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rdkit/External/ChemDraw/test_6k.cpp
Brian Kelley 22be7245df Add suppresions for AppleClang and ChemDraw (#9147)
2026-03-04 08:27:30 +01:00

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//
// Copyright (c) 2025 Glysade Inc and other RDkit contributors
// All rights reserved.
//
// Redistribution and use in source and binary forms, with or without
// modification, are permitted provided that the following conditions are
// met:
//
// * Redistributions of source code must retain the above copyright
// notice, this list of conditions and the following disclaimer.
// * Redistributions in binary form must reproduce the above
// copyright notice, this list of conditions and the following
// disclaimer in the documentation and/or other materials provided
// with the distribution.
// * Neither the name of Novartis Institutes for BioMedical Research Inc.
// nor the names of its contributors may be used to endorse or promote
// products derived from this software without specific prior written
// permission.
//
// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS
// "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT
// LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR
// A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT
// OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
// SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT
// LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE,
// DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY
// THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
// (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
// OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
//
#include "chemdraw.h"
#include "chemdraw_doc.h"
#include <catch2/catch_all.hpp>
#include "RDGeneral/test.h"
#include <RDGeneral/Invariant.h>
#include <GraphMol/RDKitBase.h>
#include <GraphMol/ChemTransforms/ChemTransforms.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 "ChemDrawStartInclude.h"
#include "chemdraw/CDXStdObjects.h"
#include "ChemDrawEndInclude.h"
#include <filesystem>
using namespace RDKit;
using namespace RDKit::v2;
namespace {
std::string replace(std::string &istr, const std::string &from,
const std::string &to) {
std::string str(istr);
size_t start_pos = str.find(from);
if (start_pos == std::string::npos) {
return str;
}
str.replace(start_pos, from.length(), to);
return str;
}
bool hasNonSupportedFeatures(CDXDocument &document, const std::string &fname) {
// check for monomers
std::ifstream ifs(fname);
std::stringstream xml;
xml << ifs.rdbuf();
// We should be able to figure this out from the node but...
if (xml.str().find("monomerAttachmentStructure_") != std::string::npos ||
xml.str().find("Name=\"monomerAttachments") != std::string::npos) {
return true;
}
for (auto node : document.ContainedObjects()) {
auto id = (CDXDatumID)node.second->GetTag();
switch (id) {
case kCDXObj_Page:
for (auto frag : node.second->ContainedObjects()) {
auto id = (CDXDatumID)frag.second->GetTag();
if (id == kCDXObj_Fragment) {
auto &fragment = (CDXFragment &)(*frag.second);
if (fragment.m_sequenceType == kCDXSeqType_Unknown) {
return true;
}
} else if (id == kCDXObj_BracketAttachment ||
id == kCDXObj_BracketedGroup) {
return true;
}
}
break;
case kCDXObj_ObjectTag: {
CDXObject &object = *((CDXObject *)node.second);
id = (CDXDatumID)object.GetTag();
// Check for monomers
break;
}
default:
break;
}
}
return false;
}
bool hasNonSupportedFeatures(const std::string &fname) {
auto doc = ChemDraw::ChemDrawToDocument(fname);
return hasNonSupportedFeatures(*doc, fname);
}
TEST_CASE("Round TRIP") {
std::string path =
std::string(getenv("RDBASE")) + "/External/ChemDraw/test_data/CDXML6K/";
SECTION("round trip") {
// if we can't find the CDXML6K path, then don't run the test
if (!std::filesystem::exists(path)) {
return;
}
int failed = 0;
int saniFailed = 0;
int total = 0;
int parseable = 0;
int nomol = 0;
int badparse = 0;
int success = 0;
int smimatches = 0;
int nonSupported = 0;
int no_mol_in_doc = 0;
int bad_chemdraw_mol = 0;
RDLog::LogStateSetter blocker;
std::string cdxpath = path + "CDXML/";
std::string molpath = path + "mol/";
std::string smipath = path + "smiles/";
std::string failpath = path + "FAILED/";
std::string nomolpath = path + "NOMOL/";
std::string badparsepath = path + "BADPARSE/";
std::string sanitizationpath = path + "SANI/";
std::set<std::string> known_failures{
"INDMUMLL1117_2025-01-24-17-23-14_304.cdxml", // Dative oxygen gets set
// to a radical
"INDMUMLL1117_2025-01-24-17-26-06_1010.cdxml", // The next batch has a
// type of stereochem I
// don't know how to
// parse yet
"INDMUMLL1117_2025-01-24-17-26-06_1012.cdxml",
"INDMUMLL1117_2025-01-24-17-26-06_1022.cdxml",
"INDMUMLL1117_2025-01-24-17-26-06_1024.cdxml",
"INDMUMLL1117_2025-01-24-17-26-06_1026.cdxml",
"INDMUMLL1117_2025-01-24-17-26-06_1032.cdxml",
"INDMUMLL1117_2025-01-24-17-26-06_1034.cdxml",
"INDMUMLL1117_2025-01-24-17-26-06_1036.cdxml",
"INDMUMLL1117_2025-01-24-17-26-06_1040.cdxml",
"INDMUMLL1117_2025-01-24-17-26-06_1042.cdxml",
"INDMUMLL1117_2025-01-24-17-26-06_1048.cdxml", // Stereo chem batch
// ends here
"INDMUMLL1117_2025-01-24-17-26-13_1690.cdxml", // RDKit shows a radical
// for the dative ->[O]
"INDMUMLL1117_2025-01-24-17-27-11_6877.cdxml", // The next batch has a
// type of stereochem I
// don't know how to
// parse yet (same as
// before)
"INDMUMLL1117_2025-01-24-17-27-11_6878.cdxml",
"INDMUMLL1117_2025-01-24-17-27-11_6883.cdxml",
"INDMUMLL1117_2025-01-24-17-27-11_6884.cdxml",
"INDMUMLL1117_2025-01-24-17-27-11_6889.cdxml",
"INDMUMLL1117_2025-01-24-17-27-11_6896.cdxml",
"INDMUMLL1117_2025-01-24-17-27-30_8574.cdxml", // Stereo chem batch
// ends here
"INDMUMLL1117_2025-01-24-17-27-31_8633.cdxml", // RDkit is missing a
// dummy atom molecule
"INDMUMLL1117_2025-01-24-17-27-31_8651.cdxml", // RDkit is missing a
// dummy atom molecule
"INDMUMLL1117_2025-01-24-17-27-53_10330.cdxml", // 2D projection of 3D
// stereo, we fail this
// one
"INDMUMLL1117_2025-01-24-17-27-53_10332.cdxml", // 2D projection of 3D
// stereo, we fail this
// one
"INDMUMLL1117_2025-01-24-17-27-54_10336.cdxml", // RDKit Smiles keeps
// any bonds ~,
// ChemDraw doesn't
"INDMUMLL1117_2025-01-24-17-28-02_10942.cdxml", // Chemdraw smiles
// doesn't support
// quadruple bond $
"INDMUMLL1117_2025-01-24-17-28-15_11666.cdxml", // RDKit Smiles keeps
// any bonds ~,
// ChemDraw doesn't
"INDMUMLL1117_2025-01-24-17-28-20_12011.cdxml", // RDKit gets stereo
// from the 3D data and
// the wedging
"INDMUMLL1117_2025-01-24-17-28-20_12012.cdxml", // RDKit gets stereo
// from the 3D data and
// the wedging
"INDMUMLL1117_2025-01-24-17-28-21_12031.cdxml", // 2D projection of 3D
// stereo, we fail this
// one
"INDMUMLL1117_2025-01-24-17-28-30_12568.cdxml", // 2D projection of 3D
// stereo, we fail this
// one
"INDMUMLL1117_2025-01-24-17-29-06_14654.cdxml", // Dative oxygen gets
// set to a radical
"INDMUMLL1117_2025-01-24-17-29-08_14775.cdxml", // RDKit Smiles keeps
// any bonds ~,
// ChemDraw doesn't
"INDMUMLL1117_2025-01-24-17-29-09_14896.cdxml", // We apparently do a
// bit of a better job
// than chemdraw here
// in parsing R/S
"INDMUMLL1117_2025-01-24-17-29-09_14897.cdxml" // RDKit just gets very
// different stereo
// chem, no idea why
};
for (auto p : {failpath, nomolpath, badparsepath, sanitizationpath}) {
if (std::filesystem::exists(p)) {
std::filesystem::remove_all(p);
}
std::filesystem::create_directory(p);
}
for (const auto &entry :
std::filesystem::recursive_directory_iterator(cdxpath)) {
if (entry.is_regular_file()) {
std::string fname = entry.path().filename().string();
// issue here - graphite nanotube
if (fname == "INDMUMLL1117_2025-01-24-17-28-02_10946.cdxml") {
continue; // nanotube takes forever
}
auto molfname = molpath + replace(fname, ".cdxml", ".mol");
auto smifname = smipath + replace(fname, ".cdxml", ".smi");
// if chemscript couldn't make an output, ignore it
total++;
if (!std::filesystem::exists(molfname) ||
!std::filesystem::exists(smifname)) {
no_mol_in_doc++;
continue;
}
// Get the ChemScript mol and smiles
std::unique_ptr<RWMol> mol;
//= nullptr;
try {
mol.reset(MolFileToMol(molfname));
} catch (...) {
bad_chemdraw_mol++;
continue;
}
// REQUIRE(mols.size());
std::ifstream ifs(smifname);
std::string smiles_in;
ifs >> smiles_in;
std::string smiles;
{
try {
auto smimol = SmilesToMol(smiles_in);
if (!smimol) {
smiles = smiles_in;
} else {
smiles = MolToSmiles(*smimol);
delete smimol;
}
} catch (...) {
smiles = smiles_in;
}
}
parseable++;
// Read the cdxml
std::vector<std::unique_ptr<RWMol>> mols;
bool santizationFailure = false;
try {
mols = MolsFromChemDrawFile(entry.path().string());
if (mols.size() == 0) {
ChemDrawParserParams params;
params.sanitize = false;
mols = MolsFromChemDrawFile(entry.path().string(), params);
santizationFailure = true;
}
if (!mols.size()) {
if (smiles.size() == 0) {
// At least we match the chemscript non-mol
success++;
} else if (hasNonSupportedFeatures(entry.path().string())) {
// std::cerr << "[NOMOL (Unsupported)]: " << entry.path().string()
// << std::endl;
nonSupported++;
} else {
std::cerr << "[NOMOL]: " << entry.path().string() << std::endl;
std::filesystem::copy(
entry.path().string(),
nomolpath + entry.path().filename().string());
nomol++;
}
continue;
}
} catch (...) {
std::cerr << "[BADPARSE]: " << entry.path().string() << std::endl;
std::filesystem::copy(
entry.path(), badparsepath + entry.path().filename().string());
badparse++;
continue;
}
std::unique_ptr<ROMol> m = std::make_unique<ROMol>(*mols[0]);
for (size_t i = 1; i < mols.size(); i++) {
m.reset(combineMols(*m, *mols[i]));
}
auto rdkit_smi = MolToSmiles(*m);
auto mol_smi = mol.get() ? MolToSmiles(*mol) : "";
if (mol_smi != rdkit_smi) {
// Do we match chemscripts smiles output at least?
if (rdkit_smi == smiles) {
smimatches++;
continue;
}
if (hasNonSupportedFeatures(entry.path().string())) {
nonSupported++;
continue; // has unsupported features
}
if (santizationFailure) {
std::cerr << "[SANI]: " << entry.path() << std::endl;
std::filesystem::copy(
entry.path(),
sanitizationpath + entry.path().filename().string());
saniFailed++;
} else {
if (known_failures.find(entry.path().filename().string()) !=
known_failures.end()) {
continue; // we know this failure and it's ok for now
}
std::cerr << "[FAIL]: " << entry.path() << std::endl;
std::filesystem::copy(entry.path(),
failpath + entry.path().filename().string());
failed++;
}
std::cerr << "rdkit: " << rdkit_smi << std::endl;
std::cerr << "chemscript (mol): " << mol_smi << std::endl;
std::cerr << "chemscript (smiles): " << smiles << std::endl;
std::cerr << molfname << std::endl;
std::cerr << smifname << std::endl;
} else {
success++;
}
}
}
std::cerr << "Total:" << total << std::endl;
std::cerr << "Parseable (has chemscript output):" << parseable << std::endl;
std::cerr << "Success:" << success + smimatches << std::endl;
std::cerr << "skipped (non supported features):" << nonSupported
<< std::endl;
std::cerr << "skipped (no mol in doc):" << no_mol_in_doc << std::endl;
std::cerr << "Chemscript smiles matches not chemscript mol: " << smimatches
<< std::endl;
std::cerr << "Failed:" << failed << std::endl;
std::cerr << "Sanitization:" << saniFailed << std::endl;
std::cerr << "Nomol:" << nomol << std::endl;
std::cerr << "Badparse:" << badparse << std::endl;
std::cerr << "Bad ChemDraw Mol:" << bad_chemdraw_mol << std::endl;
REQUIRE(failed == 0);
}
}
} // namespace
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