc[nH]c1C2");
    // we removed all the S groups:
    CHECK(getSubstanceGroups(*mol).empty());
  }
  SECTION("removal leaves other s groups intact") {
    auto mol = R"CTAB(
  Mrv1810 02022006062D          
 
  0  0  0     0  0            999 V3000
M  V30 BEGIN CTAB
M  V30 COUNTS 6 6 2 0 0
M  V30 BEGIN ATOM
M  V30 1 C 2.1256 -2.5487 0 0
M  V30 2 C 1.2204 -1.3027 0 0
M  V30 3 N 2.1256 -0.0569 0 0
M  V30 4 C 3.5902 -0.5327 0 0
M  V30 5 C 3.5902 -2.0727 0 0
M  V30 6 C 4.8361 -2.9778 0 0
M  V30 END ATOM
M  V30 BEGIN BOND
M  V30 1 4 1 2
M  V30 2 4 2 3
M  V30 3 4 3 4
M  V30 4 4 1 5
M  V30 5 4 4 5
M  V30 6 1 5 6
M  V30 END BOND
M  V30 BEGIN SGROUP
M  V30 1 DAT 0 ATOMS=(1 6) FIELDNAME=some_data -
M  V30 FIELDDISP="    4.8361   -2.9778    DAU   ALL  0       0" -
M  V30 MRV_FIELDDISP=0 FIELDDATA=foo
M  V30 2 DAT 0 ATOMS=(1 3) FIELDNAME=MRV_IMPLICIT_H -
M  V30 FIELDDISP="    0.0000    0.0000    DR    ALL  0       0" -
M  V30 FIELDDATA=IMPL_H1
M  V30 END SGROUP
M  V30 END CTAB
M  END
)CTAB"_ctab;
    REQUIRE(mol);
    CHECK(MolToSmiles(*mol) == "Cc1cc[nH]c1");
    CHECK(getSubstanceGroups(*mol).size() == 1);
  }
}

TEST_CASE("extra v3k mol file properties", "[ctab][v3k]") {
  SECTION("ATTCHPT") {
    auto mol = R"CTAB(
  Mrv2007 03132014352D          

  0  0  0     0  0            999 V3000
M  V30 BEGIN CTAB
M  V30 COUNTS 3 2 0 0 0
M  V30 BEGIN ATOM
M  V30 1 C -16.625 7.1667 0 0 ATTCHPT=2
M  V30 2 C -15.2913 7.9367 0 0 ATTCHPT=1
M  V30 3 N -13.9576 7.1667 0 0
M  V30 END ATOM
M  V30 BEGIN BOND
M  V30 1 1 1 2
M  V30 2 1 2 3
M  V30 END BOND
M  V30 END CTAB
M  END
)CTAB"_ctab;
    REQUIRE(mol);
    CHECK(mol->getAtomWithIdx(0)->getProp<int>(
              common_properties::molAttachPoint) == 2);
    CHECK(mol->getAtomWithIdx(1)->getProp<int>(
              common_properties::molAttachPoint) == 1);
    auto molb = MolToV3KMolBlock(*mol);
    CHECK(molb.find("ATTCHPT=1") != std::string::npos);
    CHECK(molb.find("ATTCHPT=2") != std::string::npos);
  }
  SECTION("others") {
    // this is not reasonable; just there to ensure that the reading/writing is
    // working
    auto mol = R"CTAB(really fake
  Mrv2007 03132015062D          

  0  0  0     0  0            999 V3000
M  V30 BEGIN CTAB
M  V30 COUNTS 5 4 0 0 0
M  V30 BEGIN ATOM
M  V30 1 C -22.5833 11.0833 0 0 EXACHG=1
M  V30 2 C -21.2497 11.8533 0 0 INVRET=2
M  V30 3 C -23.917 11.8533 0 0 ATTCHORD=3
M  V30 4 C -25.2507 11.0833 0 0 CLASS=foo
M  V30 5 C -26.5844 11.8533 0 0 SEQID=4
M  V30 END ATOM
M  V30 BEGIN BOND
M  V30 1 1 1 2
M  V30 2 1 1 3
M  V30 3 1 3 4
M  V30 4 1 4 5
M  V30 END BOND
M  V30 END CTAB
M  END
)CTAB"_ctab;
    REQUIRE(mol);
    CHECK(mol->getAtomWithIdx(0)->getProp<int>(
              common_properties::molRxnExactChange) == 1);
    CHECK(mol->getAtomWithIdx(1)->getProp<int>(
              common_properties::molInversionFlag) == 2);
    CHECK(mol->getAtomWithIdx(2)->getProp<int>(
              common_properties::molAttachOrder) == 3);
    CHECK(mol->getAtomWithIdx(3)->getProp<std::string>(
              common_properties::molAtomClass) == "foo");
    CHECK(mol->getAtomWithIdx(4)->getProp<int>(
              common_properties::molAtomSeqId) == 4);
    auto molb = MolToV3KMolBlock(*mol);
    CHECK(molb.find("EXACHG=1") != std::string::npos);
    CHECK(molb.find("INVRET=2") != std::string::npos);
    CHECK(molb.find("ATTCHORD=3") != std::string::npos);
    CHECK(molb.find("CLASS=foo") != std::string::npos);
    CHECK(molb.find("SEQID=4") != std::string::npos);
  }
  SECTION("SUBST") {
    auto mol = R"CTAB(test
  Mrv2007 03132018122D          

  0  0  0     0  0            999 V3000
M  V30 BEGIN CTAB
M  V30 COUNTS 4 3 0 0 0
M  V30 BEGIN ATOM
M  V30 1 C -16.6248 7.1666 0 0 SUBST=3
M  V30 2 C -15.2911 7.9366 0 0 SUBST=-2
M  V30 3 N -13.9574 7.1666 0 0 SUBST=-1
M  V30 4 C -17.9585 7.9366 0 0 SUBST=6
M  V30 END ATOM
M  V30 BEGIN BOND
M  V30 1 1 1 2
M  V30 2 1 2 3
M  V30 3 1 1 4
M  V30 END BOND
M  V30 END CTAB
M  END
)CTAB"_ctab;
    REQUIRE(mol);

    auto smarts = MolToSmarts(*mol);
    CHECK(smarts == "[#6&D3](-[#6&D2]-[#7&D0])-[#6&D{6-}]");

    auto molb = MolToV3KMolBlock(*mol);
    CHECK(molb.find("SUBST=3") != std::string::npos);
    CHECK(molb.find("SUBST=-2") != std::string::npos);
    CHECK(molb.find("SUBST=-1") != std::string::npos);
  }
  SECTION("bond props") {
    auto mol = R"CTAB(bogus example
  Mrv2007 03132017102D          

  0  0  0     0  0            999 V3000
M  V30 BEGIN CTAB
M  V30 COUNTS 8 7 0 0 0
M  V30 BEGIN ATOM
M  V30 1 C -28.125 8.2067 0 0
M  V30 2 C -26.7913 7.4367 0 0
M  V30 3 C -26.7913 5.8967 0 0
M  V30 4 C -28.125 5.1267 0 0
M  V30 5 N -29.4587 5.8967 0 0
M  V30 6 C -29.4587 7.4367 0 0
M  V30 7 * -27.2359 7.18 0 0
M  V30 8 R# -25.2354 8.335 0 0 RGROUPS=(1 1)
M  V30 END ATOM
M  V30 BEGIN BOND
M  V30 1 1 1 2
M  V30 2 2 2 3
M  V30 3 1 3 4
M  V30 4 2 4 5
M  V30 5 1 5 6 
M  V30 6 2 1 6 RXCTR=1
M  V30 7 1 7 8 ENDPTS=(3 1 2 3) ATTACH=ANY
M  V30 END BOND
M  V30 END CTAB
M  END)CTAB"_ctab;
    REQUIRE(mol);

    auto molb = MolToV3KMolBlock(*mol);
    CHECK(molb.find("ENDPTS=(3 1 2 3) ATTACH=ANY") != std::string::npos);
    CHECK(molb.find("RXCTR=1") != std::string::npos);
  }
}

TEST_CASE(
    "Problems parsing SGroup abbreviations with multiple attachment points",
    "[bug][parser]") {
  std::string rdbase = getenv("RDBASE");
  SECTION("basics") {
    std::string fName =
        rdbase + "/Code/GraphMol/FileParsers/test_data/sgroup_ap_bug.mol";
    std::unique_ptr<RWMol> mol(MolFileToMol(fName));
    REQUIRE(mol);

    const auto &sgroups = getSubstanceGroups(*mol);
    CHECK(sgroups.size() == 3);
    CHECK(sgroups[0].hasProp("TYPE"));
    CHECK(sgroups[0].getProp<std::string>("TYPE") == "SUP");
    CHECK(sgroups[0].getAttachPoints().size() == 1);
    CHECK(sgroups[1].hasProp("TYPE"));
    CHECK(sgroups[1].getProp<std::string>("TYPE") == "SUP");
    CHECK(sgroups[1].getAttachPoints().size() == 1);
    CHECK(sgroups[2].hasProp("TYPE"));
    CHECK(sgroups[2].getProp<std::string>("TYPE") == "SUP");
    CHECK(sgroups[2].getAttachPoints().size() == 2);
  }
}

TEST_CASE(
    "github #3207: Attachment point info not being read from V2000 mol blocks",
    "[ctab][bug]") {
  SECTION("ATTCHPT") {
    auto mol = R"CTAB(
  Mrv1824 06092009122D          

  3  2  0  0  0  0            999 V2000
   -8.9061    3.8393    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -8.1917    4.2518    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -7.4772    3.8393    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  2  3  1  0  0  0  0
M  APO  2   1   2   2   1
M  END
)CTAB"_ctab;
    REQUIRE(mol);
    CHECK(mol->getAtomWithIdx(0)->getProp<int>(
              common_properties::molAttachPoint) == 2);
    CHECK(mol->getAtomWithIdx(1)->getProp<int>(
              common_properties::molAttachPoint) == 1);
    auto molb = MolToV3KMolBlock(*mol);
    CHECK(molb.find("ATTCHPT=1") != std::string::npos);
    CHECK(molb.find("ATTCHPT=2") != std::string::npos);
  }
  SECTION("Val=-1") {
    auto mol = R"CTAB(
  Mrv1824 06092009122D          

  3  2  0  0  0  0            999 V2000
   -8.9061    3.8393    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -8.1917    4.2518    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -7.4772    3.8393    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  2  3  1  0  0  0  0
M  APO  2   1   3   2   1
M  END
)CTAB"_ctab;
    REQUIRE(mol);
    CHECK(mol->getAtomWithIdx(0)->getProp<int>(
              common_properties::molAttachPoint) == -1);
    CHECK(mol->getAtomWithIdx(1)->getProp<int>(
              common_properties::molAttachPoint) == 1);
    auto molb = MolToV3KMolBlock(*mol);
    CHECK(molb.find("ATTCHPT=1") != std::string::npos);
    CHECK(molb.find("ATTCHPT=-1") != std::string::npos);
  }
}

TEST_CASE("XBHEAD and XBCORR causing parser failures", "[bug][reader]") {
  std::string rdbase = getenv("RDBASE");
  SECTION("basics") {
    std::string fName =
        rdbase +
        "/Code/GraphMol/FileParsers/sgroup_test_data/repeat_groups_query1.mol";
    std::unique_ptr<RWMol> mol(MolFileToMol(fName));
    REQUIRE(mol);
    const auto &sgroups = getSubstanceGroups(*mol);
    CHECK(sgroups.size() == 1);
    CHECK(sgroups[0].hasProp("TYPE"));
    CHECK(sgroups[0].getProp<std::string>("TYPE") == "SRU");
    CHECK(sgroups[0].hasProp("XBHEAD"));
    auto v = sgroups[0].getProp<std::vector<unsigned int>>("XBHEAD");
    CHECK(v.size() == 2);
    CHECK(v[0] == 5);
    CHECK(v[1] == 0);

    CHECK(sgroups[0].hasProp("XBCORR"));
    CHECK(sgroups[0].getProp<std::vector<unsigned int>>("XBCORR").size() == 4);

    auto mb = MolToV3KMolBlock(*mol);
    CHECK(mb.find("XBHEAD=(2 6 1)") != std::string::npos);
    CHECK(mb.find("XBCORR=(4 6 6 1 1)") != std::string::npos);
  }
}
TEST_CASE("LINKNODE information being ignored", "[ctab][bug]") {
  SECTION("v3000") {
    auto mol = R"CTAB(
  Mrv2007 06212005162D          

  0  0  0     0  0            999 V3000
M  V30 BEGIN CTAB
M  V30 COUNTS 5 5 0 0 0
M  V30 BEGIN ATOM
M  V30 1 C -3.25 12.2683 0 0
M  V30 2 C -4.4959 11.3631 0 0
M  V30 3 C -4.02 9.8986 0 0
M  V30 4 C -2.48 9.8986 0 0
M  V30 5 C -2.0041 11.3631 0 0
M  V30 END ATOM
M  V30 BEGIN BOND
M  V30 1 1 1 2
M  V30 2 1 2 3
M  V30 3 1 3 4
M  V30 4 1 4 5
M  V30 5 1 1 5
M  V30 END BOND
M  V30 LINKNODE 1 3 2 1 2 1 5
M  V30 LINKNODE 1 4 2 4 3 4 5
M  V30 END CTAB
M  END
)CTAB"_ctab;
    REQUIRE(mol);
    CHECK(mol->getProp<std::string>(common_properties::molFileLinkNodes) ==
          "1 3 2 1 2 1 5|1 4 2 4 3 4 5");
    auto molb = MolToV3KMolBlock(*mol);
    CHECK(molb.find("LINKNODE 1 3 2 1 2 1 5") != std::string::npos);
    CHECK(molb.find("LINKNODE 1 4 2 4 3 4 5") != std::string::npos);
  }
  SECTION("v2000") {
    auto mol = R"CTAB(
  Mrv2007 06222015182D          

  5  5  0  0  0  0            999 V2000
   -1.7411    6.5723    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4085    6.0874    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1536    5.3028    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3286    5.3028    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0736    6.0874    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  2  3  1  0  0  0  0
  3  4  1  0  0  0  0
  4  5  1  0  0  0  0
  1  5  1  0  0  0  0
M  LIN  2   1   3   2   5   4   4   3   5
M  END
)CTAB"_ctab;
    REQUIRE(mol);
    CHECK(mol->getProp<std::string>(common_properties::molFileLinkNodes) ==
          "1 3 2 1 2 1 5|1 4 2 4 3 4 5");
    auto molb = MolToV3KMolBlock(*mol);
    CHECK(molb.find("LINKNODE 1 3 2 1 2 1 5") != std::string::npos);
    CHECK(molb.find("LINKNODE 1 4 2 4 3 4 5") != std::string::npos);
  }
}
TEST_CASE("more complex queries in CTAB parsers", "[ctab]") {
  SECTION("v3000") {
    auto mol = R"CTAB(*.*.*.*.*.*.*.* |$;Q_e;M_p;X_p;AH_p;QH_p;MH_p;XH_p$|
  manual  06272007272D          

  0  0  0     0  0            999 V3000
M  V30 BEGIN CTAB
M  V30 COUNTS 8 0 0 0 0
M  V30 BEGIN ATOM
M  V30 1 A -3.2083 5.25 0 0
M  V30 2 Q -0.25 6 0 0
M  V30 3 M 4.5417 6.0417 0 0
M  V30 4 X 1.2917 4.2083 0 0
M  V30 5 AH -4.2083 5.25 0 0
M  V30 6 QH -1.25 6 0 0
M  V30 7 MH 3.5417 6.0417 0 0
M  V30 8 XH 0.2917 4.2083 0 0
M  V30 END ATOM
M  V30 END CTAB
M  END
)CTAB"_ctab;
    REQUIRE(mol);
    for (const auto atom : mol->atoms()) {
      REQUIRE(atom->hasQuery());
      CHECK(!atom->getQuery()->getTypeLabel().empty());
    }
    std::string pkl;
    MolPickler::pickleMol(*mol, pkl);
    ROMol cp(pkl);
    for (const auto atom : cp.atoms()) {
      REQUIRE(atom->hasQuery());
      CHECK(!atom->getQuery()->getTypeLabel().empty());
      CHECK(atom->getQuery()->getTypeLabel() ==
            mol->getAtomWithIdx(atom->getIdx())->getQuery()->getTypeLabel());
    }
    auto molb = MolToV3KMolBlock(*mol);
    CHECK(molb.find(" A ") != std::string::npos);
    CHECK(molb.find(" AH ") != std::string::npos);
    CHECK(molb.find(" Q ") != std::string::npos);
    CHECK(molb.find(" QH ") != std::string::npos);
    CHECK(molb.find(" M ") != std::string::npos);
    CHECK(molb.find(" MH ") != std::string::npos);
    CHECK(molb.find(" X ") != std::string::npos);
    CHECK(molb.find(" XH ") != std::string::npos);
  }
  SECTION("v2000") {
    auto mol = R"CTAB(*.*.*.*.*.*.*.* |$;Q_e;M_p;X_p;AH_p;QH_p;MH_p;XH_p$|
  manual  06272007272D          

  8  0  0  0  0  0            999 V2000
   -3.2083    5.2500    0.0000 A   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2500    6.0000    0.0000 Q   0  0  0  0  0  0  0  0  0  0  0  0
    4.5417    6.0417    0.0000 M   0  0  0  0  0  0  0  0  0  0  0  0
    1.2917    4.2083    0.0000 X   0  0  0  0  0  0  0  0  0  0  0  0
   -4.2083    5.2500    0.0000 AH  0  0  0  0  0  0  0  0  0  0  0  0
   -1.2500    6.0000    0.0000 QH  0  0  0  0  0  0  0  0  0  0  0  0
    3.5417    6.0417    0.0000 MH  0  0  0  0  0  0  0  0  0  0  0  0
    0.2917    4.2083    0.0000 XH  0  0  0  0  0  0  0  0  0  0  0  0
M  END
)CTAB"_ctab;
    REQUIRE(mol);
    for (const auto atom : mol->atoms()) {
      REQUIRE(atom->hasQuery());
      CHECK(!atom->getQuery()->getTypeLabel().empty());
    }
    std::string pkl;
    MolPickler::pickleMol(*mol, pkl);
    ROMol cp(pkl);
    for (const auto atom : cp.atoms()) {
      REQUIRE(atom->hasQuery());
      CHECK(!atom->getQuery()->getTypeLabel().empty());
      CHECK(atom->getQuery()->getTypeLabel() ==
            mol->getAtomWithIdx(atom->getIdx())->getQuery()->getTypeLabel());
    }
    auto molb = MolToMolBlock(*mol);
    CHECK(molb.find(" A ") != std::string::npos);
    CHECK(molb.find(" AH ") != std::string::npos);
    CHECK(molb.find(" Q ") != std::string::npos);
    CHECK(molb.find(" QH ") != std::string::npos);
    CHECK(molb.find(" M ") != std::string::npos);
    CHECK(molb.find(" MH ") != std::string::npos);
    CHECK(molb.find(" X ") != std::string::npos);
    CHECK(molb.find(" XH ") != std::string::npos);
    /// SMARTS-based queries are not written for these:
    CHECK(molb.find("V    ") == std::string::npos);
  }
}

TEST_CASE("read metadata from PNG", "[reader][PNG]") {
  std::string rdbase = getenv("RDBASE");
  SECTION("basics") {
    std::string fname =
        rdbase + "/Code/GraphMol/FileParsers/test_data/colchicine.png";
    auto metadata = PNGFileToMetadata(fname);

    auto iter =
        std::find_if(metadata.begin(), metadata.end(),
                     [](const std::pair<std::string, std::string> &val) {
                       return boost::starts_with(val.first, PNGData::smilesTag);
                     });
    REQUIRE(iter != metadata.end());
    CHECK(
        iter->second ==
        "COc1cc2c(-c3ccc(OC)c(=O)cc3[C@@H](NC(C)=O)CC2)c(OC)c1OC "
        "|(6.46024,1.03002,;5.30621,1.98825,;3.89934,1.46795,;2.74531,2.42618,;"
        "1.33844,1.90588,;1.0856,0.427343,;-0.228013,-0.296833,;0.1857,-1."
        "73865,;-0.683614,-2.96106,;-2.18134,-3.04357,;-2.75685,-4.42878,;-4."
        "24422,-4.62298,;-3.17967,-1.92404,;-4.62149,-2.33775,;-2.92683,-0."
        "445502,;-1.61322,0.278673,;-2.02693,1.72049,;-3.50547,1.97333,;-4."
        "02577,3.3802,;-5.50431,3.63304,;-3.06754,4.53423,;-1.15762,2.9429,;0."
        "340111,3.02541,;2.23963,-0.530891,;1.98679,-2.00943,;3.14082,-2.96766,"
        ";3.6465,-0.0105878,;4.80053,-0.968822,;4.54769,-2.44736,)|");
  }
  SECTION("no metadata") {
    std::string fname =
        rdbase +
        "/Code/GraphMol/FileParsers/test_data/colchicine.no_metadata.png";
    auto metadata = PNGFileToMetadata(fname);
    REQUIRE(metadata.empty());
  }
  SECTION("bad PNG") {
    std::string text = "NOT A PNG";
    REQUIRE_THROWS_AS(PNGStringToMetadata(text), FileParseException);
  }

  SECTION("truncated PNG") {
    std::string fname =
        rdbase + "/Code/GraphMol/FileParsers/test_data/colchicine.png";
    auto istr = std::ifstream(fname, std::ios_base::binary);
    istr.seekg(0, istr.end);
    auto sz = istr.tellg();
    istr.seekg(0, istr.beg);
    char *buff = new char[sz];
    istr.read(buff, sz);
    std::string data(buff, sz);
    delete[] buff;
    auto metadata = PNGStringToMetadata(data);
    REQUIRE(!metadata.empty());
    REQUIRE_THROWS_AS(PNGStringToMetadata(data.substr(1000)),
                      FileParseException);
  }
#ifdef RDK_USE_BOOST_IOSTREAMS
  SECTION("compressed metadata") {
    std::string fname =
        rdbase + "/Code/GraphMol/FileParsers/test_data/colchicine.mrv.png";
    auto metadata = PNGFileToMetadata(fname);
    auto iter =
        std::find_if(metadata.begin(), metadata.end(),
                     [](const std::pair<std::string, std::string> &val) {
                       return val.first == "molSource";
                     });
    REQUIRE(iter != metadata.end());
    CHECK(iter->second.find("<MChemicalStruct>") != std::string::npos);
  }
#endif
}

TEST_CASE("write metadata to PNG", "[writer][PNG]") {
  std::string rdbase = getenv("RDBASE");
  SECTION("basics") {
    std::string fname =
        rdbase +
        "/Code/GraphMol/FileParsers/test_data/colchicine.no_metadata.png";
    std::vector<std::pair<std::string, std::string>> metadata;
    metadata.push_back(std::make_pair(
        PNGData::smilesTag,
        std::string(
            "COc1cc2c(-c3ccc(OC)c(=O)cc3[C@@H](NC(C)=O)CC2)c(OC)c1OC "
            "|(6.46024,1.03002,;5.30621,1.98825,;3.89934,1.46795,;2.74531,2."
            "42618,;1.33844,1.90588,;1.0856,0.427343,;-0.228013,-0.296833,;0."
            "1857,-1.73865,;-0.683614,-2.96106,;-2.18134,-3.04357,;-2.75685,-4."
            "42878,;-4.24422,-4.62298,;-3.17967,-1.92404,;-4.62149,-2.33775,;-"
            "2.92683,-0.445502,;-1.61322,0.278673,;-2.02693,1.72049,;-3.50547,"
            "1.97333,;-4.02577,3.3802,;-5.50431,3.63304,;-3.06754,4.53423,;-1."
            "15762,2.9429,;0.340111,3.02541,;2.23963,-0.530891,;1.98679,-2."
            "00943,;3.14082,-2.96766,;3.6465,-0.0105878,;4.80053,-0.968822,;4."
            "54769,-2.44736,)|")));
    auto pngData = addMetadataToPNGFile(fname, metadata);
    std::ofstream ofs("write_metadata.png");
    ofs.write(pngData.c_str(), pngData.size());
    ofs.flush();
    auto ometadata = PNGStringToMetadata(pngData);
    REQUIRE(ometadata.size() == metadata.size());
    for (unsigned int i = 0; i < ometadata.size(); ++i) {
      CHECK(ometadata[i].first == metadata[i].first);
      CHECK(ometadata[i].second == metadata[i].second);
    }
  }
}

TEST_CASE("read molecule from PNG", "[reader][PNG]") {
  std::string rdbase = getenv("RDBASE");
  SECTION("smiles") {
    std::string fname =
        rdbase + "/Code/GraphMol/FileParsers/test_data/colchicine.png";
    std::unique_ptr<ROMol> mol(PNGFileToMol(fname));
    REQUIRE(mol);
    CHECK(mol->getNumAtoms() == 29);
    CHECK(mol->getNumConformers() == 1);
  }
  SECTION("mol") {
    std::string fname =
        rdbase + "/Code/GraphMol/FileParsers/test_data/colchicine.mol.png";
    std::unique_ptr<ROMol> mol(PNGFileToMol(fname));
    REQUIRE(mol);
    CHECK(mol->getNumAtoms() == 29);
    CHECK(mol->getNumConformers() == 1);
  }
  SECTION("no metadata") {
    std::string fname =
        rdbase +
        "/Code/GraphMol/FileParsers/test_data/colchicine.no_metadata.png";
    REQUIRE_THROWS_AS(PNGFileToMol(fname), FileParseException);
  }
}

TEST_CASE("write molecule to PNG", "[writer][PNG]") {
  std::string rdbase = getenv("RDBASE");
  SECTION("basics") {
    std::string fname =
        rdbase +
        "/Code/GraphMol/FileParsers/test_data/colchicine.no_metadata.png";
    std::ifstream strm(fname, std::ios::in | std::ios::binary);
    auto colchicine =
        "COc1cc2c(c(OC)c1OC)-c1ccc(OC)c(=O)cc1[C@@H](NC(C)=O)CC2"_smiles;
    REQUIRE(colchicine);
    auto pngString = addMolToPNGStream(*colchicine, strm);
    // read it back out
    std::unique_ptr<ROMol> mol(PNGStringToMol(pngString));
    REQUIRE(mol);
    CHECK(mol->getNumAtoms() == 29);
    CHECK(mol->getNumConformers() == 0);
  }
  SECTION("use SMILES") {
    std::string fname =
        rdbase +
        "/Code/GraphMol/FileParsers/test_data/colchicine.no_metadata.png";
    std::ifstream strm(fname, std::ios::in | std::ios::binary);
    auto colchicine =
        "COc1cc2c(c(OC)c1OC)-c1ccc(OC)c(=O)cc1[C@@H](NC(C)=O)CC2"_smiles;
    REQUIRE(colchicine);
    bool includePkl = false;
    auto pngString = addMolToPNGStream(*colchicine, strm, includePkl);
    // read it back out
    std::unique_ptr<ROMol> mol(PNGStringToMol(pngString));
    REQUIRE(mol);
    CHECK(mol->getNumAtoms() == 29);
    CHECK(mol->getNumConformers() == 0);
  }
  SECTION("use MOL") {
    std::string fname =
        rdbase +
        "/Code/GraphMol/FileParsers/test_data/colchicine.no_metadata.png";
    std::ifstream strm(fname, std::ios::in | std::ios::binary);
    auto colchicine =
        "COc1cc2c(c(OC)c1OC)-c1ccc(OC)c(=O)cc1[C@@H](NC(C)=O)CC2"_smiles;
    REQUIRE(colchicine);
    bool includePkl = false;
    bool includeSmiles = false;
    bool includeMol = true;
    auto pngString = addMolToPNGStream(*colchicine, strm, includePkl,
                                       includeSmiles, includeMol);
    // read it back out
    std::unique_ptr<ROMol> mol(PNGStringToMol(pngString));
    REQUIRE(mol);
    CHECK(mol->getNumAtoms() == 29);
    CHECK(mol->getNumConformers() == 1);
  }
}
TEST_CASE("multiple molecules in the PNG", "[writer][PNG]") {
  std::string rdbase = getenv("RDBASE");

  std::vector<std::string> smiles = {"c1ccccc1", "CCCOC", "c1ncccc1"};
  std::vector<std::unique_ptr<ROMol>> mols;
  for (const auto &smi : smiles) {
    mols.emplace_back(SmilesToMol(smi));
  }
  SECTION("pickles") {
    std::vector<std::pair<std::string, std::string>> metadata;
    for (const auto &mol : mols) {
      std::string pkl;
      MolPickler::pickleMol(*mol, pkl);
      metadata.push_back(std::make_pair(PNGData::pklTag, pkl));
    }
    // for the purposes of this test we'll add the metadata to an unrelated
    // PNG
    std::string fname =
        rdbase +
        "/Code/GraphMol/FileParsers/test_data/colchicine.no_metadata.png";
    std::ifstream strm(fname, std::ios::in | std::ios::binary);
    auto png = addMetadataToPNGStream(strm, metadata);
    std::stringstream pngstrm(png);
    auto molsRead = PNGStreamToMols(pngstrm);
    REQUIRE(molsRead.size() == mols.size());
    for (unsigned i = 0; i < molsRead.size(); ++i) {
      CHECK(MolToSmiles(*molsRead[i]) == MolToSmiles(*mols[i]));
    }
  }
  SECTION("SMILES") {
    std::vector<std::pair<std::string, std::string>> metadata;
    for (const auto &mol : mols) {
      std::string pkl = "BOGUS";
      // add bogus pickle data so we know that's not being read
      metadata.push_back(std::make_pair(PNGData::pklTag, pkl));
      metadata.push_back(std::make_pair(PNGData::smilesTag, MolToSmiles(*mol)));
    }
    // for the purposes of this test we'll add the metadata to an unrelated
    // PNG
    std::string fname =
        rdbase +
        "/Code/GraphMol/FileParsers/test_data/colchicine.no_metadata.png";
    std::ifstream strm(fname, std::ios::in | std::ios::binary);
    auto png = addMetadataToPNGStream(strm, metadata);
    std::stringstream pngstrm(png);
    auto molsRead = PNGStreamToMols(pngstrm, PNGData::smilesTag);
    REQUIRE(molsRead.size() == mols.size());
    for (unsigned i = 0; i < molsRead.size(); ++i) {
      CHECK(MolToSmiles(*molsRead[i]) == MolToSmiles(*mols[i]));
    }
  }
}

TEST_CASE("multiple molecules in the PNG, second example", "[writer][PNG]") {
  std::string rdbase = getenv("RDBASE");

  std::vector<std::string> smiles = {"c1ccccc1", "CCO", "CC(=O)O", "c1ccccn1"};
  std::vector<std::unique_ptr<ROMol>> mols;
  for (const auto &smi : smiles) {
    mols.emplace_back(SmilesToMol(smi));
  }
  SECTION("pickles") {
    std::string fname =
        rdbase + "/Code/GraphMol/FileParsers/test_data/multiple_mols.png";
    std::ifstream strm(fname, std::ios::in | std::ios::binary);
    auto molsRead = PNGStreamToMols(strm);
    REQUIRE(molsRead.size() == mols.size());
    for (unsigned i = 0; i < molsRead.size(); ++i) {
      CHECK(MolToSmiles(*molsRead[i]) == MolToSmiles(*mols[i]));
    }
  }
  SECTION("SMILES") {
    std::vector<std::pair<std::string, std::string>> metadata;
    for (const auto &mol : mols) {
      std::string pkl = "BOGUS";
      // add bogus pickle data so we know that's not being read
      metadata.push_back(std::make_pair(PNGData::pklTag, pkl));
      metadata.push_back(std::make_pair(PNGData::smilesTag, MolToSmiles(*mol)));
    }
    // for the purposes of this test we'll add the metadata to an unrelated
    // PNG
    std::string fname =
        rdbase +
        "/Code/GraphMol/FileParsers/test_data/colchicine.no_metadata.png";
    std::ifstream strm(fname, std::ios::in | std::ios::binary);
    auto png = addMetadataToPNGStream(strm, metadata);
    std::stringstream pngstrm(png);
    auto molsRead = PNGStreamToMols(pngstrm, PNGData::smilesTag);
    REQUIRE(molsRead.size() == mols.size());
    for (unsigned i = 0; i < molsRead.size(); ++i) {
      CHECK(MolToSmiles(*molsRead[i]) == MolToSmiles(*mols[i]));
    }
  }
}

TEST_CASE("github #3413: V3K mol blocks with no atoms fail to parse", "[bug]") {
  SECTION("basics") {
    auto m = R"CTAB(6065
     RDKit          2D

  0  0  0  0  0  0  0  0  0  0999 V3000
M  V30 BEGIN CTAB
M  V30 COUNTS 0 0 0 0 0
M  V30 BEGIN ATOM
M  V30 END ATOM
M  V30 END CTAB
M  END)CTAB"_ctab;
    REQUIRE(m);
    CHECK(m->getNumAtoms() == 0);
    CHECK(m->getNumBonds() == 0);
  }
}

TEST_CASE("github #3415: problem parsing SGroup data containing \" ", "[bug]") {
  SECTION("basics") {
    auto m = R"CTAB(
  Mrv2014 09172018222D          

  0  0  0     0  0            999 V3000
M  V30 BEGIN CTAB
M  V30 COUNTS 6 6 1 0 0
M  V30 BEGIN ATOM
M  V30 1 C 1.3337 2.31 0 0
M  V30 2 C 2.6674 1.54 0 0
M  V30 3 C 2.6674 -0 0 0
M  V30 4 C 1.3337 -0.77 0 0
M  V30 5 C 0 0 0 0
M  V30 6 C 0 1.54 0 0
M  V30 END ATOM
M  V30 BEGIN BOND
M  V30 1 2 1 2
M  V30 2 1 2 3
M  V30 3 2 3 4
M  V30 4 1 4 5
M  V30 5 2 5 6
M  V30 6 1 1 6
M  V30 END BOND
M  V30 BEGIN SGROUP
M  V30 1 DAT 0 ATOMS=(1 1) FIELDNAME=Tempstruct FIELDINFO="""" -
M  V30 FIELDDISP="    2.1037    1.5400    DA    ALL  0       0" QUERYOP="""" -
M  V30 FIELDDATA=Foo1
M  V30 END SGROUP
M  V30 END CTAB
M  END
)CTAB"_ctab;
    REQUIRE(m);
    CHECK(m->getNumAtoms() == 6);
    CHECK(m->getNumBonds() == 6);
    auto sgs = getSubstanceGroups(*m);
    REQUIRE(sgs.size() == 1);
    CHECK(sgs[0].getProp<std::string>("TYPE") == "DAT");
    CHECK(sgs[0].getProp<std::string>("FIELDINFO") == "\"");
    CHECK(sgs[0].getProp<std::string>("QUERYOP") == "\"");
  }
  SECTION("empty string") {
    auto m = R"CTAB(
  Mrv2014 09172018222D          

  0  0  0     0  0            999 V3000
M  V30 BEGIN CTAB
M  V30 COUNTS 6 6 1 0 0
M  V30 BEGIN ATOM
M  V30 1 C 1.3337 2.31 0 0
M  V30 2 C 2.6674 1.54 0 0
M  V30 3 C 2.6674 -0 0 0
M  V30 4 C 1.3337 -0.77 0 0
M  V30 5 C 0 0 0 0
M  V30 6 C 0 1.54 0 0
M  V30 END ATOM
M  V30 BEGIN BOND
M  V30 1 2 1 2
M  V30 2 1 2 3
M  V30 3 2 3 4
M  V30 4 1 4 5
M  V30 5 2 5 6
M  V30 6 1 1 6
M  V30 END BOND
M  V30 BEGIN SGROUP
M  V30 1 DAT 0 ATOMS=(1 1) FIELDNAME=Tempstruct FIELDINFO="" -
M  V30 FIELDDISP="    2.1037    1.5400    DA    ALL  0       0" QUERYOP="""" -
M  V30 FIELDDATA=Foo1
M  V30 END SGROUP
M  V30 END CTAB
M  END
)CTAB"_ctab;
    REQUIRE(m);
    CHECK(m->getNumAtoms() == 6);
    CHECK(m->getNumBonds() == 6);
    auto sgs = getSubstanceGroups(*m);
    REQUIRE(sgs.size() == 1);
    CHECK(sgs[0].getProp<std::string>("TYPE") == "DAT");
    CHECK(sgs[0].getProp<std::string>("FIELDINFO").empty());
    CHECK(sgs[0].getProp<std::string>("QUERYOP") == "\"");
  }
}

TEST_CASE("github #3597: Scientific notation in SDF V3000 files", "[bug]") {
  SECTION("basics") {
    auto m = R"CTAB(
  Mrv2020 11302014062D          

  2  1  0  0  0  0            999 V2000
   -2.8125    1.9196    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0980    2.3321    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
M  END
)CTAB"_ctab;
    REQUIRE(m);
    m->getConformer().getAtomPos(0).z = 1e-6;
    m->getConformer().getAtomPos(1).z = 1e-4;
    auto mb = MolToV3KMolBlock(*m);
    CHECK(mb.find("1e-06") == std::string::npos);
  }
  SECTION("toosmall") {
    auto m = R"CTAB(
  Mrv2020 11302014062D          

  2  1  0  0  0  0            999 V2000
   -2.8125    1.9196    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0980    2.3321    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
M  END
)CTAB"_ctab;
    REQUIRE(m);
    m->getConformer().getAtomPos(0).z = 1e-17;
    m->getConformer().getAtomPos(1).z = 1e-4;
    auto mb = MolToV3KMolBlock(*m);
    // std::cerr<<mb<<std::endl;
    CHECK(mb.find("M  V30 1 C -2.812500 1.919600 0.000000 0") !=
          std::string::npos);
  }
}

TEST_CASE("github #3620: V3K mol block parser not saving the chiral flag",
          "[bug]") {
  SECTION("basics") {
    auto m = R"CTAB(
  Mrv2014 12082009582D          

  0  0  0     0  0            999 V3000
M  V30 BEGIN CTAB
M  V30 COUNTS 4 3 0 0 1
M  V30 BEGIN ATOM
M  V30 1 C -1.875 6.0417 0 0 CFG=2
M  V30 2 C -0.5413 6.8117 0 0
M  V30 3 F -3.2087 6.8117 0 0
M  V30 4 Cl -1.875 4.5017 0 0
M  V30 END ATOM
M  V30 BEGIN BOND
M  V30 1 1 1 3
M  V30 2 1 1 4
M  V30 3 1 1 2 CFG=1
M  V30 END BOND
M  V30 END CTAB
M  END
)CTAB"_ctab;
    REQUIRE(m);
    unsigned int chiralFlag = 0;
    CHECK(
        m->getPropIfPresent(common_properties::_MolFileChiralFlag, chiralFlag));
    CHECK(chiralFlag == 1);
    auto mb = MolToV3KMolBlock(*m);
    CHECK(mb.find("4 3 0 0 1") != std::string::npos);
  }
}

TEST_CASE("test bond flavors when writing PDBs", "[bug]") {
  SECTION("basics") {
    std::unique_ptr<RWMol> m{SequenceToMol("G")};
    REQUIRE(m);
    int confId = -1;
    {
      int flavor = 0;
      auto pdb = MolToPDBBlock(*m, confId, flavor);
      CHECK(pdb.find("CONECT    1    2\n") != std::string::npos);
      CHECK(pdb.find("CONECT    3    4    4    5\n") != std::string::npos);
    }
    {
      int flavor = 2;
      auto pdb = MolToPDBBlock(*m, confId, flavor);
      CHECK(pdb.find("CONECT    1    2\n") == std::string::npos);
      CHECK(pdb.find("CONECT    3    4    4\n") != std::string::npos);
    }
    {
      int flavor = 8;
      auto pdb = MolToPDBBlock(*m, confId, flavor);
      CHECK(pdb.find("CONECT    1    2\n") != std::string::npos);
      CHECK(pdb.find("CONECT    3    4    5\n") != std::string::npos);
    }
    {
      int flavor = 2 | 8;
      auto pdb = MolToPDBBlock(*m, confId, flavor);
      CHECK(pdb.find("CONECT") == std::string::npos);
    }
  }
}