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rdkit/Code/GraphMol/FileParsers/cdxml_parser_catch.cpp
Brian Kelley b417465e93 Adds MolToCDXMLBlock to FileParsers (#9291) 
* Adds MolToCDXMLBlock to FileParsers

* Simplified code, removed warning

* Fix C# wrapper for MolToCDX

* Add C# test, fix cscode in swig

* Fix typo in tests

* Set default format to CDXML for MolToCDXML

Co-authored-by: Greg Landrum <greg.landrum@gmail.com>

* Add CDXML writer smoke tests

---------

Co-authored-by: Greg Landrum <greg.landrum@gmail.com>
2026-05-29 05:36:35 +02:00

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//
// Copyright (c) 2022 Brian P Kelley
// 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 <catch2/catch_all.hpp>
#include <RDGeneral/Invariant.h>
#include <GraphMol/RDKitBase.h>
#include <GraphMol/FileParsers/FileParsers.h>
#include <GraphMol/SmilesParse/SmilesWrite.h>
#include <GraphMol/SmilesParse/SmilesParse.h>
#include <GraphMol/SmilesParse/SmartsWrite.h>
#include <RDGeneral/FileParseException.h>
#include <boost/algorithm/string.hpp>
#include <RDGeneral/BadFileException.h>
#include <GraphMol/SmilesParse/CanonicalizeStereoGroups.h>
#include <filesystem>
using namespace RDKit;
using namespace RDKit::v2::CDXMLParser;
std::string canon(const std::string &smi) {
auto *m = SmilesToMol(smi);
auto res = MolToSmiles(*m);
delete m;
return res;
}
void check_smiles_and_roundtrip(const RWMol &m, const std::string &expected) {
CHECK(MolToSmiles(m) == expected);
// std::cout << "*********" << std::endl;
// std::cout << MolToMolBlock(m) << std::endl;
std::unique_ptr<RWMol> mol(MolBlockToMol(MolToMolBlock(m)));
CHECK(MolToSmiles(*mol) == expected);
}
TEST_CASE("CDXML") {
std::string cdxmlbase =
std::string(getenv("RDBASE")) + "/Code/GraphMol/test_data/CDXML/";
SECTION("SIMPLE") {
std::string cdxml1 = R"(<?xml version="1.0" encoding="UTF-8" ?>
<!DOCTYPE CDXML SYSTEM "http://www.cambridgesoft.com/xml/cdxml.dtd" >
<CDXML
CreationProgram="ChemDraw JS 2.0.0.9"
Name="ACS Document 1996"
BoundingBox="94.75 178.16 154.89 211.17"
WindowPosition="0 0"
WindowSize="0 0"
FractionalWidths="yes"
InterpretChemically="yes"
ShowAtomQuery="yes"
ShowAtomStereo="no"
ShowAtomEnhancedStereo="yes"
ShowAtomNumber="no"
ShowResidueID="no"
ShowBondQuery="yes"
ShowBondRxn="yes"
ShowBondStereo="no"
ShowTerminalCarbonLabels="no"
ShowNonTerminalCarbonLabels="no"
HideImplicitHydrogens="no"
Magnification="666"
LabelFont="24"
LabelSize="10"
LabelFace="96"
CaptionFont="24"
CaptionSize="10"
HashSpacing="2.50"
MarginWidth="1.60"
LineWidth="0.60"
BoldWidth="2"
BondLength="14.40"
BondSpacing="18"
ChainAngle="120"
LabelJustification="Auto"
CaptionJustification="Left"
AminoAcidTermini="HOH"
ShowSequenceTermini="yes"
ShowSequenceBonds="yes"
ShowSequenceUnlinkedBranches="no"
ResidueWrapCount="40"
ResidueBlockCount="10"
ResidueZigZag="yes"
NumberResidueBlocks="no"
PrintMargins="36 36 36 36"
MacPrintInfo="0003000001200120000000000B6608A0FF84FF880BE309180367052703FC0002000001200120000000000B6608A0000100000064000000010001010100000001270F000100010000000000000000000000000002001901900000000000400000000000000000000100000000000000000000000000000000"
ChemPropName=""
ChemPropFormula="Chemical Formula: "
ChemPropExactMass="Exact Mass: "
ChemPropMolWt="Molecular Weight: "
ChemPropMOverZ="m/z: "
ChemPropAnalysis="Elemental Analysis: "
ChemPropBoilingPt="Boiling Point: "
ChemPropMeltingPt="Melting Point: "
ChemPropCritTemp="Critical Temp: "
ChemPropCritPres="Critical Pres: "
ChemPropCritVol="Critical Vol: "
ChemPropGibbs="Gibbs Energy: "
ChemPropLogP="Log P: "
ChemPropMR="MR: "
ChemPropHenry="Henry&apos;s Law: "
ChemPropEForm="Heat of Form: "
ChemProptPSA="tPSA: "
ChemPropID=""
ChemPropFragmentLabel=""
color="0"
bgcolor="1"
RxnAutonumberStart="1"
RxnAutonumberConditions="no"
RxnAutonumberStyle="Roman"
><colortable>
<color r="1" g="1" b="1"/>
<color r="0" g="0" b="0"/>
<color r="1" g="0" b="0"/>
<color r="1" g="1" b="0"/>
<color r="0" g="1" b="0"/>
<color r="0" g="1" b="1"/>
<color r="0" g="0" b="1"/>
<color r="1" g="0" b="1"/>
</colortable><fonttable>
<font id="24" charset="utf-8" name="Arial"/>
</fonttable><page
id="32"
BoundingBox="0 0 542 354"
Width="542"
Height="354"
HeaderPosition="36"
FooterPosition="36"
PageOverlap="0"
PrintTrimMarks="yes"
HeightPages="1"
WidthPages="1"
DrawingSpace="poster"
><fragment
id="10"
BoundingBox="94.75 178.16 154.89 211.17"
Z="4"
><n
id="7"
p="95.05 187.47"
Z="1"
AS="N"
/><n
id="9"
p="95.05 201.87"
Z="3"
AS="N"
/><n
id="11"
p="106.31 210.84"
Z="5"
AS="N"
/><n
id="13"
p="120.35 207.64"
Z="7"
AS="N"
/><n
id="15"
p="126.59 194.67"
Z="9"
AS="N"
/><n
id="17"
p="120.35 181.69"
Z="11"
AS="N"
/><n
id="19"
p="106.31 178.49"
Z="13"
AS="N"
/><n
id="28"
p="140.99 194.67"
Z="22"
NodeType="Nickname"
NeedsClean="yes"
AS="N"
><fragment
id="33"
><n
id="34"
p="148.17 207.09"
Element="8"
NumHydrogens="0"
/><n
id="35"
p="162.52 207.09"
/><n
id="36"
p="176.87 207.09"
/><n
id="37"
p="169.69 194.67"
/><n
id="38"
p="169.69 219.52"
/><n
id="39"
p="140.99 194.67"
/><n
id="40"
p="148.17 182.24"
Element="8"
NumHydrogens="0"
/><n
id="41"
p="126.64 194.67"
NodeType="ExternalConnectionPoint"
/><b
id="42"
B="39"
E="40"
Order="2"
/><b
id="43"
B="35"
E="38"
/><b
id="44"
B="35"
E="36"
/><b
id="45"
B="35"
E="37"
/><b
id="46"
B="34"
E="35"
/><b
id="47"
B="34"
E="39"
/><b
id="48"
B="41"
E="39"
/></fragment><t
p="137.66 198.28"
BoundingBox="137.66 189.64 154.89 198.28"
LabelJustification="Left"
LabelAlignment="Left"
><s font="24" size="9.95" color="0" face="96">Boc</s></t></n><b
id="21"
Z="15"
B="7"
E="9"
BS="N"
/><b
id="22"
Z="16"
B="9"
E="11"
BS="N"
/><b
id="23"
Z="17"
B="11"
E="13"
BS="N"
/><b
id="24"
Z="18"
B="13"
E="15"
BS="N"
/><b
id="25"
Z="19"
B="15"
E="17"
BS="N"
/><b
id="26"
Z="20"
B="17"
E="19"
BS="N"
/><b
id="27"
Z="21"
B="19"
E="7"
BS="N"
/><b
id="29"
Z="23"
B="15"
E="28"
BS="N"
/></fragment></page></CDXML>)";
{
std::stringstream iss(cdxml1);
auto mols = MolsFromCDXMLDataStream(iss);
for (auto &mol : mols) {
CHECK(MolToSmiles(*mol) == "CC(C)(C)OC(=O)C1CCCCCC1");
}
}
{
std::stringstream iss(cdxml1);
// v1 api
auto mols = CDXMLDataStreamToMols(iss);
for (auto &mol : mols) {
CHECK(MolToSmiles(*mol) == "CC(C)(C)OC(=O)C1CCCCCC1");
}
}
}
SECTION("REACTION") {
std::string fname = cdxmlbase + "reaction-with-boc.cdxml";
std::vector<std::string> expected = {"CC(C)(C)OC(=O)C1CCCCCC1[*:1]",
"c1ccc([*:1])cc1", "C1CC1", "C1CCC1"};
{
auto mols = MolsFromCDXMLFile(fname);
CHECK(mols.size() == expected.size());
int i = 0;
for (auto &mol : mols) {
CHECK(MolToSmiles(*mol) == expected[i++]);
}
}
{
// v1 api
auto mols = CDXMLFileToMols(fname);
CHECK(mols.size() == expected.size());
int i = 0;
for (auto &mol : mols) {
CHECK(MolToSmiles(*mol) == expected[i++]);
}
}
}
SECTION("RING CHIRALITY") {
std::string fname = cdxmlbase + "ring-stereo1.cdxml";
std::vector<std::string> expected = {"C1CC[C@H]2CCCC[C@H]2C1"};
auto mols = MolsFromCDXMLFile(fname);
CHECK(mols.size() == expected.size());
int i = 0;
for (auto &mol : mols) {
CHECK(MolToSmiles(*mol) == expected[i++]);
}
}
SECTION("SIMPLE CHIRAL") {
std::string fname = cdxmlbase + "chirality1.cdxml";
std::vector<std::string> expected = {"C[C@H](N)C[C@H](C)N"};
auto mols = MolsFromCDXMLFile(fname);
CHECK(mols.size() == expected.size());
int i = 0;
for (auto &mol : mols) {
CHECK(MolToSmiles(*mol) == expected[i++]);
}
}
SECTION("CDXML-CISTRANS") {
auto fname = cdxmlbase + "cistrans1.cdxml";
std::vector<std::string> expected = {"F/C(I)=C(\\Cl)Br"};
auto mols = MolsFromCDXMLFile(fname);
CHECK(mols.size() == expected.size());
int i = 0;
for (auto &mol : mols) {
CHECK(MolToSmiles(*mol) == expected[i++]);
}
}
SECTION("REACTION") {
auto fname = cdxmlbase + "rxn1.cdxml";
std::vector<std::string> expected = {
"Cl[c:1]1[cH:4][cH:3][cH:2][cH:6][cH:5]1",
"OC(O)B[c:7]1[cH:8][cH:9][cH:10][cH:11][cH:12]1",
"[cH:1]1[cH:4][cH:3][cH:2][c:6](-[c:7]2[cH:8][cH:9][cH:10][cH:11][cH:12]2)[cH:5]1"};
auto mols = MolsFromCDXMLFile(fname);
int i = 0;
for (auto &mol : mols) {
CHECK(mol->getProp<unsigned int>("CDX_SCHEME_ID") == 397);
CHECK(mol->getProp<unsigned int>("CDX_STEP_ID") == 398);
if (i == 0) {
CHECK(mol->getProp<unsigned int>("CDX_REAGENT_ID") == 0);
} else if (i == 1) {
CHECK(mol->getProp<unsigned int>("CDX_REAGENT_ID") == 1);
} else if (i == 2) {
CHECK(mol->getProp<unsigned int>("CDX_PRODUCT_ID") == 0);
}
CHECK(MolToSmiles(*mol) == expected[i++]);
}
}
SECTION("DEUTERIUM") {
auto fname = cdxmlbase + "deuterium.cdxml";
{
std::vector<std::string> expected = {
"[2H]c1c([2H])c([2H])c([2H])c([2H])c1[2H]"};
auto mols = MolsFromCDXMLFile(fname);
CHECK(mols.size() == expected.size());
int i = 0;
for (auto &mol : mols) {
CHECK(MolToSmiles(*mol) == expected[i++]);
}
}
{
std::vector<std::string> expected = {
"[2H]C1=C([2H])C([2H])=C([2H])C([2H])=C1[2H]"};
CDXMLParserParams params;
params.sanitize = false;
params.removeHs = false;
auto mols = MolsFromCDXMLFile(fname, params);
CHECK(mols.size() == expected.size());
int i = 0;
for (auto &mol : mols) {
CHECK(MolToSmiles(*mol) == expected[i++]);
}
}
{
std::vector<std::string> expected = {
"[2H]C1=C([2H])C([2H])=C([2H])C([2H])=C1[2H]"};
CDXMLParserParams params;
params.sanitize = false;
params.removeHs = true;
auto mols = MolsFromCDXMLFile(fname, params);
CHECK(mols.size() == expected.size());
int i = 0;
for (auto &mol : mols) {
CHECK(MolToSmiles(*mol) == expected[i++]);
}
}
}
SECTION("Queries") {
{
auto fname = cdxmlbase + "query-atoms.cdxml";
std::vector<std::string> expected = {"*c1ccccc1", "*c1ccccc1",
"*c1ccccc1"};
std::vector<std::string> expected_smarts = {
"[#6]1:[#6]:[#6]:[#6]:[#6]:[#6]:1-*",
"[#6]1:[#6]:[#6]:[#6]:[#6]:[#6]:1-[!#1]",
"[#6]1:[#6]:[#6]:[#6]:[#6]:[#6]:1-[!#6&!#1]"};
auto mols = MolsFromCDXMLFile(fname);
CHECK(mols.size() == expected.size());
int i = 0;
for (auto &mol : mols) {
CHECK(MolToSmarts(*mol) == expected_smarts[i]);
CHECK(MolToSmiles(*mol) == expected[i++]);
}
}
{
auto fname = cdxmlbase + "anybond.cdxml";
auto mols = MolsFromCDXMLFile(fname);
CHECK(mols.size() == 1);
CHECK(MolToSmiles(*mols[0]) == "C1CCC~CC1");
CHECK(MolToSmarts(*mols[0]) == "[#6]1~[#6]-[#6]-[#6]-[#6]-[#6]-1");
}
}
SECTION("ElementList") {
auto fname = cdxmlbase + "element-list.cdxml";
std::vector<std::string> expected = {"[C]CC"};
std::vector<std::string> expected_smarts = {"[#6]-[#6]-[#6,#7,#8,#16]"};
auto mols = MolsFromCDXMLFile(fname);
CHECK(mols.size() == expected.size());
int i = 0;
for (auto &mol : mols) {
CHECK(MolToSmarts(*mol) == expected_smarts[i]);
CHECK(MolToSmiles(*mol) == expected[i++]);
}
}
SECTION("Enhanced Stereo") {
auto fname = cdxmlbase + "beta-cypermethrin.cdxml";
std::vector<std::string> expected = {
"CC1(C)[C@H](C=C(Cl)Cl)[C@H]1C(=O)O[C@@H](C#N)c1cccc(Oc2ccccc2)c1"};
std::vector<std::string> expected_cx = {
"CC1(C)[C@H](C=C(Cl)Cl)[C@@H]1C(=O)O[C@H](C#N)c1cccc(Oc2ccccc2)c1 |&1:3,&2:8,12|"};
auto mols = MolsFromCDXMLFile(fname);
CHECK(mols.size() == expected.size());
int i = 0;
for (auto &mol : mols) {
mol.get()->clearConformers();
CHECK(MolToSmiles(*mol) == expected[i]);
CHECK(MolToCXSmiles(*mol) == expected_cx[i++]);
}
}
SECTION("Enhanced Stereo 2") {
auto fname = cdxmlbase + "beta-cypermethrin-or-abs.cdxml";
std::vector<std::string> expected = {
"CC1(C)[C@H](C=C(Cl)Cl)[C@H]1C(=O)O[C@@H](C#N)c1cccc(Oc2ccccc2)c1"};
std::vector<std::string> expected_cx = {
"CC1(C)[C@H](C=C(Cl)Cl)[C@@H]1C(=O)O[C@H](C#N)c1cccc(Oc2ccccc2)c1 |a:3,o1:8,12|"};
auto mols = MolsFromCDXMLFile(fname);
CHECK(mols.size() == expected.size());
int i = 0;
SmilesWriteParams wp;
for (auto &mol : mols) {
auto tomol = std::unique_ptr<ROMol>(mol.release());
tomol.get()->clearConformers();
RDKit::canonicalizeStereoGroups(tomol);
CHECK(MolToSmiles(*tomol) == expected[i]);
CHECK(MolToCXSmiles(*tomol, wp) == expected_cx[i++]);
}
}
SECTION("Bad CDXML") {
auto fname = cdxmlbase + "bad-cdxml.cdxml";
// Only one passes sanitization
{
std::vector<std::string> expected = {"*c1ccccc1"};
std::vector<std::string> expected_smarts = {
"[#6]1:[#6]:[#6]:[#6]:[#6]:[#6]:1-*",
};
auto mols = MolsFromCDXMLFile(fname);
CHECK(mols.size() == expected.size());
int i = 0;
for (auto &mol : mols) {
CHECK(MolToSmarts(*mol) == expected_smarts[i]);
CHECK(MolToSmiles(*mol) == expected[i++]);
}
}
// setting sanitization to false, we get both
std::vector<std::string> expected = {"*C1=C([H])C([H])=C([H])C([H])=C1[H]",
"*C1=C([H])N([H])=C([H])C([H])=C1[H]"};
std::vector<std::string> expected_smarts = {
"[#6]1(=[#6](-[#6](=[#6](-[#6](=[#6]-1-*)-[H])-[H])-[H])-[H])-[H]",
"[#6]1(=[#6](-[#6](=[#7](-[#6](=[#6]-1-[!#1])-[H])-[H])-[H])-[H])-[H]",
};
CDXMLParserParams params;
params.sanitize = false;
auto mols = MolsFromCDXMLFile(fname, params);
CHECK(mols.size() == expected.size());
int i = 0;
for (auto &mol : mols) {
CHECK(MolToSmarts(*mol) == expected_smarts[i]);
CHECK(MolToSmiles(*mol) == expected[i++]);
}
}
SECTION("Fusion with chirality") {
auto fname = cdxmlbase + "fusion-chiral.cdxml";
auto mols = MolsFromCDXMLFile(fname);
std::vector<std::string> expected = {"C[C@@H](O)[C@@H](C)O"};
CHECK(mols.size() == expected.size());
int i = 0;
for (auto &mol : mols) {
CHECK(MolToSmiles(*mol) == expected[i++]);
}
}
SECTION("ChemDraw Template from the synthesis-workshop") {
// this was hella fun to validate the stereo-chemistry...
auto fname = cdxmlbase + "chemdraw_template1.cdxml";
auto mols = MolsFromCDXMLFile(fname);
#ifndef RDK_BUILD_CHEMDRAW_SUPPORT
std::vector<std::string> expected = {
"CCC/C=C/C=C/C(=O)O[C@H]1/C(=C/C(=O)OC)C[C@H]2C[C@H]([C@@H](C)O)OC(=O)C[C@H](O)C[C@@H]3C[C@H](OC(C)=O)C(C)(C)[C@](O)(C[C@@H]4C/C(=C/C(=O)OC)C[C@H](/C=C/C(C)(C)[C@]1(O)O2)O4)O3",
"[B]",
"*",
"[C]",
"Cc1ccc2n1[C@@H]1[C@@H]3O[C@]([C@H](C)O)(C=C2)[C@H]1c1ccc(C)n1[C@@H]3C", // this is may or may not be correct, but the structure is drawn incorrectly. There's a test below which fixes this
"Cc1ccc2n1[C@H](C)C(=O)[C@@H]1[C@H]2C(=O)C=Cc2ccc(C)n21",
"Cc1ccc2ccc(=O)ccn12",
"Cc1cccn1[C@H](C)C=O",
"Cc1ccc2ccc([O-])cc[n+]1-2",
"Cc1ccc2ccc(=O)ccn12",
"Cc1cccn1[C@H](C)C(C#N)O[Si](C)(C)C",
"CC1CCC2(O)C3(OC4(O)C[C@]2(C)C2(O)[C@H](OC(=O)c5ccc[nH]5)C(O)(C(C)C)C4(C)C32O)C1O",
"C=C(C)[C@H]1CC(=O)CC2=C(C1)[C@H]1C(=O)O[C@H]3C[C@@](C)(O)[C@@H](C2=O)[C@@H]13"};
#else
// the new cdxml parser handles stereo a lot better
std::vector<std::string> expected = {
"CCC/C=C/C=C/C(=O)O[C@H]1/C(=C/C(=O)OC)C[C@H]2C[C@H]([C@@H](C)O)OC(=O)C[C@H](O)C[C@@H]3C[C@H](OC(C)=O)C(C)(C)[C@](O)(C[C@@H]4C/C(=C/C(=O)OC)C[C@H](/C=C/C(C)(C)[C@]1(O)O2)O4)O3",
"[B]",
"*",
"[C]",
"Cc1ccc2n1[C@@H]1[C@@H]3O[C@]([C@H](C)O)(C=C2)[C@H]1c1ccc(C)n1[C@@H]3C",
// this is may or may not be correct, but the structure is drawn
// incorrectly.
// There's a test below which fixes this
"Cc1ccc2n1[C@H](C)C(=O)[C@@H]1[C@H]2C(=O)C=Cc2ccc(C)n21",
"Cc1ccc2ccc(=O)ccn12",
"Cc1cccn1[C@H](C)C=O",
"Cc1ccc2ccc([O-])cc[n+]1-2",
"Cc1ccc2ccc(=O)ccn12",
"Cc1cccn1[C@H](C)C(C#N)O[Si](C)(C)C",
"CC1CC[C@]2(O)[C@]3(C)C[C@]4(O)O[C@@]2([C@@H]1O)C1(O)C4(C)C(O)(C(C)C)[C@@H](OC(=O)c2ccc[nH]2)[C@]13O",
"C=C(C)[C@H]1CC(=O)CC2=C(C1)[C@H]1C(=O)O[C@H]3C[C@@](C)(O)[C@@H](C2=O)[C@@H]13"};
#endif
CHECK(mols.size() == expected.size());
int i = 0;
for (auto &mol : mols) {
CHECK(MolToSmiles(*mol) == expected[i++]);
}
}
SECTION("deuterium atom") {
auto fname = cdxmlbase + "deuterium-atom.cdxml";
CDXMLParserParams params;
params.sanitize = false;
params.removeHs = false;
auto mols = MolsFromCDXMLFile(fname, params);
std::vector<std::string> expected = {"[2H]"};
CHECK(mols.size() == expected.size());
int i = 0;
for (auto &mol : mols) {
CHECK(MolToSmiles(*mol) == expected[i++]);
}
}
SECTION("ChemDraw Template 2 from the synthesis-workshop") {
// this was another hella fun to validate the stereo-chemistry...
// there were so many stereo warnings in chemdraw, I'm just going to
// assume
// the rdkit is correct here...
auto fname = cdxmlbase + "chemdraw_template2.cdxml";
auto mols = MolsFromCDXMLFile(fname);
#ifndef RDK_BUILD_CHEMDRAW_SUPPORT
std::vector<std::string> expected = {
"CCN1CC2(COC)CCC(OC)C34C5CC6C(OC)CC(O)(C(CC23)C14)C5C6O",
"*",
"C",
"[F]",
"[B]",
"[C]",
"[2H]",
"CCN1CC2(COC)CCC(OC)C34C5CC6C(OC)CC(O)(C(CC23)C14)C5C6O",
"*",
"C",
"[F]",
"[B]",
"[C]",
"[2H]",
"CCN1CC2(COC)CCC(OC)C34C5CC6C(OC)CC(O)(C(CC23)C14)C5C6O",
"*",
"C",
"[F]",
"[B]",
"[C]",
"[2H]",
"CCN1CC2(COC)CCC(OC)C34C5CC6C(OC)CC(O)(C(CC23)C14)C5C6O",
"*",
"C",
"[F]",
"[B]",
"[C]",
"[2H]",
"CCN1CC2(COC)CCC(OC)C34C5CC6C(OC)CC(O)(C(CC23)C14)C5C6O",
"CCN1CC2(COC)CCC(OC)C34C5CC6C(OC)CC(O)(C(CC23)C14)C5C6O",
"*",
"[B]",
"[C]",
"[2H]",
"C",
"[F]",
"*",
"C",
"[F]",
"[B]",
"[C]",
"[2H]",
"CCN1CC2(COC)CCC(OC)C34C5CC6C(OC)CC(O)(C(CC23)C14)C5C6O",
"*",
"C",
"[F]",
"[B]",
"[C]",
"[2H]",
"CCN1CC2(COC)CCC(OC)C34C5CC6C(OC)CC(O)(C(CC23)C14)C5C6O",
"*",
"C",
"[F]",
"[B]",
"[C]",
"[2H]",
"CC1CCC2(O)C3(OC4(O)C[C@]2(C)C2(O)[C@H](O)C(O)(C(C)C)C4(C)C32O)C1O",
"CC1=C(C(C)C)[C@@H](O)C2(O)C1(O)C13OC(=O)C[C@@]2(C)C1(O)CCC(C)C3O",
"CC1=CC23OC(=O)C[C@@](C)(C2(O)CC1)C1(O)[C@H](O)C2(C(C)C)OC2(C)C31O",
"*",
"[B]",
"[C]",
"CC1CCC2C3(C1)OC1C[C@]2(C)C2CC(C(C)C)C1(C)C23",
"[2H]",
"*",
"[B]",
"[C]",
"C",
"CC1CCC2(O)C3(OC4(O)C[C@]2(C)C2(O)[C@H](O)C(O)(C(C)C)C4(C)C32O)C1O",
"[2H]"};
#else
// The new cdxml parser handles stereo a LOT better
std::string talatisamine = "CCN1C[C@]2(COC)CCC(OC)[C@@]34[C@@H]5C[C@@H]6C(OC)C[C@@](O)([C@H]5[C@H]6O)[C@@H](C[C@H]23)[C@H]14";
std::vector<std::string> expected = {
talatisamine, //0
"*",
"C",
"[F]",
"[B]",
"[C]",
"[2H]",
talatisamine,
"*",
"C",
"[F]", // 10
"[B]",
"[C]",
"[2H]",
talatisamine,
"*",
"C",
"[F]",
"[B]",
"[C]",
"[2H]", // 20
talatisamine,
"*",
"C",
"[F]",
"[B]",
"[C]",
"[2H]",
talatisamine,
"CCN1C[C@]2(COC)CC[C@H](OC)[C@]34C1C(C[C@H]23)[C@@]1(O)CC(OC)[C@H]2C[C@@H]4[C@@H]1[C@H]2O",
"*", // 30
"[B]",
"[C]",
"[2H]",
"C",
"[F]",
"*",
"C",
"[F]",
"[B]",
"[C]", // 40
"[2H]",
talatisamine,
"*",
"C",
"[F]",
"[B]",
"[C]",
"[2H]",
talatisamine,
"*", // 50
"C",
"[F]",
"[B]",
"[C]",
"[2H]",
"CC1CC[C@]2(O)[C@]3(C)C[C@]4(O)O[C@@]2([C@@H]1O)C1(O)C4(C)C(O)(C(C)C)[C@@H](O)[C@]13O",
"CC1=C(C(C)C)[C@@H](O)[C@@]2(O)[C@@]3(C)CC(=O)O[C@@]4([C@H](O)C(C)CC[C@]34O)[C@@]12O",
"CC1=C[C@@]23OC(=O)C[C@@](C)([C@@]2(O)CC1)[C@]1(O)[C@H](O)C2(C(C)C)OC2(C)[C@@]31O",
"*",
"[B]", // 60
"[C]",
"CC1CC[C@@H]2[C@]3(C)C[C@@H]4O[C@@]2(C1)C1[C@@H]3CC(C(C)C)C14C",
"[2H]",
"*",
"[B]",
"[C]",
"C",
"CC1CC[C@]2(O)[C@]3(C)C[C@]4(O)O[C@@]2([C@@H]1O)C1(O)C4(C)C(O)(C(C)C)[C@@H](O)[C@]13O",
"[2H]"};
#endif
CHECK(mols.size() == expected.size());
int i = 0;
for (auto &mol : mols) {
INFO(i);
CHECK(MolToSmiles(*mol) == expected[i++]);
}
}
SECTION("ChemDraw Template 3 from the synthesis-workshop") {
// this was another hella fun to validate the stereo-chemistry...
// there were so many stereo warnings in chemdraw, I'm just going to
// assume
// the rdkit is correct here...
auto fname = cdxmlbase + "chemdraw_template3.cdxml";
auto mols = MolsFromCDXMLFile(fname);
std::vector<std::string> expected = {
"CCC/C=C/C=C/C(=O)O[C@H]1/C(=C/C(=O)OC)C[C@H]2C[C@H]([C@@H](C)O)OC(=O)C[C@H](O)C[C@@H]3C[C@H](OC(C)=O)C(C)(C)[C@](O)(C[C@@H]4C/C(=C/C(=O)OC)C[C@H](/C=C/C(C)(C)[C@]1(O)O2)O4)O3",
"[B]",
"*",
"[C]",
"CCC/C=C/C=C/C(=O)O[C@H]1/C(=C/C(=O)OC)C[C@H]2C[C@H]([C@@H](C)O)OC(=O)C[C@H](O)C[C@@H]3C[C@H](OC(C)=O)C(C)(C)[C@](O)(C[C@@H]4C/C(=C/C(=O)OC)C[C@H](/C=C/C(C)(C)[C@]1(O)O2)O4)O3",
"[B]",
"*",
"[C]",
"CCC/C=C/C=C/C(=O)O[C@H]1/C(=C/C(=O)OC)C[C@@H](C[C@@H](O)[C@@H](C)O)O[C@@]1(O)C(C)(C)/C=C/C=O",
"*",
"[C]",
"C=C(C[C@H]([O])C[C@]1(O)O[C@H](C[C@@H](O)CC(=O)O)C[C@H](OC(C)=O)C1(C)C)C[Si](C)(C)C",
"*.CC[Si](CC)CC",
"CC[Si](C)(CC)CC",
"CC[Si](C)(CC)CC",
"CC",
"CC",
"*",
"C=C(C[C@H]([O])C[C@]1(O)O[C@H](C[C@@H](O)CC(=O)O)C[C@H](OC(C)=O)C1(C)C)C[Si](C)(C)C",
"*.CC[Si](CC)CC",
"CCC/C=C/C=C/C(=O)O[C@H]1/C(=C/C(=O)OC)C[C@@H](C[C@@H](O)[C@@H](C)O)O[C@@]1(O)C(C)(C)/C=C/C=O",
"[C]"};
int i = 0;
for (auto &mol : mols) {
INFO(i);
check_smiles_and_roundtrip(*mol, expected[i++]);
}
}
SECTION("protecting group") {
auto fname = cdxmlbase + "protecting-groups.cdxml";
auto mols = MolsFromCDXMLFile(fname);
std::vector<std::string> expected = {"CC[Si](C)(CC)CC", "CC"};
CHECK(mols.size() == expected.size());
int i = 0;
for (auto &mol : mols) {
check_smiles_and_roundtrip(*mol, expected[i++]);
}
}
SECTION("protecting group 2") {
auto fname = cdxmlbase + "protecting-groups2.cdxml";
auto mols = MolsFromCDXMLFile(fname);
std::vector<std::string> expected = {"CC[Si](C)(CC)CC", "CC"};
CHECK(mols.size() == expected.size());
int i = 0;
for (auto &mol : mols) {
check_smiles_and_roundtrip(*mol, expected[i++]);
}
}
SECTION("floating protecting group") {
auto fname = cdxmlbase + "floating-protecting-group.cdxml";
// This is a weird one, chemdraw simply ignores the error that causes the
// bond issue, we should probably drop the floating fragment here if
// we are sanitizing
auto mols = MolsFromCDXMLFile(fname);
std::vector<std::string> expected = {
"*",
"C=C(C[C@H]([O])C[C@]1(O)O[C@H](C[C@@H](O)CC(=O)O)C[C@H](OC(C)=O)C1(C)C)C[Si](C)(C)C",
"*.CC[Si](CC)CC"};
CHECK(mols.size() == expected.size());
int i = 0;
for (auto &mol : mols) {
INFO(i);
check_smiles_and_roundtrip(*mol, expected[i++]);
}
}
SECTION("Missing File Name") {
try {
auto mols = MolsFromCDXMLFile("missing file");
CHECK(0); // Bad file exception not caught
} catch (RDKit::BadFileException &) {
}
}
SECTION("Aromatic ring (bondorder==4") {
auto fname = cdxmlbase + "aromatic.cdxml";
auto mols = MolsFromCDXMLFile(fname);
std::vector<std::string> expected = {"c1ccccc1"};
CHECK(mols.size() == expected.size());
int i = 0;
for (auto &mol : mols) {
check_smiles_and_roundtrip(*mol, expected[i++]);
}
}
SECTION("Malformed") {
auto fname = cdxmlbase + "malformed.cdxml";
try {
auto mols = MolsFromCDXMLFile(fname);
CHECK(0);
} catch (FileParseException &e) {
#ifndef RDK_BUILD_CHEMDRAW_SUPPORT
CHECK(std::string(e.what()) == "expected > at line: 373");
#else
CHECK(std::string(e.what()).find("Failed parsing XML with error code 5") !=
std::string::npos);
#endif
}
}
SECTION("Lots of stereo") {
{
auto fname = cdxmlbase + "stereo.cdxml";
std::vector<std::string> expected = {
"C[C@@H](Cl)[C@H](N)O.C[C@@H](F)[C@H](N)O.C[C@H](Br)[C@@H](N)O.C[C@H](I)[C@@H](N)O"};
auto mols = MolsFromCDXMLFile(fname);
CHECK(mols.size() == expected.size());
int i = 0;
for (auto &mol : mols) {
check_smiles_and_roundtrip(*mol, expected[i++]);
}
}
{ // The above, but broken out for easier testing
std::vector<std::string> filenames = {"stereo1.cdxml", "stereo2.cdxml",
"stereo3.cdxml", "stereo4.cdxml"};
std::vector<std::string> expected = {
"C[C@H](I)[C@@H](N)O", "C[C@@H](I)[C@H](N)O", "C[C@@H](Cl)[C@H](N)O",
"C[C@H](Br)[C@@H](N)O"};
for (auto i = 0u; i < filenames.size(); ++i) {
auto fname = cdxmlbase + filenames[i];
auto mols = MolsFromCDXMLFile(fname);
CHECK(mols.size() == 1);
auto &m = *mols.back();
check_smiles_and_roundtrip(m, expected[i]);
}
}
{
auto fname = cdxmlbase + "wavy.cdxml";
std::vector<std::string> expected = {"Cc1cccc(C)c1NC(=O)N=C1CCCN1C",
"Cc1cccc(C)c1NC(=O)/N=C1\\CCCN1C"};
auto mols = MolsFromCDXMLFile(fname);
CHECK(mols.size() == expected.size());
int i = 0;
for (auto &mol : mols) {
if (i == 0) {
CHECK(mol->getBondWithIdx(11)->getStereo() ==
Bond::BondStereo::STEREOANY);
}
check_smiles_and_roundtrip(*mol, expected[i++]);
}
}
{
auto fname = cdxmlbase + "wavy-single.cdxml";
std::vector<std::string> expected = {"CCCC"};
auto mols = MolsFromCDXMLFile(fname);
CHECK(mols.size() == expected.size());
int i = 0;
for (auto &mol : mols) {
CHECK(mol->getBondWithIdx(0)->getBondDir() == Bond::BondDir::NONE);
CHECK(mol->getBondWithIdx(1)->getBondDir() == Bond::BondDir::NONE);
CHECK(mol->getBondWithIdx(2)->getBondDir() == Bond::BondDir::NONE);
check_smiles_and_roundtrip(*mol, expected[i++]);
}
}
}
SECTION("Lots of bad molecules") {
{
auto fname = cdxmlbase + "bad-id.cdxml";
auto mols = MolsFromCDXMLFile(fname);
CHECK(mols.size() == 0);
}
{
auto fname = cdxmlbase + "bad-coords.cdxml";
auto mols = MolsFromCDXMLFile(fname);
CHECK(mols.size() == 0);
}
{
auto fname = cdxmlbase + "bad-bondorder.cdxml";
auto mols = MolsFromCDXMLFile(fname);
#ifndef RDK_BUILD_CHEMDRAW_SUPPORT
CHECK(mols.size() == 0);
#else
CHECK(mols.size() == 1); // The original chemdraw reader makes unknowns single bonds
#endif
}
{
auto fname = cdxmlbase + "bad-bondorder2.cdxml";
auto mols = MolsFromCDXMLFile(fname);
CHECK(mols.size() == 0);
}
}
}
TEST_CASE("atropisomers") {
std::string cdxmlbase =
std::string(getenv("RDBASE")) + "/Code/GraphMol/test_data/CDXML/";
SECTION("atropisomer") {
{
std::vector<std::string> filenames = {"atrop1.cdxml"};
#ifndef RDK_BUILD_CHEMDRAW_SUPPORT
std::vector<std::string> expected = {
"C[C]1[C][CH]C(Cl)C(C)=C1c1c(C)ccc(Cl)c1C |(-2.936,-0.12,;-2.936,-1.66,;-1.602,-2.43,;-1.602,-3.97,;-2.936,-4.74,;-2.93,-6.28,;-4.27,-3.97,;-5.603,-4.74,;-4.27,-2.43,;-5.603,-1.66,;-5.603,-0.12,;-4.27,0.64,;-6.937,0.64,;-8.271,-0.12,;-8.271,-1.66,;-9.604,-2.43,;-6.937,-2.43,;-6.937,-3.97,),^1:1,3,^2:2,wU:8.8|"};
#else
std::vector<std::string> expected = {
"C[C]1[C][CH]C(Cl)C(C)=C1c1c(C)ccc(Cl)c1C |(-2.936,-0.12,;-2.936,-1.66,;-1.602,-2.43,;-1.602,-3.97,;-2.936,-4.74,;-2.93,-6.28,;-4.27,-3.97,;-5.603,-4.74,;-4.27,-2.43,;-5.603,-1.66,;-5.603,-0.12,;-4.27,0.639999,;-6.937,0.639999,;-8.271,-0.12,;-8.271,-1.66,;-9.604,-2.43,;-6.937,-2.43,;-6.937,-3.97,),^1:1,3,^2:2,wU:8.8|"};
#endif
for (auto i = 0u; i < filenames.size(); ++i) {
auto fname = cdxmlbase + filenames[i];
auto mol = MolsFromCDXMLFile(fname);
SmilesWriteParams ps;
auto smi = MolToCXSmiles(*(mol[0].get()), ps,
SmilesWrite::CXSmilesFields::CX_ALL);
CHECK(smi == expected[i]);
}
}
}
}
TEST_CASE("bad stereo in a natural product") {
std::string cdxmlbase =
std::string(getenv("RDBASE")) + "/Code/GraphMol/test_data/CDXML/";
SECTION("case 1") {
auto fname = cdxmlbase + "stereo5.cdxml";
auto mols = MolsFromCDXMLFile(fname);
REQUIRE(mols.size() == 1);
CHECK(
MolToSmiles(*mols[0]) ==
"Cc1ccc2n1[C@@H]1[C@@H]3O[C@]([C@H](C)O)(C=C2)[C@H]1c1ccc(C)n1[C@@H]3C");
}
}
TEST_CASE("Github #6262: preserve bond wedging") {
std::string cdxmlbase =
std::string(getenv("RDBASE")) + "/Code/GraphMol/test_data/CDXML/";
SECTION("case 1") {
auto fname = cdxmlbase + "stereo6.cdxml";
auto mols = MolsFromCDXMLFile(fname);
REQUIRE(mols.size() == 1);
{
REQUIRE(mols[0]->getBondBetweenAtoms(2, 5));
unsigned int cfg = 0;
CHECK(mols[0]->getBondBetweenAtoms(2, 5)->getPropIfPresent(
common_properties::_MolFileBondCfg, cfg));
CHECK(cfg == 1);
}
{
REQUIRE(mols[0]->getBondBetweenAtoms(1, 4));
unsigned int cfg = 0;
CHECK(mols[0]->getBondBetweenAtoms(1, 4)->getPropIfPresent(
common_properties::_MolFileBondCfg, cfg));
CHECK(cfg == 3);
}
{
REQUIRE(mols[0]->getBondBetweenAtoms(3, 8));
unsigned int cfg = 0;
CHECK(mols[0]->getBondBetweenAtoms(3, 8)->getPropIfPresent(
common_properties::_MolFileBondCfg, cfg));
CHECK(cfg == 2);
}
}
}
TEST_CASE("Github #6887: and1 or1 in same mol") {
SECTION("case 1") {
std::string cdxml1 = R"(<?xml version="1.0" encoding="UTF-8" ?>
<!DOCTYPE CDXML SYSTEM "http://www.cambridgesoft.com/xml/cdxml.dtd" >
<CDXML
CreationProgram="ChemDraw 21.0.0.28"
Name="Untitled A4 Document-2"
BoundingBox="115.75 357.32 272.13 406.58"
WindowPosition="0 0"
WindowSize="0 0"
FractionalWidths="yes"
InterpretChemically="yes"
ShowAtomQuery="yes"
ShowAtomStereo="no"
ShowAtomEnhancedStereo="yes"
ShowAtomNumber="no"
ShowResidueID="no"
ShowBondQuery="yes"
ShowBondRxn="yes"
ShowBondStereo="no"
ShowTerminalCarbonLabels="no"
ShowNonTerminalCarbonLabels="no"
HideImplicitHydrogens="no"
LabelFont="21"
LabelSize="10"
LabelFace="96"
CaptionFont="510"
CaptionSize="12"
HashSpacing="2.70"
MarginWidth="2"
LineWidth="1"
BoldWidth="4"
BondLength="30"
BondSpacing="12"
ChainAngle="120"
LabelJustification="Auto"
CaptionJustification="Left"
AminoAcidTermini="HOH"
ShowSequenceTermini="yes"
ShowSequenceBonds="yes"
ShowSequenceUnlinkedBranches="no"
ResidueWrapCount="40"
ResidueBlockCount="10"
ResidueZigZag="yes"
NumberResidueBlocks="no"
PrintMargins="36 36 36 36"
color="0"
bgcolor="1"
><colortable>
<color r="1" g="1" b="1"/>
<color r="0" g="0" b="0"/>
<color r="1" g="0" b="0"/>
<color r="1" g="1" b="0"/>
<color r="0" g="1" b="0"/>
<color r="0" g="1" b="1"/>
<color r="0" g="0" b="1"/>
<color r="1" g="0" b="1"/>
</colortable><fonttable>
<font id="21" charset="x-mac-roman" name="Helvetica"/>
<font id="510" charset="x-mac-roman" name="Times New Roman"/>
</fonttable><page
id="24"
BoundingBox="0 0 523 770"
HeaderPosition="36"
FooterPosition="36"
PrintTrimMarks="yes"
HeightPages="1"
WidthPages="1"
><fragment
id="3"
BoundingBox="115.75 357.32 272.13 406.58"
Z="2"
><n
id="2"
p="116 406"
Z="1"
AS="N"
/><n
id="4"
p="141.98 391"
Z="3"
Geometry="Tetrahedral"
AS="N"
BondOrdering="5 7 0 17"
EnhancedStereoType="And"
EnhancedStereoGroupNum="1"
><objecttag
TagType="Unknown"
Name="enhancedstereo"
><t
p="137.96 401.37"
BoundingBox="138.29 396 145.62 401.50"
CaptionLineHeight="variable"
><s font="21" size="7.5" color="0">&amp;1</s></t></objecttag></n><n
id="6"
p="167.96 406"
Z="5"
AS="N"
/><n
id="8"
p="193.94 391"
Z="7"
Geometry="Tetrahedral"
AS="N"
BondOrdering="9 11 0 19"
EnhancedStereoType="Or"
EnhancedStereoGroupNum="2"
><objecttag
TagType="Unknown"
Name="enhancedstereo"
><t
p="188.54 401.26"
BoundingBox="188.76 396 199.07 401.41"
CaptionLineHeight="variable"
><s font="21" size="7.5" color="0">or2</s></t></objecttag></n><n
id="10"
p="219.92 406"
Z="9"
AS="N"
/><n
id="12"
p="245.90 391"
Z="11"
Geometry="Tetrahedral"
AS="N"
BondOrdering="13 15 0 21"
EnhancedStereoType="Or"
EnhancedStereoGroupNum="1"
><objecttag
TagType="Unknown"
Name="enhancedstereo"
><t
p="241.11 401.22"
BoundingBox="241.32 396 250.43 401.36"
CaptionLineHeight="variable"
><s font="21" size="7.5" color="0">or1</s></t></objecttag></n><n
id="14"
p="271.88 406"
Z="13"
AS="N"
/><n
id="16"
p="141.98 361"
Z="15"
NodeType="Fragment"
NeedsClean="yes"
AS="N"
><fragment
id="25"
><n
id="26"
p="141.98 361"
Element="8"
NumHydrogens="0"
/><n
id="27"
p="116 346"
NumHydrogens="3"
/><n
id="28"
p="141.98 391"
NodeType="ExternalConnectionPoint"
/><b
id="29"
B="26"
E="27"
/><b
id="30"
B="28"
E="26"
Display="WedgeBegin"
/></fragment><t
p="138.09 364.68"
BoundingBox="138.48 357.32 159.33 364.89"
LabelJustification="Left"
LabelAlignment="Left"
><s font="21" size="10" color="0" face="96">OMe</s></t></n><n
id="18"
p="193.94 361"
Z="17"
Element="17"
NumHydrogens="0"
NeedsClean="yes"
AS="N"
><t
p="190.33 364.68"
BoundingBox="190.77 357.32 199.10 364.87"
LabelJustification="Left"
LabelAlignment="Left"
><s font="21" size="10" color="0" face="96">Cl</s></t></n><n
id="20"
p="245.90 361"
Z="19"
Element="35"
NumHydrogens="0"
NeedsClean="yes"
AS="N"
><t
p="242.57 364.59"
BoundingBox="243.31 357.41 252.45 364.59"
LabelJustification="Left"
LabelAlignment="Left"
><s font="21" size="10" color="0" face="96">Br</s></t></n><b
id="5"
Z="4"
B="2"
E="4"
BS="N"
/><b
id="7"
Z="6"
B="4"
E="6"
BS="N"
/><b
id="9"
Z="8"
B="6"
E="8"
BS="N"
/><b
id="11"
Z="10"
B="8"
E="10"
BS="N"
/><b
id="13"
Z="12"
B="10"
E="12"
BS="N"
/><b
id="15"
Z="14"
B="12"
E="14"
BS="N"
/><b
id="17"
Z="16"
B="4"
E="16"
Display="WedgeBegin"
BS="N"
/><b
id="19"
Z="18"
B="8"
E="18"
Display="WedgeBegin"
BS="N"
/><b
id="21"
Z="20"
B="12"
E="20"
Display="WedgeBegin"
BS="N"
/></fragment></page></CDXML>
)";
auto mols = MolsFromCDXML(cdxml1);
mols[0]->clearConformers();
CHECK(MolToCXSmiles(*mols[0]) ==
"CO[C@H](C)C[C@H](Cl)C[C@H](C)Br |o1:5,o2:8,&1:2|");
}
}
TEST_CASE("Github #7528 - read fragments in groups") {
std::string cdxmlbase =
std::string(getenv("RDBASE")) + "/Code/GraphMol/test_data/CDXML/";
SECTION("case 1") {
auto fname = cdxmlbase + "github7467-grouped-fragments.cdxml";
CDXMLParserParams params;
params.sanitize = false;
auto mols = MolsFromCDXMLFile(fname, params);
REQUIRE(mols.size() == 2);
}
}
TEST_CASE("Github #7501 - dative bonds") {
std::string cdxmlbase =
std::string(getenv("RDBASE")) + "/Code/GraphMol/test_data/CDXML/";
SECTION("case 1") {
auto fname = cdxmlbase + "github7501-dative.cdxml";
CDXMLParserParams params;
auto mols = MolsFromCDXMLFile(fname, params);
CHECK(MolToSmiles(*mols[0]) ==
"C[CH2](C)->[Os]12<-[CH3]CC[NH]->1CC=[NH]->2"); // All datives to the
// Osmium
}
}
#ifdef RDK_BUILD_CHEMDRAW_SUPPORT
struct format_check {
std::string filename;
bool stream, iscdx, cdxres, cdxmlres, autores;
};
TEST_CASE("CDX and Formats") {
std::string cdxmlbase =
std::string(getenv("RDBASE")) + "/Code/GraphMol/test_data/CDXML/";
std::string cdxbase =
std::string(getenv("RDBASE")) + "/Code/GraphMol/test_data/CDX/";
SECTION("READ CDX") {
auto cdxfname = cdxmlbase + "ring-stereo1.cdx";
auto cdxmlfname = cdxmlbase + "ring-stereo1.cdxml";
// should default to CDXFormat Auto
auto mols1 = MolsFromCDXMLFile(cdxfname);
auto mols2 = MolsFromCDXMLFile(cdxmlfname);
CHECK(MolToSmiles(*mols1[0]) == MolToSmiles(*mols2[0]));
}
SECTION("Read CDX Files/Streams") {
const std::vector<std::pair<std::string, std::string>> tests {
{"structure_1.cdx", "C1CCOC1"},
{"structure_2.cdx", "C1=CCN=C1"},
{"structure_3.cdx", "CS(C)=O"},
{"structure_4.cdx", "CCO"},
{"structure_5.cdx", "c1cc[nH]c1"},
{"structure_6.cdx", "c1ccoc1"}
};
for(const auto &test : tests) {
auto fname = cdxbase + test.first;
// Read the file
auto m = MolsFromCDXMLFile(fname);
CHECK(MolToSmiles(*m[0]) == test.second);
// Read the CDX stream
auto size = std::filesystem::file_size(fname);
std::string content(size, '\0');
std::ifstream in(fname, std::ios::binary);
in.read(&content[0], size);
auto m2 = MolsFromCDXML(content);
CHECK(MolToSmiles(*m2[0]) == test.second);
}
}
SECTION("READ CDX/CDXML Blocks") {
auto cdxfname = cdxmlbase + "ring-stereo1.cdx";
auto cdxmlfname = cdxmlbase + "ring-stereo1.cdxml";
auto size = std::filesystem::file_size(cdxfname);
std::string content(size, '\0');
std::ifstream in(cdxfname, std::ios::binary);
in.read(&content[0], size);
auto mols1 = MolsFromCDXML(content);
auto size2 = std::filesystem::file_size(cdxmlfname);
std::string content2(size2, ' ');
std::ifstream in2(cdxmlfname, std::ios::binary);
in2.read(&content2[0], size2);
auto mols2 = MolsFromCDXML(content2);
CHECK(MolToSmiles(*mols1[0]) == MolToSmiles(*mols2[0]));
}
SECTION("Check Formats") {
auto cdxfilename = cdxmlbase + "ring-stereo1.cdx";
auto cdxmlfilename = cdxmlbase + "ring-stereo1.cdxml";
std::vector<format_check> checks { {cdxfilename, true, true, true, false, false},
{cdxfilename, false, true, true, false, true},
{cdxmlfilename, true, false, false, true, true},
{cdxmlfilename, false, false, false, true, true},
};
std::vector<CDXMLFormat> formats = { CDXMLFormat::CDX, CDXMLFormat::CDXML, CDXMLFormat::Auto };
for(auto &check : checks) {
if(check.stream) {
} else {
for(auto format : formats) {
bool hasmols = false;
bool exception = false;
try {
auto mols = MolsFromCDXMLFile(check.filename, CDXMLParserParams(true, true, format));
hasmols = mols.size() > 0;
// std::cerr << check.filename << " not stream " << (unsigned)format << " hasmols: " << hasmols << std::endl;
} catch (...) {
exception = true;
// std::cerr << check.filename << " not stream " << (unsigned)format << " exception" << std::endl;
}
bool expected = false;
if (format == CDXMLFormat::CDX) {
expected = check.cdxres;
} else if (format == CDXMLFormat::CDXML) {
expected = check.cdxmlres;
} else {
expected = check.autores;
}
if (exception) {
CHECK(expected == false);
} else {
CHECK(expected == hasmols);
}
}
}
}
}
SECTION("Check MolToCDXMLBlock") {
if(hasChemDrawCDXSupport()) {
auto mol = "c1ccccc1"_smiles;
REQUIRE(mol);
auto block = MolToCDXMLBlock(*mol);
CHECK(block.find("<CDXML") != std::string::npos);
auto cdx = MolToCDXMLBlock(*mol, CDXMLFormat::CDX);
CHECK(cdx.find("<CDXML") == std::string::npos);
auto mols = MolsFromCDXML(block, {true, true, CDXMLFormat::CDXML});
CHECK(mols.size() == 1);
CHECK(MolToSmiles(*mols[0]) == "c1ccccc1");
mols = MolsFromCDXML(cdx, {true, true, CDXMLFormat::CDX});
CHECK(mols.size() == 1);
CHECK(MolToSmiles(*mols[0]) == "c1ccccc1");
}
}
}
#endif
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