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rdkit/Code/GraphMol/FileParsers/file_parsers_catch.cpp
Greg Landrum 2ee798ddca Add support for the rest of the v3000 atom properties (#3007) 
* Add convenience functions for generating v3K mol blocks and mol files

* first pass at parsing/writing the remaining atom properties from the CTAB spec

* handle SUBST

* write out the bond props that were being read but not written

* add an additional test

* fix a couple of problems caught in review
2020-03-14 04:58:07 +01:00

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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/FileParsers/FileParsers.h>
#include <GraphMol/SmilesParse/SmilesWrite.h>
#include <GraphMol/SmilesParse/SmilesParse.h>
#include <GraphMol/SmilesParse/SmartsWrite.h>
using namespace RDKit;
TEST_CASE("Basic SVG Parsing", "[SVG,parser]") {
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,parser]") {
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", "[parser,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",
"[parser,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);
}
}
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