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d2f716a2e43af940688a4b75933ec6ca75d49ff7
rdkit/Code/GraphMol/FileParsers/testMolSupplier.cpp
Brian Kelley d2f716a2e4 Adds gzstream stream, exposes to swig (#2314) 
* Move RDBoostStreams to RDStreams

* RDBoostStreams->RDStreams

* RDBoostStreams->RDStreams

* Wrap SWIG (with Java test)

* Fix missing declaration

* Use the file that already exists

* Revert to original version

* Revert to CXSMiles version

* Update boost version

* Remove redundant code

* Add zlib

* check for win32

* FileParsers now builds static on windows
2019-03-18 05:32:42 +01:00

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// $Id$
//
// Copyright (C) 2002-2008 Greg Landrum and Rational Discovery LLC
//
// @@ 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 <GraphMol/RDKitBase.h>
#include <string>
#include <iostream>
#include <fstream>
#include <map>
#include <memory>
#include "MolSupplier.h"
#include "MolWriters.h"
#include "FileParsers.h"
#include "FileParserUtils.h"
#include <RDGeneral/FileParseException.h>
#include <RDGeneral/BadFileException.h>
#include <RDGeneral/RDLog.h>
#include <RDStreams/streams.h>
#include <GraphMol/SmilesParse/SmilesWrite.h>
#include <GraphMol/SmilesParse/SmilesParse.h>
#include <GraphMol/Depictor/RDDepictor.h>
#include <boost/iostreams/device/file.hpp>
#include <boost/iostreams/filtering_stream.hpp>
namespace io = boost::iostreams;
using namespace RDKit;
int testMolSup() {
std::string rdbase = getenv("RDBASE");
std::string fname =
rdbase + "/Code/GraphMol/FileParsers/test_data/NCI_aids_few.sdf";
{
SDMolSupplier sdsup(fname);
unsigned int i = 0;
while (!sdsup.atEnd()) {
ROMol *nmol = sdsup.next();
if (nmol) {
TEST_ASSERT(nmol->hasProp(common_properties::_Name));
TEST_ASSERT(nmol->hasProp("NCI_AIDS_Antiviral_Screen_Conclusion"));
delete nmol;
}
i++;
}
TEST_ASSERT(i == 16);
}
{
SDMolSupplier sdsup(fname);
for (unsigned int i = 0; i < 16; ++i) {
ROMol *nmol = sdsup.next();
if (nmol) {
TEST_ASSERT(nmol->hasProp(common_properties::_Name));
TEST_ASSERT(nmol->hasProp("NCI_AIDS_Antiviral_Screen_Conclusion"));
delete nmol;
}
}
// test issue 3524949:
TEST_ASSERT(sdsup.atEnd());
bool ok = false;
try {
sdsup.next();
} catch (FileParseException &) {
ok = true;
}
TEST_ASSERT(ok);
}
{
std::ifstream strm(fname.c_str());
SDMolSupplier sdsup(&strm, false);
unsigned int i = 0;
while (!sdsup.atEnd()) {
ROMol *nmol = sdsup.next();
if (nmol) {
TEST_ASSERT(nmol->hasProp(common_properties::_Name));
TEST_ASSERT(nmol->hasProp("NCI_AIDS_Antiviral_Screen_Conclusion"));
delete nmol;
}
i++;
}
TEST_ASSERT(i == 16);
}
{
auto *strm = new std::ifstream(fname.c_str());
SDMolSupplier sdsup(strm, true);
unsigned int i = 0;
while (!sdsup.atEnd()) {
ROMol *nmol = sdsup.next();
if (nmol) {
TEST_ASSERT(nmol->hasProp(common_properties::_Name));
TEST_ASSERT(nmol->hasProp("NCI_AIDS_Antiviral_Screen_Conclusion"));
delete nmol;
}
i++;
}
TEST_ASSERT(i == 16);
}
#ifdef RDK_BUILD_COORDGEN_SUPPORT
{
fname = rdbase + "/Code/GraphMol/FileParsers/test_data/NCI_aids_few.mae";
MaeMolSupplier maesup(fname);
std::shared_ptr<ROMol> nmol;
for (unsigned int i = 0; i < 16; ++i) {
nmol.reset(maesup.next());
if (nmol) {
TEST_ASSERT(nmol->hasProp(common_properties::_Name));
TEST_ASSERT(nmol->getNumAtoms() > 0);
if (i == 0) {
auto smiles = MolToSmiles(*nmol);
TEST_ASSERT(smiles ==
"CCC1=[O+][Cu]2([O+]=C(CC)C1)[O+]=C(CC)CC(CC)=[O+]2");
}
}
}
TEST_ASSERT(maesup.atEnd());
bool ok = false;
try {
maesup.next();
} catch (FileParseException &) {
ok = true;
}
TEST_ASSERT(ok);
}
#endif // RDK_BUILD_COORDGEN_SUPPORT
return 1;
}
void testRandMolSup() {
std::string rdbase = getenv("RDBASE");
std::string fname =
rdbase + "/Code/GraphMol/FileParsers/test_data/NCI_aids_few.sdf";
// std::string fname("../test_data/NCI_aids_few.sdf");
SDMolSupplier sdsup(fname);
ROMol *tmol = sdsup[7];
delete tmol;
CHECK_INVARIANT(sdsup.length() == 16, "");
STR_VECT names;
names.push_back(std::string("48"));
names.push_back(std::string("128"));
names.push_back(std::string("164"));
names.push_back(std::string("180"));
names.push_back(std::string("192"));
names.push_back(std::string("210"));
names.push_back(std::string("213"));
names.push_back(std::string("229"));
int i;
for (i = 0; i < 8; i++) {
ROMol *mol = sdsup[2 * i];
std::string mname;
mol->getProp(common_properties::_Name, mname);
CHECK_INVARIANT(mname == names[i], "");
delete mol;
}
// get a random molecule
ROMol *mol = sdsup[5];
TEST_ASSERT(mol);
std::string mname;
mol->getProp(common_properties::_Name, mname);
delete mol;
CHECK_INVARIANT(mname == "170", "");
// get the last molecule:
mol = sdsup[15];
TEST_ASSERT(mol);
delete mol;
// and make sure we're at the end:
TEST_ASSERT(sdsup.atEnd());
// now make sure we can grab earlier mols (was sf.net issue 1904170):
mol = sdsup[0];
TEST_ASSERT(mol);
delete mol;
// Issue 113: calling length before grabbing a molecule results in crashes:
SDMolSupplier sdsup2(fname);
CHECK_INVARIANT(sdsup2.length() == 16, "");
}
void testSmilesSup() {
std::string mname;
std::string fname;
ROMol *mol;
std::string rdbase = getenv("RDBASE");
fname = rdbase + "/Code/GraphMol/FileParsers/test_data/fewSmi.2.csv";
{
SmilesMolSupplier nSup2(fname, ",", 1, 0, true);
TEST_ASSERT(nSup2.length() == 10);
}
{
SmilesMolSupplier nSup2(fname, ",", 1, 0, true);
mol = nSup2[3];
TEST_ASSERT(!nSup2.atEnd())
TEST_ASSERT(nSup2.length() == 10);
mol->getProp(common_properties::_Name, mname);
CHECK_INVARIANT(mname == "4", "");
mol->getProp("TPSA", mname);
CHECK_INVARIANT(mname == "82.78", "");
delete mol;
mol = nSup2[9];
TEST_ASSERT(mol);
delete mol;
// now make sure we can grab earlier mols (was sf.net issue 1904170):
mol = nSup2[0];
TEST_ASSERT(mol);
delete mol;
}
{
std::ifstream strm(fname.c_str(), std::ios_base::binary);
SmilesMolSupplier nSup2(&strm, false, ",", 1, 0, true);
mol = nSup2[3];
CHECK_INVARIANT(nSup2.length() == 10, "");
mol->getProp(common_properties::_Name, mname);
CHECK_INVARIANT(mname == "4", "");
mol->getProp("TPSA", mname);
CHECK_INVARIANT(mname == "82.78", "");
delete mol;
mol = nSup2[9];
TEST_ASSERT(mol);
delete mol;
// now make sure we can grab earlier mols (was sf.net issue 1904170):
mol = nSup2[0];
TEST_ASSERT(mol);
delete mol;
}
fname = rdbase + "/Code/GraphMol/FileParsers/test_data/first_200.tpsa.csv";
SmilesMolSupplier smiSup(fname, ",", 0, -1);
mol = smiSup[16];
mol->getProp("TPSA", mname);
CHECK_INVARIANT(mname == "46.25", "");
delete mol;
mol = smiSup[8];
mol->getProp("TPSA", mname);
CHECK_INVARIANT(mname == "65.18", "");
delete mol;
int len = smiSup.length();
CHECK_INVARIANT(len == 200, "");
smiSup.reset();
int i = 0;
mol = smiSup.next();
while (1) {
std::string mname;
mol->getProp(common_properties::_Name, mname);
i++;
delete mol;
try {
mol = smiSup.next();
} catch (FileParseException &) {
break;
}
}
CHECK_INVARIANT(i == 200, "");
fname = rdbase + "/Code/GraphMol/FileParsers/test_data/fewSmi.csv";
SmilesMolSupplier *nSup = new SmilesMolSupplier(fname, ",", 1, 0, false);
// check the length before we read anything out...
// this was a problem at one point (Issue 113)
CHECK_INVARIANT(nSup->length() == 10, "");
mol = (*nSup)[3];
mol->getProp(common_properties::_Name, mname);
CHECK_INVARIANT(mname == "4", "");
mol->getProp("Column_2", mname);
CHECK_INVARIANT(mname == "82.78", "");
delete nSup;
nSup = new SmilesMolSupplier(fname, ",", 1, 0, false);
unsigned int nRead = 0;
while (!nSup->atEnd()) {
delete mol;
mol = nSup->next();
TEST_ASSERT(mol);
nRead++;
}
TEST_ASSERT(nSup->length() == 10);
TEST_ASSERT(nRead == 10);
delete nSup;
delete mol;
}
void testSmilesSupFromText() {
std::string mname;
std::string fname;
ROMol *mol;
SmilesMolSupplier nSup2;
std::string text;
bool failed;
int nAts;
// this was a delightful boundary condition:
BOOST_LOG(rdErrorLog)
<< "------------------------------------------------------" << std::endl;
text = "CC\n"
"CCC\n"
"CCOC\n"
"CCCCOC";
{
nSup2.setData(text, " ", 0, -1, false, true);
// BOOST_LOG(rdErrorLog) << "SIZE: " << nSup2.length() << std::endl;
mol = nSup2.next();
nAts = mol->getNumAtoms();
delete mol;
TEST_ASSERT(nAts == 2);
mol = nSup2[3];
nAts = mol->getNumAtoms();
delete mol;
TEST_ASSERT(nAts == 6);
TEST_ASSERT(nSup2.length() == 4);
failed = false;
try {
mol = nSup2[4];
delete mol;
} catch (FileParseException &) {
failed = true;
}
TEST_ASSERT(failed);
mol = nSup2[2];
nAts = mol->getNumAtoms();
TEST_ASSERT(nAts == 4);
TEST_ASSERT(mol->hasProp(common_properties::_Name));
mol->getProp(common_properties::_Name, mname);
TEST_ASSERT(mname == "2");
delete mol;
}
{
nSup2.setData(text, " ", 0, -1, false, true);
mol = nSup2[2];
TEST_ASSERT(mol);
nAts = mol->getNumAtoms();
TEST_ASSERT(nAts == 4);
TEST_ASSERT(mol->hasProp(common_properties::_Name));
mol->getProp(common_properties::_Name, mname);
TEST_ASSERT(mname == "2");
delete mol;
mol = nSup2[3];
TEST_ASSERT(mol);
nAts = mol->getNumAtoms();
TEST_ASSERT(nAts == 6);
TEST_ASSERT(mol->hasProp(common_properties::_Name));
mol->getProp(common_properties::_Name, mname);
TEST_ASSERT(mname == "3");
delete mol;
}
{
nSup2.setData(text, " ", 0, -1, false, true);
mol = nSup2[3];
TEST_ASSERT(mol);
nAts = mol->getNumAtoms();
TEST_ASSERT(nAts == 6);
TEST_ASSERT(mol->hasProp(common_properties::_Name));
mol->getProp(common_properties::_Name, mname);
TEST_ASSERT(mname == "3");
delete mol;
mol = nSup2[2];
TEST_ASSERT(mol);
nAts = mol->getNumAtoms();
TEST_ASSERT(nAts == 4);
TEST_ASSERT(mol->hasProp(common_properties::_Name));
mol->getProp(common_properties::_Name, mname);
TEST_ASSERT(mname == "2");
delete mol;
}
// --------------
// basics:
text = "Id SMILES Column_2\n"
"mol-1 C 1.0\n"
"mol-2 CC 4.0\n"
"mol-3 CCC 9.0\n"
"mol-4 CCCC 16.0\n";
#if 1
nSup2.setData(text, " ", 1, 0, true, true);
mol = nSup2[3];
// BOOST_LOG(rdErrorLog) << "SIZE: " << nSup2.length() << std::endl;
CHECK_INVARIANT(nSup2.length() == 4, "");
mol->getProp(common_properties::_Name, mname);
TEST_ASSERT(mname == "mol-4");
mol->getProp("Column_2", mname);
TEST_ASSERT(mname == "16.0");
delete mol;
// ensure that we can call setData a second time:
text = "Id SMILES Column_2\n"
"mol-1 C 1.0\n"
"mol-2 CC 4.0\n"
"mol-3 CCC 9.0\n";
nSup2.setData(text, " ", 1, 0, true, true);
CHECK_INVARIANT(nSup2.length() == 3, "");
mol = nSup2[2];
mol->getProp(common_properties::_Name, mname);
TEST_ASSERT(mname == "mol-3");
mol->getProp("Column_2", mname);
TEST_ASSERT(mname == "9.0");
delete mol;
// now test for failure handling:
text = "Id SMILES Column_2\n"
"mol-1 C 1.0\n"
"mol-2 CC 4.0\n"
"mol-3 fail 9.0\n"
"mol-4 CCCC 16.0\n";
nSup2.setData(text, " ", 1, 0, true, true);
mol = nSup2[3];
// BOOST_LOG(rdErrorLog) << "SIZE: " << nSup2.length() << std::endl;
TEST_ASSERT(nSup2.length() == 4);
mol->getProp(common_properties::_Name, mname);
TEST_ASSERT(mname == "mol-4");
mol->getProp("Column_2", mname);
TEST_ASSERT(mname == "16.0");
delete mol;
// failures should give null molecules:
mol = nSup2[2];
TEST_ASSERT(!mol);
delete mol;
#endif
// issue 114, no \n at EOF:
text = "Id SMILES Column_2\n"
"mol-1 C 1.0\n"
"mol-2 CC 4.0\n"
"mol-4 CCCC 16.0\n";
nSup2.setData(text, " ", 1, 0, true, true);
// BOOST_LOG(rdErrorLog) << "SIZE: " << nSup2.length() << std::endl;
TEST_ASSERT(nSup2.length() == 3);
mol = nSup2[2];
TEST_ASSERT(mol);
mol->getProp(common_properties::_Name, mname);
TEST_ASSERT(mname == "mol-4");
mol->getProp("Column_2", mname);
TEST_ASSERT(mname == "16.0");
TEST_ASSERT(nSup2.atEnd());
delete mol;
text = "Id SMILES Column_2\n"
"mol-1 C 1.0\n"
"mol-2 CC 4.0\n"
"mol-4 CCCC 16.0";
nSup2.setData(text, " ", 1, 0, true, true);
// BOOST_LOG(rdErrorLog) << "SIZE: " << nSup2.length() << std::endl;
TEST_ASSERT(nSup2.length() == 3);
mol = nSup2[2];
TEST_ASSERT(mol);
mol->getProp(common_properties::_Name, mname);
TEST_ASSERT(mname == "mol-4");
mol->getProp("Column_2", mname);
TEST_ASSERT(mname == "16.0");
TEST_ASSERT(nSup2.atEnd());
delete mol;
try {
mol = nSup2[3];
delete mol;
} catch (FileParseException &) {
failed = true;
}
TEST_ASSERT(failed);
text = "mol-1 C 1.0\n"
"mol-2 CC 4.0\n"
"mol-4 CCCC 16.0";
nSup2.setData(text, " ", 1, 0, false, true);
// BOOST_LOG(rdErrorLog) << "SIZE: " << nSup2.length() << std::endl;
TEST_ASSERT(nSup2.length() == 3);
mol = nSup2[2];
TEST_ASSERT(mol);
mol->getProp(common_properties::_Name, mname);
TEST_ASSERT(mname == "mol-4");
mol->getProp("Column_2", mname);
TEST_ASSERT(mname == "16.0");
delete mol;
text = "C\n"
"CC\n"
"CCCC";
nSup2.setData(text, " ", 0, -1, false, true);
// BOOST_LOG(rdErrorLog) << "SIZE: " << nSup2.length() << std::endl;
TEST_ASSERT(nSup2.length() == 3);
mol = nSup2[2];
TEST_ASSERT(mol);
TEST_ASSERT(mol->getNumAtoms() == 4);
delete mol;
// this was a delightful boundary condition:
BOOST_LOG(rdErrorLog)
<< "------------------------------------------------------" << std::endl;
text = "CC\n"
"CCC\n"
"CCOC\n"
"CCCCOC";
nSup2.setData(text, " ", 0, -1, false, true);
// BOOST_LOG(rdErrorLog) << "SIZE: " << nSup2.length() << std::endl;
mol = nSup2.next();
delete mol;
mol = nSup2[3];
TEST_ASSERT(nSup2.length() == 4);
delete mol;
failed = false;
try {
mol = nSup2[4];
delete mol;
} catch (FileParseException &) {
failed = true;
}
TEST_ASSERT(failed);
BOOST_LOG(rdErrorLog)
<< "------------------------------------------------------" << std::endl;
// this was a delightful boundary condition:
text = "CC\n"
"CCC\n"
"CCOC\n"
"CCCCOC";
nSup2.setData(text, " ", 0, -1, false, true);
// BOOST_LOG(rdErrorLog) << "SIZE: " << nSup2.length() << std::endl;
failed = false;
try {
mol = nSup2[4];
delete mol;
} catch (FileParseException &) {
failed = true;
}
TEST_ASSERT(failed);
BOOST_LOG(rdErrorLog) << ">>> This may result in an infinite loop. It "
"should finish almost immediately:"
<< std::endl;
TEST_ASSERT(nSup2.length() == 4);
BOOST_LOG(rdErrorLog) << "<<< done." << std::endl;
nSup2.reset();
unsigned int nDone = 0;
while (!nSup2.atEnd()) {
mol = nSup2.next();
nDone++;
delete mol;
}
TEST_ASSERT(nDone == nSup2.length());
// ensure that we can call setData a second time:
text = "Id SMILES Column_2\n"
"# comment, ignore\n"
"mol-1 C 1.0\n"
"mol-2 CC 4.0\n"
"mol-3 CCC 9.0\n"
"mol-4 CCCC 16.0\n";
nSup2.setData(text, " ", 1, 0, true, true);
mol = nSup2[2];
mol->getProp(common_properties::_Name, mname);
TEST_ASSERT(mname == "mol-3");
mol->getProp("Column_2", mname);
TEST_ASSERT(mname == "9.0");
delete mol;
mol = nSup2[1];
mol->getProp(common_properties::_Name, mname);
TEST_ASSERT(mname == "mol-2");
mol->getProp("Column_2", mname);
TEST_ASSERT(mname == "4.0");
delete mol;
// this was a delightful boundary condition:
text = "CC\n"
"CCC\n"
"CCOC\n"
"CCCCOC\n"
"\n"
"\n";
nSup2.setData(text, " ", 0, -1, false, true);
TEST_ASSERT(nSup2.length() == 4);
nSup2.reset();
nDone = 0;
while (!nSup2.atEnd()) {
mol = nSup2.next();
nDone++;
delete mol;
}
TEST_ASSERT(nDone == nSup2.length());
};
void testSmilesWriter() {
std::string rdbase = getenv("RDBASE");
std::string fname =
rdbase + "/Code/GraphMol/FileParsers/test_data/fewSmi.csv";
// std::string fname = "../test_data/fewSmi.csv";
SmilesMolSupplier *nSup = new SmilesMolSupplier(fname, ",", 1, 0, false);
std::string oname =
rdbase + "/Code/GraphMol/FileParsers/test_data/outSmiles_molsupplier.csv";
// std::string oname = "../test_data/outSmiles.csv";
STR_VECT propNames;
propNames.push_back(std::string("Column_2"));
SmilesWriter *writer = new SmilesWriter(oname, " ");
writer->setProps(propNames);
STR_VECT names;
STR_VECT props;
ROMol *mol = nSup->next();
// BOOST_LOG(rdErrorLog) << "WRITING" << std::endl;
while (mol) {
// BOOST_LOG(rdErrorLog) << "MOL: " << MolToSmiles(*mol) << std::endl;
std::string mname, pval;
mol->getProp(common_properties::_Name, mname);
mol->getProp("Column_2", pval);
names.push_back(mname);
props.push_back(pval);
writer->write(*mol);
delete mol;
try {
mol = nSup->next();
} catch (FileParseException &) {
break;
}
}
writer->flush();
delete nSup;
// now read the molecules back in a check if we have the same properties etc
nSup = new SmilesMolSupplier(oname);
int i = 0;
mol = nSup->next();
while (mol) {
std::string mname, pval;
mol->getProp(common_properties::_Name, mname);
mol->getProp("Column_2", pval);
CHECK_INVARIANT(mname == names[i], "");
CHECK_INVARIANT(pval == props[i], "");
i++;
delete mol;
try {
mol = nSup->next();
} catch (FileParseException &) {
break;
}
}
TEST_ASSERT(nSup->length() == writer->numMols());
writer->close();
delete writer;
delete nSup;
}
void testSDWriter() {
std::string rdbase = getenv("RDBASE");
std::string fname =
rdbase + "/Code/GraphMol/FileParsers/test_data/NCI_aids_few.sdf";
SDMolSupplier sdsup(fname);
std::string ofile =
rdbase +
"/Code/GraphMol/FileParsers/test_data/outNCI_few_molsupplier.sdf";
auto *writer = new SDWriter(ofile);
STR_VECT names;
while (!sdsup.atEnd()) {
ROMol *mol = sdsup.next();
std::string mname;
mol->getProp(common_properties::_Name, mname);
names.push_back(mname);
writer->write(*mol);
delete mol;
}
writer->flush();
CHECK_INVARIANT(writer->numMols() == 16, "");
writer->close();
delete writer;
// now read in the file we just finished writing
SDMolSupplier reader(ofile);
int i = 0;
while (!reader.atEnd()) {
ROMol *mol = reader.next();
std::string mname;
mol->getProp(common_properties::_Name, mname);
BOOST_LOG(rdInfoLog) << mname << "\n";
// CHECK_INVARIANT(mname == names[i], "");
delete mol;
i++;
}
BOOST_LOG(rdInfoLog) << i << "\n";
/*
// now read in a file with aromatic information on the bonds
std::string infile = rdbase +
"/Code/GraphMol/FileParsers/test_data/outNCI_arom.sdf";
SDMolSupplier nreader(infile);
i = 0;
while (!nreader.atEnd()) {
ROMol *mol = nreader.next();
std::string mname;
mol->getProp(common_properties::_Name, mname);
BOOST_LOG(rdInfoLog) << mname << "\n";
//CHECK_INVARIANT(mname == names[i], "");
i++;
delete mol;
}*/
}
void testSDSupplierEnding() {
std::string rdbase = getenv("RDBASE");
// test the SD supplier to check if it properly handle the end of sd file
// conditions
// should work fine if the sd file end with a $$$$ follwed by blank line or
// no
// no blank lines
std::string infile =
rdbase + "/Code/GraphMol/FileParsers/test_data/esters_end.sdf";
int i = 0;
SDMolSupplier reader(infile);
while (!reader.atEnd()) {
ROMol *mol = reader.next();
std::string mname;
mol->getProp(common_properties::_Name, mname);
i++;
delete mol;
}
CHECK_INVARIANT(i == 6, "");
}
void testSuppliersEmptyFile() {
std::string rdbase = getenv("RDBASE");
{
std::string infile =
rdbase + "/Code/GraphMol/FileParsers/test_data/empty.sdf";
SDMolSupplier reader(infile);
TEST_ASSERT(reader.atEnd());
}
{
std::string infile =
rdbase + "/Code/GraphMol/FileParsers/test_data/empty.smi";
SmilesMolSupplier smiSup(infile, ",", 0, -1);
TEST_ASSERT(smiSup.atEnd());
}
// tests for GitHub issue 19:
{
std::string infile =
rdbase + "/Code/GraphMol/FileParsers/test_data/empty2.sdf";
SDMolSupplier reader(infile);
TEST_ASSERT(reader.length() == 0);
}
{
std::string infile =
rdbase + "/Code/GraphMol/FileParsers/test_data/empty2.sdf";
SDMolSupplier reader(infile);
TEST_ASSERT(reader.atEnd());
bool failed = false;
try {
reader[0];
} catch (FileParseException &) {
failed = true;
}
TEST_ASSERT(failed);
TEST_ASSERT(reader.length() == 0);
}
{
std::string infile =
rdbase + "/Code/GraphMol/FileParsers/test_data/empty2.sdf";
SDMolSupplier reader(infile);
bool failed = false;
try {
reader[0];
} catch (FileParseException &) {
failed = true;
}
TEST_ASSERT(failed);
TEST_ASSERT(reader.length() == 0);
}
{
SDMolSupplier reader;
reader.setData("");
TEST_ASSERT(reader.atEnd());
bool failed = false;
try {
reader[0];
} catch (FileParseException &) {
failed = true;
}
TEST_ASSERT(failed);
TEST_ASSERT(reader.length() == 0);
}
{
SDMolSupplier reader;
reader.setData("");
bool failed = false;
try {
reader[0];
} catch (FileParseException &) {
failed = true;
}
TEST_ASSERT(failed);
TEST_ASSERT(reader.length() == 0);
}
{
SDMolSupplier reader;
reader.setData("");
TEST_ASSERT(reader.length() == 0);
}
}
void testCisTrans() {
std::string text;
text = "mol-1 ClC(C)=C(Br)C\n"
"mol-2 C1=COC=CC1C(Cl)=C(Br)C\n"
"mol-3 C1=COC=CC1\\C(Cl)=C(Br)\\C";
SmilesMolSupplier smiSup;
smiSup.setData(text, " ", 1, 0, false, true);
std::string ofile = "cisTrans_molsupplier.sdf";
SDWriter writer(ofile);
while (!smiSup.atEnd()) {
ROMol *mol = smiSup.next();
TEST_ASSERT(mol);
RDDepict::compute2DCoords(*mol);
writer.write(*mol);
delete mol;
}
writer.close();
// do the round t;est
// parse the sd file and write it out to smiles
SDMolSupplier *reader;
try {
reader = new SDMolSupplier("cisTrans_molsupplier.sdf");
} catch (FileParseException &) {
reader = nullptr;
}
TEST_ASSERT(reader);
while (!reader->atEnd()) {
ROMol *mol = reader->next();
std::string mname;
mol->getProp(common_properties::_Name, mname);
BOOST_LOG(rdInfoLog) << mname << " ";
BOOST_LOG(rdInfoLog) << MolToSmiles(*mol, 1) << "\n";
delete mol;
}
delete reader;
}
void testStereoRound() {
// - we will read ina bunch of cdk2 smiles with stereo on them
// - generate the canonical smiles for each one
// - generate 2D coordinates, write to an sdf file
// - read the sdf file back in and compare the canonical smiles
std::string rdbase = getenv("RDBASE");
std::string infile =
rdbase + "/Code/GraphMol/FileParsers/test_data/cdk2_stereo.csv";
SmilesMolSupplier *smiSup;
try {
smiSup = new SmilesMolSupplier(infile, ",", 0, 1, false, true);
} catch (FileParseException &) {
smiSup = nullptr;
}
TEST_ASSERT(smiSup)
std::map<std::string, std::string> nameSmi;
std::string ofile =
rdbase +
"/Code/GraphMol/FileParsers/test_data/cdk2_stereo_molsupplier.sdf";
auto *writer = new SDWriter(ofile);
int count = 0;
while (!smiSup->atEnd()) {
ROMol *mol = smiSup->next();
// mol->debugMol(std::cout);
std::string mname;
mol->getProp(common_properties::_Name, mname);
nameSmi[mname] = MolToSmiles(*mol, 1);
ROMol *nmol = SmilesToMol(nameSmi[mname]);
// nmol->debugMol(std::cout);
std::string nsmi = MolToSmiles(*nmol, 1);
// BOOST_LOG(rdErrorLog) << mname << "\n";
if (nameSmi[mname] != nsmi) {
BOOST_LOG(rdInfoLog) << mname << " " << nameSmi[mname] << " " << nsmi
<< "\n";
}
RDDepict::compute2DCoords(*mol);
writer->write(*mol);
count++;
delete mol;
delete nmol;
if (count % 50 == 0) {
BOOST_LOG(rdInfoLog) << count << " " << mname << "\n";
}
}
writer->close();
delete smiSup;
delete writer;
// now read the SD file back in check if the canonical smiles are the same
SDMolSupplier *reader;
try {
reader = new SDMolSupplier(ofile);
} catch (FileParseException &) {
reader = nullptr;
}
TEST_ASSERT(reader);
count = 0;
while (!reader->atEnd()) {
ROMol *mol = reader->next();
// mol->debugMol(std::cout);
std::string smiles = MolToSmiles(*mol, 1);
std::string mname;
mol->getProp(common_properties::_Name, mname);
if (nameSmi[mname] != smiles) {
BOOST_LOG(rdInfoLog) << mname << " " << nameSmi[mname] << " " << smiles
<< "\n";
}
delete mol;
count++;
}
delete reader;
}
void testIssue226() {
std::string rdbase = getenv("RDBASE");
std::string fname =
rdbase + "/Code/GraphMol/FileParsers/test_data/Issue226.sdf";
SDMolSupplier sdsup(fname);
ROMol *mol;
mol = sdsup.next();
TEST_ASSERT(mol);
TEST_ASSERT(mol->hasProp("E1"));
TEST_ASSERT(mol->hasProp("E2"));
delete mol;
mol = sdsup.next();
TEST_ASSERT(mol);
TEST_ASSERT(mol->hasProp("E1"));
TEST_ASSERT(mol->hasProp("E2"));
delete mol;
}
int testTDTSupplier1() {
std::string rdbase = getenv("RDBASE");
std::string fname =
rdbase + "/Code/GraphMol/FileParsers/test_data/acd_few.tdt";
{
TDTMolSupplier suppl(fname, "PN");
unsigned int i = 0;
while (!suppl.atEnd()) {
ROMol *nmol = suppl.next();
if (nmol) {
std::string prop1, prop2;
TEST_ASSERT(nmol->getNumAtoms() > 0);
TEST_ASSERT(nmol->hasProp("PN"));
TEST_ASSERT(nmol->hasProp(common_properties::_Name));
TEST_ASSERT(nmol->hasProp("MFCD"));
nmol->getProp("PN", prop1);
nmol->getProp(common_properties::_Name, prop2);
TEST_ASSERT(prop1 == prop2);
// we didn't ask for 2D conformers, so there should be a property 2D:
TEST_ASSERT(nmol->hasProp(common_properties::TWOD));
// and no conformer:
TEST_ASSERT(!nmol->getNumConformers());
delete nmol;
i++;
}
}
TEST_ASSERT(i == 10);
}
{
std::ifstream strm(fname.c_str(), std::ios_base::binary);
TDTMolSupplier suppl(&strm, false, "PN");
unsigned int i = 0;
while (!suppl.atEnd()) {
ROMol *nmol = suppl.next();
if (nmol) {
std::string prop1, prop2;
TEST_ASSERT(nmol->getNumAtoms() > 0);
TEST_ASSERT(nmol->hasProp("PN"));
TEST_ASSERT(nmol->hasProp(common_properties::_Name));
TEST_ASSERT(nmol->hasProp("MFCD"));
nmol->getProp("PN", prop1);
nmol->getProp(common_properties::_Name, prop2);
TEST_ASSERT(prop1 == prop2);
// we didn't ask for 2D conformers, so there should be a property 2D:
TEST_ASSERT(nmol->hasProp(common_properties::TWOD));
// and no conformer:
TEST_ASSERT(!nmol->getNumConformers());
delete nmol;
i++;
}
}
TEST_ASSERT(i == 10);
}
return 1;
}
int testTDTSupplier2() {
std::string rdbase = getenv("RDBASE");
std::string fname =
rdbase + "/Code/GraphMol/FileParsers/test_data/acd_few.tdt";
int i;
std::string prop1, prop2;
TDTMolSupplier suppl(fname, "PN", 2);
i = 0;
while (!suppl.atEnd()) {
ROMol *nmol = suppl.next();
if (nmol) {
TEST_ASSERT(nmol->getNumAtoms() > 0);
TEST_ASSERT(nmol->hasProp("PN"));
TEST_ASSERT(nmol->hasProp(common_properties::_Name));
TEST_ASSERT(nmol->hasProp("MFCD"));
nmol->getProp("PN", prop1);
nmol->getProp(common_properties::_Name, prop2);
TEST_ASSERT(prop1 == prop2);
// we asked for 2D conformers, so there should be no property 2D:
TEST_ASSERT(!nmol->hasProp(common_properties::TWOD));
// and a conformer:
TEST_ASSERT(nmol->getNumConformers() == 1);
// with id "2":
TEST_ASSERT(nmol->beginConformers()->get()->getId() == 2);
delete nmol;
i++;
}
}
TEST_ASSERT(i == 10);
return 1;
}
int testTDTSupplier3() {
std::string data;
int i;
std::string prop1, prop2;
TDTMolSupplier suppl;
data = "$SMI<Cc1nnc(N)nc1C>\n"
"CAS<17584-12-2>\n"
"|\n"
"$SMI<Cc1n[nH]c(=O)nc1N>\n"
"CAS<~>\n"
"|\n"
"$SMI<Cc1n[nH]c(=O)[nH]c1=O>\n"
"CAS<932-53-6>\n"
"|\n"
"$SMI<Cc1nnc(NN)nc1O>\n"
"CAS<~>\n"
"|\n";
suppl.setData(data, "CAS");
i = 0;
while (!suppl.atEnd()) {
ROMol *nmol = suppl.next();
if (nmol) {
TEST_ASSERT(nmol->getNumAtoms() > 0);
TEST_ASSERT(nmol->hasProp("CAS"));
TEST_ASSERT(nmol->hasProp(common_properties::_Name));
nmol->getProp("CAS", prop1);
nmol->getProp(common_properties::_Name, prop2);
TEST_ASSERT(prop1 == prop2);
// no conformers should have been read:
TEST_ASSERT(nmol->getNumConformers() == 0);
delete nmol;
i++;
}
}
TEST_ASSERT(i == 4);
TEST_ASSERT(suppl.length() == 4);
// now make sure we can grab earlier mols (was sf.net issue 1904170):
ROMol *mol = suppl[0];
TEST_ASSERT(mol);
delete mol;
// make sure we can reset the supplier and still process it properly;
suppl.setData(data, "CAS");
i = 0;
while (!suppl.atEnd()) {
ROMol *nmol = suppl.next();
if (nmol) {
TEST_ASSERT(nmol->getNumAtoms() > 0);
TEST_ASSERT(nmol->hasProp("CAS"));
TEST_ASSERT(nmol->hasProp(common_properties::_Name));
nmol->getProp("CAS", prop1);
nmol->getProp(common_properties::_Name, prop2);
TEST_ASSERT(prop1 == prop2);
// no conformers should have been read:
TEST_ASSERT(nmol->getNumConformers() == 0);
delete nmol;
i++;
}
}
TEST_ASSERT(i == 4);
return 1;
}
void testSDSupplierFromText() {
std::string text;
int i = 0;
SDMolSupplier reader;
text =
"Structure1\n"
"csChFnd70/05230312262D\n"
"\n"
" 5 4 0 0 0 0 0 0 0 0999 V2000\n"
" 1.2124 0.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0\n"
" 2.4249 0.7000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n"
" 3.6373 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n"
" 2.4249 2.1000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0\n"
" 0.0000 0.7000 0.0000 Y 0 0 0 0 0 0 0 0 0 0 0 0\n"
" 1 2 1 0 0 0 0\n"
" 2 3 1 0 0 0 0\n"
" 2 4 2 0 0 0 0\n"
" 1 5 1 0 0 0 0\n"
"M END\n"
"> <ID> (3)\n"
"Lig1\n"
"\n"
"$$$$\n"
"Structure1\n"
"csChFnd70/05230312262D\n"
"\n"
" 6 5 0 0 0 0 0 0 0 0999 V2000\n"
" 1.2124 0.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0\n"
" 2.4249 0.7000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n"
" 3.6373 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n"
" 2.4249 2.1000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0\n"
" 0.0000 0.7000 0.0000 Y 0 0 0 0 0 0 0 0 0 0 0 0\n"
" 4.8477 0.6988 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n"
" 1 2 1 0 0 0 0\n"
" 2 3 1 0 0 0 0\n"
" 2 4 2 0 0 0 0\n"
" 1 5 1 0 0 0 0\n"
" 3 6 1 0 0 0 0\n"
"M END\n"
"> <ID> (4)\n"
"Lig2\n"
"\n"
"$$$$\n";
reader.setData(text);
i = 0;
while (!reader.atEnd()) {
ROMol *mol = reader.next();
std::string mname;
TEST_ASSERT(mol->hasProp(common_properties::_Name));
TEST_ASSERT(mol->hasProp("ID"));
i++;
delete mol;
}
TEST_ASSERT(i == 2);
}
void testSDSupplierFromTextStrLax1() {
std::string text;
text =
"Structure1\n"
"csChFnd70/05230312262D\n"
"\n"
" 5 4 0 0 0 0 0 0 0 0999 V2000\n"
" 1.2124 0.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0\n"
" 2.4249 0.7000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n"
" 3.6373 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n"
" 2.4249 2.1000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0\n"
" 0.0000 0.7000 0.0000 Y 0 0 0 0 0 0 0 0 0 0 0 0\n"
" 1 2 1 0 0 0 0\n"
" 2 3 1 0 0 0 0\n"
" 2 4 2 0 0 0 0\n"
" 1 5 1 0 0 0 0\n"
"M END\n"
"blah\n"
"\n"
"blah after blank line\n"
"> <ID> (3)\n"
"Lig1\n"
"\n"
"This will be ignored\n"
"> <ANOTHER_PROPERTY> (4)\n"
"Value\n"
"\n"
"$$$$\n"
"Structure1\n"
"csChFnd70/05230312262D\n"
"\n"
" 6 5 0 0 0 0 0 0 0 0999 V2000\n"
" 1.2124 0.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0\n"
" 2.4249 0.7000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n"
" 3.6373 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n"
" 2.4249 2.1000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0\n"
" 0.0000 0.7000 0.0000 Y 0 0 0 0 0 0 0 0 0 0 0 0\n"
" 4.8477 0.6988 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n"
" 1 2 1 0 0 0 0\n"
" 2 3 1 0 0 0 0\n"
" 2 4 2 0 0 0 0\n"
" 1 5 1 0 0 0 0\n"
" 3 6 1 0 0 0 0\n"
"M END\n"
"> <ID> (4)\n"
"Lig2\n"
"\n"
"This will be ignored\n"
"\n"
"> <ANOTHER_PROPERTY> (4)\n"
"Value\n"
"\n"
"This will be ignored\n"
"\n"
"$$$$\n";
// strict
{
SDMolSupplier reader;
reader.setData(text, true, true, true);
int i = 0;
while (!reader.atEnd()) {
ROMol *mol = reader.next();
TEST_ASSERT(mol->hasProp(common_properties::_Name));
if (i == 0)
TEST_ASSERT(!mol->hasProp("ID"));
TEST_ASSERT(!mol->hasProp("ANOTHER_PROPERTY"));
i++;
delete mol;
}
TEST_ASSERT(i == 2);
}
// lax
{
SDMolSupplier reader;
reader.setData(text, true, true, false);
int i = 0;
while (!reader.atEnd()) {
ROMol *mol = reader.next();
TEST_ASSERT(mol->hasProp(common_properties::_Name));
TEST_ASSERT(mol->hasProp("ID"));
TEST_ASSERT(mol->hasProp("ANOTHER_PROPERTY"));
i++;
delete mol;
}
TEST_ASSERT(i == 2);
}
}
void testSDSupplierFromTextStrLax2() {
std::string text;
text =
"Structure1\n"
"csChFnd70/05230312262D\n"
"\n"
" 5 4 0 0 0 0 0 0 0 0999 V2000\n"
" 1.2124 0.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0\n"
" 2.4249 0.7000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n"
" 3.6373 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n"
" 2.4249 2.1000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0\n"
" 0.0000 0.7000 0.0000 Y 0 0 0 0 0 0 0 0 0 0 0 0\n"
" 1 2 1 0 0 0 0\n"
" 2 3 1 0 0 0 0\n"
" 2 4 2 0 0 0 0\n"
" 1 5 1 0 0 0 0\n"
"M END\n"
"> <ID> (3)\n"
"Lig1\n"
"\n"
"> <ANOTHER_PROPERTY> (4)\n"
"No blank line before dollars\n"
"$$$$\n"
"Structure1\n"
"csChFnd70/05230312262D\n"
"\n"
" 6 5 0 0 0 0 0 0 0 0999 V2000\n"
" 1.2124 0.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0\n"
" 2.4249 0.7000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n"
" 3.6373 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n"
" 2.4249 2.1000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0\n"
" 0.0000 0.7000 0.0000 Y 0 0 0 0 0 0 0 0 0 0 0 0\n"
" 4.8477 0.6988 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n"
" 1 2 1 0 0 0 0\n"
" 2 3 1 0 0 0 0\n"
" 2 4 2 0 0 0 0\n"
" 1 5 1 0 0 0 0\n"
" 3 6 1 0 0 0 0\n"
"M END\n"
"> <ID> (3)\n"
"Lig2\n"
"\n"
"> <ANOTHER_PROPERTY> (4)\n"
"Value2\n"
"\n"
"$$$$\n";
// strict
{
SDMolSupplier reader;
reader.setData(text, true, true, true);
int i = 0;
while (!reader.atEnd()) {
ROMol *mol = reader.next();
TEST_ASSERT(mol->hasProp(common_properties::_Name));
TEST_ASSERT(mol->hasProp("ID"));
TEST_ASSERT(mol->hasProp("ANOTHER_PROPERTY"));
std::string s;
mol->getProp("ID", s);
TEST_ASSERT(s == "Lig1");
mol->getProp("ANOTHER_PROPERTY", s);
TEST_ASSERT(s == "No blank line before dollars\n"
"$$$$\n"
"Structure1\n"
"csChFnd70/05230312262D");
i++;
delete mol;
}
TEST_ASSERT(i == 1);
}
// lax
{
SDMolSupplier reader;
reader.setData(text, true, true, false);
int i = 0;
while (!reader.atEnd()) {
ROMol *mol = reader.next();
TEST_ASSERT(mol->hasProp(common_properties::_Name));
TEST_ASSERT(mol->hasProp("ID"));
TEST_ASSERT(mol->hasProp("ANOTHER_PROPERTY"));
std::string s;
mol->getProp("ID", s);
TEST_ASSERT(s == "Lig2");
mol->getProp("ANOTHER_PROPERTY", s);
TEST_ASSERT(s == "Value2");
i++;
delete mol;
}
TEST_ASSERT(i == 1);
}
}
void testSDSupplierStrLax1() {
std::string rdbase = getenv("RDBASE");
std::string fname =
rdbase + "/Code/GraphMol/FileParsers/test_data/strictLax1.sdf";
// strict
{
SDMolSupplier reader(fname, true, true, true);
int i = 0;
while (!reader.atEnd()) {
ROMol *mol = reader.next();
TEST_ASSERT(mol->hasProp(common_properties::_Name));
if (i == 0)
TEST_ASSERT(!mol->hasProp("ID"));
TEST_ASSERT(!mol->hasProp("ANOTHER_PROPERTY"));
i++;
delete mol;
}
TEST_ASSERT(i == 2);
}
// lax
{
SDMolSupplier reader(fname, true, true, false);
int i = 0;
while (!reader.atEnd()) {
ROMol *mol = reader.next();
TEST_ASSERT(mol->hasProp(common_properties::_Name));
TEST_ASSERT(mol->hasProp("ID"));
TEST_ASSERT(mol->hasProp("ANOTHER_PROPERTY"));
i++;
delete mol;
}
TEST_ASSERT(i == 2);
}
}
void testSDSupplierStrLax2() {
std::string rdbase = getenv("RDBASE");
std::string fname =
rdbase + "/Code/GraphMol/FileParsers/test_data/strictLax2.sdf";
// strict
{
SDMolSupplier reader(fname, true, true, true);
int i = 0;
while (!reader.atEnd()) {
ROMol *mol = reader.next();
TEST_ASSERT(mol->hasProp(common_properties::_Name));
TEST_ASSERT(mol->hasProp("ID"));
TEST_ASSERT(mol->hasProp("ANOTHER_PROPERTY"));
std::string s;
mol->getProp("ID", s);
TEST_ASSERT(s == "Lig1");
mol->getProp("ANOTHER_PROPERTY", s);
TEST_ASSERT(s == "No blank line before dollars\n"
"$$$$\n"
"Structure1\n"
"csChFnd70/05230312262D");
i++;
delete mol;
}
TEST_ASSERT(i == 1);
}
// lax
{
SDMolSupplier reader(fname, true, true, false);
int i = 0;
while (!reader.atEnd()) {
ROMol *mol = reader.next();
TEST_ASSERT(mol->hasProp(common_properties::_Name));
TEST_ASSERT(mol->hasProp("ID"));
TEST_ASSERT(mol->hasProp("ANOTHER_PROPERTY"));
std::string s;
mol->getProp("ID", s);
TEST_ASSERT(s == "Lig2");
mol->getProp("ANOTHER_PROPERTY", s);
TEST_ASSERT(s == "Value2");
i++;
delete mol;
}
TEST_ASSERT(i == 1);
}
}
void testIssue265() {
std::string rdbase = getenv("RDBASE");
std::string fname =
rdbase + "/Code/GraphMol/FileParsers/test_data/NotThere.sdf";
bool ok = false;
try {
SDMolSupplier reader(fname);
ok = false;
} catch (BadFileException &) {
ok = true;
}
TEST_ASSERT(ok);
try {
SmilesMolSupplier reader(fname);
ok = false;
} catch (BadFileException &) {
ok = true;
}
TEST_ASSERT(ok);
try {
TDTMolSupplier reader(fname);
ok = false;
} catch (BadFileException &) {
ok = true;
}
TEST_ASSERT(ok);
}
void testSDErrorHandling() {
std::string rdbase = getenv("RDBASE");
std::string fname =
rdbase + "/Code/GraphMol/FileParsers/test_data/sdErrors1.sdf";
SDMolSupplier *sdsup;
ROMol *nmol = nullptr;
// entry 1: bad properties
sdsup = new SDMolSupplier(fname);
TEST_ASSERT(!sdsup->atEnd());
nmol = sdsup->next();
TEST_ASSERT(nmol);
TEST_ASSERT(!nmol->hasProp("ID"));
delete sdsup;
delete nmol;
// case 2: can't be sanitized
fname = rdbase + "/Code/GraphMol/FileParsers/test_data/sdErrors2.sdf";
sdsup = new SDMolSupplier(fname);
TEST_ASSERT(!sdsup->atEnd());
nmol = sdsup->next();
TEST_ASSERT(!nmol);
TEST_ASSERT(sdsup->atEnd());
delete sdsup;
delete nmol;
// entry 3: bad number of atoms
fname = rdbase + "/Code/GraphMol/FileParsers/test_data/sdErrors3.sdf";
sdsup = new SDMolSupplier(fname);
TEST_ASSERT(!sdsup->atEnd());
nmol = sdsup->next();
TEST_ASSERT(!nmol);
TEST_ASSERT(sdsup->atEnd());
delete sdsup;
delete nmol;
// entry 4: bad number of bonds
fname = rdbase + "/Code/GraphMol/FileParsers/test_data/sdErrors4.sdf";
sdsup = new SDMolSupplier(fname);
TEST_ASSERT(!sdsup->atEnd());
nmol = sdsup->next();
TEST_ASSERT(!nmol);
TEST_ASSERT(sdsup->atEnd());
delete sdsup;
delete nmol;
}
void testIssue381() {
std::string rdbase = getenv("RDBASE");
std::string fname =
rdbase + "/Code/GraphMol/FileParsers/test_data/Issue381.sdf";
SDMolSupplier *sdsup;
ROMol *nmol = nullptr;
int count;
// entry 1: bad properties
sdsup = new SDMolSupplier(fname);
TEST_ASSERT(!sdsup->atEnd());
count = 0;
while (!sdsup->atEnd()) {
nmol = sdsup->next();
if (nmol)
delete nmol;
count++;
}
TEST_ASSERT(sdsup->atEnd());
TEST_ASSERT(count == 9);
TEST_ASSERT(sdsup->length() == 9);
delete sdsup;
}
void testSetStreamIndices() {
std::string rdbase = getenv("RDBASE");
std::string fname =
rdbase + "/Code/GraphMol/FileParsers/test_data/NCI_aids_few.sdf";
std::ifstream ifs(fname.c_str(), std::ios_base::binary);
std::vector<std::streampos> indices;
bool addIndex = true;
bool notEof = true;
std::streampos pos = 0;
std::string line;
while (notEof) {
if (addIndex)
pos = ifs.tellg();
notEof = (std::getline(ifs, line) ? true : false);
if (notEof) {
if (addIndex)
indices.push_back(pos);
addIndex = (line.substr(0, 4) == "$$$$");
}
}
ifs.close();
SDMolSupplier *sdsup;
ROMol *nmol = nullptr;
int count;
sdsup = new SDMolSupplier(fname);
sdsup->setStreamIndices(indices);
TEST_ASSERT(!sdsup->atEnd());
TEST_ASSERT(sdsup->length() == 16);
count = 0;
while (!sdsup->atEnd()) {
nmol = sdsup->next();
if (nmol)
delete nmol;
count++;
}
TEST_ASSERT(sdsup->atEnd());
TEST_ASSERT(count == 16);
TEST_ASSERT(sdsup->length() == 16);
delete sdsup;
}
int testMixIterAndRandom() {
std::string rdbase = getenv("RDBASE");
std::string fname =
rdbase + "/Code/GraphMol/FileParsers/test_data/esters.sdf";
bool ok;
SDMolSupplier *sdsup;
ROMol *mol;
std::string name;
sdsup = new SDMolSupplier(fname);
TEST_ASSERT(sdsup);
unsigned int i = 0;
while (!sdsup->atEnd()) {
mol = sdsup->next();
if (mol) {
TEST_ASSERT(mol->hasProp("ID"));
delete mol;
}
i++;
}
TEST_ASSERT(i == 6);
TEST_ASSERT(sdsup->length() == 6);
delete sdsup;
sdsup = new SDMolSupplier(fname);
TEST_ASSERT(sdsup);
TEST_ASSERT(sdsup->length() == 6);
mol = sdsup->next();
TEST_ASSERT(mol);
TEST_ASSERT(mol->hasProp("ID"));
mol->getProp("ID", name);
TEST_ASSERT(name == "Lig1");
delete mol;
mol = (*sdsup)[0];
TEST_ASSERT(mol);
TEST_ASSERT(mol->hasProp("ID"));
mol->getProp("ID", name);
TEST_ASSERT(name == "Lig1");
delete mol;
sdsup->reset();
mol = sdsup->next();
TEST_ASSERT(mol);
TEST_ASSERT(mol->hasProp("ID"));
mol->getProp("ID", name);
TEST_ASSERT(name == "Lig1");
delete mol;
mol = sdsup->next();
TEST_ASSERT(mol);
TEST_ASSERT(mol->hasProp("ID"));
mol->getProp("ID", name);
TEST_ASSERT(name == "Lig2");
delete mol;
delete sdsup;
fname = rdbase + "/Code/GraphMol/FileParsers/test_data/fewSmi.csv";
SmilesMolSupplier *nSup;
nSup = new SmilesMolSupplier(fname, ",", 1, 0, false);
TEST_ASSERT(nSup);
TEST_ASSERT(nSup->length() == 10);
mol = (*nSup)[0];
TEST_ASSERT(mol);
TEST_ASSERT(mol->getNumAtoms() == 9);
delete mol;
delete nSup;
nSup = new SmilesMolSupplier(fname, ",", 1, 0, false);
TEST_ASSERT(nSup);
mol = (*nSup)[0];
TEST_ASSERT(mol);
TEST_ASSERT(mol->getNumAtoms() == 9);
TEST_ASSERT(nSup->length() == 10);
delete mol;
delete nSup;
nSup = new SmilesMolSupplier(fname, ",", 1, 0, false);
TEST_ASSERT(nSup);
mol = nSup->next();
TEST_ASSERT(mol);
TEST_ASSERT(mol->getNumAtoms() == 9);
TEST_ASSERT(nSup->length() == 10);
delete mol;
mol = (*nSup)[0];
TEST_ASSERT(mol);
TEST_ASSERT(mol->getNumAtoms() == 9);
TEST_ASSERT(nSup->length() == 10);
delete mol;
mol = nSup->next();
TEST_ASSERT(mol);
TEST_ASSERT(mol->getNumAtoms() == 20);
delete nSup;
delete mol;
nSup = new SmilesMolSupplier(fname, ",", 1, 0, false);
TEST_ASSERT(nSup);
mol = nullptr;
try {
mol = (*nSup)[20];
ok = false;
} catch (FileParseException &) {
ok = true;
}
TEST_ASSERT(ok);
delete nSup;
fname = rdbase + "/Code/GraphMol/FileParsers/test_data/acd_few.tdt";
TDTMolSupplier *tSup;
tSup = new TDTMolSupplier(fname);
TEST_ASSERT(tSup);
TEST_ASSERT(tSup->length() == 10);
mol = (*tSup)[0];
TEST_ASSERT(mol);
TEST_ASSERT(mol->getNumAtoms() == 9);
delete mol;
delete tSup;
tSup = new TDTMolSupplier(fname);
TEST_ASSERT(tSup);
mol = (*tSup)[0];
TEST_ASSERT(mol);
TEST_ASSERT(mol->getNumAtoms() == 9);
TEST_ASSERT(tSup->length() == 10);
delete mol;
delete tSup;
tSup = new TDTMolSupplier(fname);
TEST_ASSERT(tSup);
mol = tSup->next();
TEST_ASSERT(mol);
TEST_ASSERT(mol->getNumAtoms() == 9);
TEST_ASSERT(tSup->length() == 10);
delete mol;
mol = (*tSup)[0];
TEST_ASSERT(mol);
TEST_ASSERT(mol->getNumAtoms() == 9);
TEST_ASSERT(tSup->length() == 10);
delete mol;
mol = tSup->next();
TEST_ASSERT(mol);
delete mol;
mol = tSup->next();
TEST_ASSERT(mol);
delete mol;
mol = tSup->next();
TEST_ASSERT(mol);
TEST_ASSERT(mol->getNumAtoms() == 10);
delete tSup;
delete mol;
tSup = new TDTMolSupplier(fname);
TEST_ASSERT(tSup);
mol = nullptr;
try {
mol = (*tSup)[20];
delete mol;
ok = false;
} catch (FileParseException &) {
ok = true;
}
TEST_ASSERT(ok);
delete tSup;
return 1;
}
int testRemoveHs() {
std::string rdbase = getenv("RDBASE");
std::string fname =
rdbase + "/Code/GraphMol/FileParsers/test_data/withHs.sdf";
SDMolSupplier sdsup(fname);
ROMol *nmol;
nmol = sdsup.next();
TEST_ASSERT(nmol);
TEST_ASSERT(nmol->getNumAtoms() == 23);
delete nmol;
nmol = sdsup.next();
TEST_ASSERT(nmol);
TEST_ASSERT(nmol->getNumAtoms() == 28);
delete nmol;
std::cerr << "build:" << std::endl;
SDMolSupplier sdsup2(fname, true, false);
nmol = sdsup2.next();
TEST_ASSERT(nmol);
// std::cerr<<" count: "<<nmol->getNumAtoms()<<std::endl;
TEST_ASSERT(nmol->getNumAtoms() == 39);
delete nmol;
nmol = sdsup2.next();
TEST_ASSERT(nmol);
TEST_ASSERT(nmol->getNumAtoms() == 30);
delete nmol;
return 1;
}
void testGetItemText() {
std::string rdbase = getenv("RDBASE");
std::string fname;
ROMol *mol1, *mol2;
std::string molB, smiles;
bool ok;
{
fname = rdbase + "/Code/GraphMol/FileParsers/test_data/NCI_aids_few.sdf";
SDMolSupplier sdsup(fname);
TEST_ASSERT(sdsup.length() == 16);
molB = sdsup.getItemText(0);
mol1 = sdsup[0];
TEST_ASSERT(mol1);
mol2 = MolBlockToMol(molB);
TEST_ASSERT(mol2);
TEST_ASSERT(mol2->getNumAtoms() == mol1->getNumAtoms());
delete mol1;
delete mol2;
// make sure getItemText() doesn't screw up the current position:
molB = sdsup.getItemText(10);
mol1 = sdsup.next();
molB = sdsup.getItemText(1);
TEST_ASSERT(mol1);
mol2 = MolBlockToMol(molB);
TEST_ASSERT(mol2);
TEST_ASSERT(mol2->getNumAtoms() == mol1->getNumAtoms());
delete mol1;
delete mol2;
// make sure getItemText() works on the last molecule
// (this was sf.net issue 1874882
molB = sdsup.getItemText(15);
mol1 = sdsup[15];
mol2 = MolBlockToMol(molB);
TEST_ASSERT(mol2);
TEST_ASSERT(mol2->getNumAtoms() == mol1->getNumAtoms());
delete mol1;
delete mol2;
try {
molB = sdsup.getItemText(16);
ok = false;
} catch (FileParseException &) {
ok = true;
}
TEST_ASSERT(ok);
try {
molB = sdsup.getItemText(20);
ok = false;
} catch (FileParseException &) {
ok = true;
}
TEST_ASSERT(ok);
}
{
fname = rdbase + "/Code/GraphMol/FileParsers/test_data/NCI_aids_few.sdf";
SDMolSupplier sdsup(fname);
// make sure getItemText() works if we haven't read at all from the
// supplier:
// (this was sf.net issue 2632960)
molB = sdsup.getItemText(0);
mol2 = MolBlockToMol(molB);
TEST_ASSERT(mol2);
mol1 = sdsup[0];
TEST_ASSERT(mol1);
TEST_ASSERT(mol2->getNumAtoms() == mol1->getNumAtoms());
delete mol1;
delete mol2;
molB = sdsup.getItemText(5);
mol2 = MolBlockToMol(molB);
TEST_ASSERT(mol2);
TEST_ASSERT(mol2->getNumAtoms() == 16);
mol1 = sdsup[5];
TEST_ASSERT(mol1);
TEST_ASSERT(mol2->getNumAtoms() == mol1->getNumAtoms());
delete mol1;
delete mol2;
}
{
fname = rdbase + "/Code/GraphMol/FileParsers/test_data/fewSmi.csv";
SmilesMolSupplier smisup(fname, ",", 1, 0, false);
TEST_ASSERT(smisup.length() == 10);
molB = smisup.getItemText(0);
TEST_ASSERT(molB == "1, CC1=CC(=O)C=CC1=O, 34.14");
mol1 = smisup[0];
TEST_ASSERT(mol1);
delete mol1;
molB = smisup.getItemText(5);
TEST_ASSERT(
molB ==
"6, OC(=O)C1=C(C=CC=C1)C2=C3C=CC(=O)C(=C3OC4=C2C=CC(=C4Br)O)Br, 87.74");
mol1 = smisup.next();
TEST_ASSERT(mol1);
TEST_ASSERT(mol1->getNumAtoms() == 20);
delete mol1;
// make sure getItemText() works on the last molecule
// (this was sf.net issue 1874882
molB = smisup.getItemText(8);
TEST_ASSERT(molB == "9, CC(=NO)C(C)=NO, 65.18");
molB = smisup.getItemText(9);
TEST_ASSERT(molB == "10, C1=CC=C(C=C1)P(C2=CC=CC=C2)C3=CC=CC=C3, 0.00");
mol1 = smisup[0];
TEST_ASSERT(mol1);
smiles = MolToSmiles(*mol1, 1);
TEST_ASSERT(smiles == "CC1=CC(=O)C=CC1=O");
TEST_ASSERT(mol1->getNumAtoms() == 9);
delete mol1;
}
{
fname = rdbase + "/Code/GraphMol/FileParsers/test_data/fewSmi.csv";
SmilesMolSupplier smisup(fname, ",", 1, 0, false);
// make sure getItemText() works if we haven't read at all from the
// supplier:
// (this was sf.net issue 2632960)
molB = smisup.getItemText(0);
TEST_ASSERT(molB == "1, CC1=CC(=O)C=CC1=O, 34.14");
molB = smisup.getItemText(5);
TEST_ASSERT(
molB ==
"6, OC(=O)C1=C(C=CC=C1)C2=C3C=CC(=O)C(=C3OC4=C2C=CC(=C4Br)O)Br, 87.74");
molB = smisup.getItemText(8);
TEST_ASSERT(molB == "9, CC(=NO)C(C)=NO, 65.18");
molB = smisup.getItemText(9);
TEST_ASSERT(molB == "10, C1=CC=C(C=C1)P(C2=CC=CC=C2)C3=CC=CC=C3, 0.00");
}
{
fname = rdbase + "/Code/GraphMol/FileParsers/test_data/fewSmi.csv";
SmilesMolSupplier smisup(fname, ",", 1, 0, false);
// make sure getItemText() flags EOF
// (this was sf.net issue 3299878)
molB = smisup.getItemText(0);
TEST_ASSERT(molB == "1, CC1=CC(=O)C=CC1=O, 34.14");
ROMol *m = smisup[9];
TEST_ASSERT(m);
delete m;
TEST_ASSERT(smisup.atEnd());
molB = smisup.getItemText(9);
TEST_ASSERT(molB == "10, C1=CC=C(C=C1)P(C2=CC=CC=C2)C3=CC=CC=C3, 0.00");
TEST_ASSERT(smisup.atEnd());
}
{
fname = rdbase + "/Code/GraphMol/FileParsers/test_data/acd_few.tdt";
TDTMolSupplier tdtsup(fname);
// make sure getItemText() works if we haven't read at all from the
// supplier:
// (this was sf.net issue 2632960)
molB = tdtsup.getItemText(0);
TEST_ASSERT(molB != "");
}
{
fname = rdbase + "/Code/GraphMol/FileParsers/test_data/acd_few.tdt";
TDTMolSupplier tdtsup(fname);
TEST_ASSERT(tdtsup.length() == 10);
molB = tdtsup.getItemText(0);
TEST_ASSERT(molB != "");
mol1 = tdtsup[0];
TEST_ASSERT(mol1);
smiles = MolToSmiles(*mol1, 1);
TEST_ASSERT(smiles == "Cc1nnc(N)nc1C");
TEST_ASSERT(mol1->getNumAtoms() == 9);
delete mol1;
// make sure getItemText doesn't screw up next()
molB = tdtsup.getItemText(5);
mol1 = tdtsup.next();
TEST_ASSERT(mol1);
TEST_ASSERT(mol1->getNumAtoms() == 9);
smiles = MolToSmiles(*mol1, 1);
TEST_ASSERT(smiles == "Cc1n[nH]c(=O)nc1N");
delete mol1;
// make sure getItemText() works on the last molecule
// (this was sf.net issue 1874882
molB = tdtsup.getItemText(9);
TEST_ASSERT(molB != "");
TEST_ASSERT(molB.substr(0, 12) == "$SMI<Cc1n[nH");
}
{
fname = rdbase + "/Code/GraphMol/FileParsers/test_data/acd_few.tdt";
TDTMolSupplier tdtsup(fname);
TEST_ASSERT(tdtsup.length() == 10);
ROMol *mol = tdtsup[9];
TEST_ASSERT(mol);
delete mol;
TEST_ASSERT(tdtsup.atEnd());
// (this was sf.net issue 3299878
molB = tdtsup.getItemText(9);
TEST_ASSERT(molB != "");
TEST_ASSERT(molB.substr(0, 12) == "$SMI<Cc1n[nH");
TEST_ASSERT(tdtsup.atEnd());
}
}
int testForwardSDSupplier() {
std::string rdbase = getenv("RDBASE");
std::string fname =
rdbase + "/Code/GraphMol/FileParsers/test_data/NCI_aids_few.sdf";
std::string fname2 =
rdbase + "/Code/GraphMol/FileParsers/test_data/NCI_aids_few.sdf.gz";
{
std::ifstream strm(fname.c_str());
ForwardSDMolSupplier sdsup(&strm, false);
unsigned int i = 0;
while (!sdsup.atEnd()) {
ROMol *nmol = sdsup.next();
TEST_ASSERT(nmol || sdsup.atEnd());
if (nmol) {
TEST_ASSERT(nmol->hasProp(common_properties::_Name));
TEST_ASSERT(nmol->hasProp("NCI_AIDS_Antiviral_Screen_Conclusion"));
delete nmol;
i++;
}
}
TEST_ASSERT(i == 16);
}
// make sure the boost::iostreams are working
{
io::filtering_istream strm;
strm.push(io::file_source(fname));
unsigned int i = 0;
while (!strm.eof()) {
std::string line;
std::getline(strm, line);
if (!strm.eof())
++i;
if (i > 1000)
break;
}
TEST_ASSERT(i == 998);
}
{
gzstream strm(fname2);
unsigned int i = 0;
while (!strm.eof()) {
std::string line;
std::getline(strm, line);
if (!strm.eof())
++i;
if (i > 1000)
break;
}
TEST_ASSERT(i == 997);
}
// looks good, now do a supplier:
{
gzstream strm(fname2);
ForwardSDMolSupplier sdsup(&strm, false);
unsigned int i = 0;
while (!sdsup.atEnd()) {
ROMol *nmol = sdsup.next();
if (nmol) {
TEST_ASSERT(nmol->hasProp(common_properties::_Name));
TEST_ASSERT(nmol->hasProp("NCI_AIDS_Antiviral_Screen_Conclusion"));
delete nmol;
i++;
}
}
TEST_ASSERT(i == 16);
}
#ifdef RDK_BUILD_COORDGEN_SUPPORT
// Now test that Maestro parsing of gz files works
std::string maefname =
rdbase + "/Code/GraphMol/FileParsers/test_data/NCI_aids_few.mae";
std::string maefname2 =
rdbase + "/Code/GraphMol/FileParsers/test_data/NCI_aids_few.maegz";
{
io::filtering_istream strm;
strm.push(io::file_source(maefname));
unsigned int i = 0;
while (!strm.eof()) {
std::string line;
std::getline(strm, line);
if (!strm.eof())
++i;
if (i > 1700)
break;
}
TEST_ASSERT(i == 1663);
}
{
gzstream strm(maefname2);
unsigned int i = 0;
while (!strm.eof()) {
std::string line;
std::getline(strm, line);
if (!strm.eof())
++i;
if (i > 1700)
break;
}
TEST_ASSERT(i == 1663);
}
// looks good, now do a supplier:
{
gzstream *strm = new gzstream(maefname2);
MaeMolSupplier maesup(strm);
unsigned int i = 0;
std::shared_ptr<ROMol> nmol;
while (!maesup.atEnd()) {
nmol.reset(maesup.next());
if (nmol != nullptr) {
i++;
}
}
TEST_ASSERT(i == 16);
}
#endif // RDK_BUILD_COORDGEN_SUPPORT
return 1;
}
void testMissingCRSDSupplier() {
std::string rdbase = getenv("RDBASE");
std::string infile =
rdbase + "/Code/GraphMol/FileParsers/test_data/missingCR.sdf";
SDMolSupplier reader(infile);
auto *mol = reader.next();
delete mol;
TEST_ASSERT(reader.atEnd());
}
void testIssue3482695() {
std::string rdbase = getenv("RDBASE");
std::string infile =
rdbase + "/Code/GraphMol/FileParsers/test_data/Issue3482695.sdf";
SDMolSupplier reader(infile);
ROMol *nmol = reader.next();
TEST_ASSERT(nmol);
TEST_ASSERT(nmol->getNumAtoms() == 0);
TEST_ASSERT(nmol->hasProp("test"));
delete nmol;
}
void testIssue3525673() {
std::string rdbase = getenv("RDBASE");
std::string infile =
rdbase + "/Code/GraphMol/FileParsers/test_data/Issue3525673.sdf";
std::ifstream ins(infile.c_str());
ForwardSDMolSupplier reader(&ins, false);
ROMol *nmol;
nmol = reader.next();
TEST_ASSERT(nmol);
delete nmol;
nmol = reader.next();
TEST_ASSERT(nmol);
TEST_ASSERT(nmol->getNumAtoms() == 37);
delete nmol;
nmol = reader.next();
TEST_ASSERT(nmol);
delete nmol;
nmol = reader.next();
TEST_ASSERT(nmol);
delete nmol;
nmol = reader.next();
TEST_ASSERT(nmol);
TEST_ASSERT(nmol->getNumAtoms() == 58);
delete nmol;
nmol = reader.next();
TEST_ASSERT(nmol);
delete nmol;
nmol = reader.next();
TEST_ASSERT(!nmol); // broken due to 'foo' in counts line!
nmol = reader.next();
TEST_ASSERT(nmol);
TEST_ASSERT(nmol->getNumAtoms() == 58);
delete nmol;
nmol = reader.next();
TEST_ASSERT(nmol);
delete nmol;
}
void testBlankLinesInProps() {
std::string rdbase = getenv("RDBASE");
std::string infile =
rdbase + "/Code/GraphMol/FileParsers/test_data/BlankPropLines.sdf";
std::ifstream ins(infile.c_str());
ForwardSDMolSupplier reader(&ins, false);
ROMol *nmol;
std::string pval;
nmol = reader.next();
TEST_ASSERT(nmol);
TEST_ASSERT(nmol->getNumAtoms() == 19);
TEST_ASSERT(nmol->hasProp("MultiLineProperty1"));
nmol->getProp("MultiLineProperty1", pval);
TEST_ASSERT(pval == "foo\nbar\n \nbaz");
TEST_ASSERT(nmol->hasProp("MultiLineProperty2"));
TEST_ASSERT(!(nmol->hasProp("fooprop")));
nmol->getProp("MultiLineProperty2", pval);
TEST_ASSERT(pval == "foo\n> <fooprop>\nbaz\n ");
delete nmol;
}
void testSkipLines() {
std::string rdbase = getenv("RDBASE");
std::string infile =
rdbase + "/Code/GraphMol/FileParsers/test_data/SkipLines.sdf";
std::ifstream ins(infile.c_str());
ForwardSDMolSupplier reader(&ins, false);
ROMol *nmol;
std::string pval;
nmol = reader.next();
TEST_ASSERT(nmol);
TEST_ASSERT(nmol->getNumAtoms() == 1);
TEST_ASSERT(nmol->hasProp("prop1"));
delete nmol;
}
void testGitHub23() {
std::string rdbase = getenv("RDBASE");
std::string ofile =
rdbase + "/Code/GraphMol/FileParsers/test_data/blah_molsupplier.sdf";
auto *writer = new SDWriter(ofile);
ROMol *mol = SmilesToMol("CCCC");
INT_VECT iv;
iv.push_back(1);
iv.push_back(2);
mol->setProp("pval", iv);
writer->write(*mol);
delete mol;
writer->close();
delete writer;
}
void testGitHub88() {
std::string rdbase = getenv("RDBASE");
std::string infile =
rdbase + "/Code/GraphMol/FileParsers/test_data/github88.v3k.sdf";
std::ifstream ins(infile.c_str());
ForwardSDMolSupplier reader(&ins, false);
ROMol *nmol;
nmol = reader.next();
TEST_ASSERT(nmol);
TEST_ASSERT(nmol->getNumAtoms() == 8);
TEST_ASSERT(nmol->hasProp("prop1"));
std::string pval;
nmol->getProp("prop1", pval);
TEST_ASSERT(pval == "4");
delete nmol;
}
void testGitHub2285() {
std::string rdbase = getenv("RDBASE");
std::string fname =
rdbase + "/Code/GraphMol/FileParsers/test_data/github2285.sdf";
std::vector<std::string> smiles;
{
SDMolSupplier sdsup(fname);
while(!sdsup.atEnd()) {
ROMol *nmol = sdsup.next();
TEST_ASSERT(nmol);
smiles.push_back(MolToSmiles(*nmol));
delete nmol;
}
}
{
SDMolSupplier sdsup(fname, true, false);
int i = 0;
while(!sdsup.atEnd()) {
ROMol *nmol = sdsup.next();
TEST_ASSERT(nmol);
ROMol *m = MolOps::removeHs(*nmol);
TEST_ASSERT(MolToSmiles(*m) == smiles[i++]);
delete nmol;
delete m;
}
TEST_ASSERT(i>0);
}
}
int main() {
RDLog::InitLogs();
#if 1
BOOST_LOG(rdErrorLog) << "\n-----------------------------------------\n";
testMolSup();
BOOST_LOG(rdErrorLog) << "Finished: testMolSup()\n";
BOOST_LOG(rdErrorLog) << "-----------------------------------------\n\n";
BOOST_LOG(rdErrorLog) << "-----------------------------------------\n";
testRandMolSup();
BOOST_LOG(rdErrorLog) << "Finished: testRandMolSup()\n";
BOOST_LOG(rdErrorLog) << "-----------------------------------------\n\n";
BOOST_LOG(rdErrorLog) << "-----------------------------------------\n";
testSmilesSup();
BOOST_LOG(rdErrorLog) << "Finished: testSmilesSup()\n";
BOOST_LOG(rdErrorLog) << "-----------------------------------------\n\n";
BOOST_LOG(rdErrorLog) << "-----------------------------------------\n";
testSmilesSupFromText();
BOOST_LOG(rdErrorLog) << "Finished: testSmilesSupFromText()\n";
BOOST_LOG(rdErrorLog) << "-----------------------------------------\n\n";
BOOST_LOG(rdErrorLog) << "-----------------------------------------\n";
testSmilesWriter();
BOOST_LOG(rdErrorLog) << "Finished: testSmilesWriter()\n";
BOOST_LOG(rdErrorLog) << "-----------------------------------------\n\n";
BOOST_LOG(rdErrorLog) << "-----------------------------------------\n";
testSDWriter();
BOOST_LOG(rdErrorLog) << "Finished: testSDWriter()\n";
BOOST_LOG(rdErrorLog) << "-----------------------------------------\n\n";
BOOST_LOG(rdErrorLog) << "-----------------------------------------\n";
testSDSupplierEnding();
BOOST_LOG(rdErrorLog) << "Finished: testSDSupplierEnding()\n";
BOOST_LOG(rdErrorLog) << "-----------------------------------------\n\n";
BOOST_LOG(rdErrorLog) << "-----------------------------------------\n";
testSuppliersEmptyFile();
BOOST_LOG(rdErrorLog) << "Finished: testSuppliersEmptyFile()\n";
BOOST_LOG(rdErrorLog) << "-----------------------------------------\n\n";
BOOST_LOG(rdErrorLog) << "-----------------------------------------\n";
testCisTrans();
BOOST_LOG(rdErrorLog) << "Finished: testCisTrans()\n";
BOOST_LOG(rdErrorLog) << "-----------------------------------------\n\n";
BOOST_LOG(rdErrorLog) << "-----------------------------------------\n";
testStereoRound();
BOOST_LOG(rdErrorLog) << "Finished: testStereoRound()\n";
BOOST_LOG(rdErrorLog) << "-----------------------------------------\n\n";
BOOST_LOG(rdErrorLog) << "-----------------------------------------\n";
testIssue226();
BOOST_LOG(rdErrorLog) << "Finished: testIssue226()\n";
BOOST_LOG(rdErrorLog) << "-----------------------------------------\n\n";
BOOST_LOG(rdErrorLog) << "-----------------------------------------\n";
testTDTSupplier1();
BOOST_LOG(rdErrorLog) << "Finished: testTDTSupplier1()\n";
BOOST_LOG(rdErrorLog) << "-----------------------------------------\n\n";
BOOST_LOG(rdErrorLog) << "-----------------------------------------\n";
testTDTSupplier2();
BOOST_LOG(rdErrorLog) << "Finished: testTDTSupplier2()\n";
BOOST_LOG(rdErrorLog) << "-----------------------------------------\n\n";
BOOST_LOG(rdErrorLog) << "-----------------------------------------\n";
testTDTSupplier3();
BOOST_LOG(rdErrorLog) << "Finished: testTDTSupplier3()\n";
BOOST_LOG(rdErrorLog) << "-----------------------------------------\n\n";
BOOST_LOG(rdErrorLog) << "-----------------------------------------\n";
testSDSupplierFromText();
BOOST_LOG(rdErrorLog) << "Finished: testSDSupplierFromText()\n";
BOOST_LOG(rdErrorLog) << "-----------------------------------------\n\n";
BOOST_LOG(rdErrorLog) << "-----------------------------------------\n";
testSDSupplierStrLax1();
BOOST_LOG(rdErrorLog) << "Finished: testSDSupplierStrLax1()\n";
BOOST_LOG(rdErrorLog) << "-----------------------------------------\n\n";
BOOST_LOG(rdErrorLog) << "-----------------------------------------\n";
testSDSupplierStrLax2();
BOOST_LOG(rdErrorLog) << "Finished: testSDSupplierStrLax2()\n";
BOOST_LOG(rdErrorLog) << "-----------------------------------------\n\n";
BOOST_LOG(rdErrorLog) << "-----------------------------------------\n";
testSDSupplierFromTextStrLax1();
BOOST_LOG(rdErrorLog) << "Finished: testSDSupplierFromTextStrLax1()\n";
BOOST_LOG(rdErrorLog) << "-----------------------------------------\n\n";
BOOST_LOG(rdErrorLog) << "-----------------------------------------\n";
testSDSupplierFromTextStrLax2();
BOOST_LOG(rdErrorLog) << "Finished: testSDSupplierFromTextStrLax2()\n";
BOOST_LOG(rdErrorLog) << "-----------------------------------------\n\n";
BOOST_LOG(rdErrorLog) << "-----------------------------------------\n";
testIssue265();
BOOST_LOG(rdErrorLog) << "Finished: testIssue265()\n";
BOOST_LOG(rdErrorLog) << "-----------------------------------------\n\n";
BOOST_LOG(rdErrorLog) << "-----------------------------------------\n";
testSDErrorHandling();
BOOST_LOG(rdErrorLog) << "Finished: testSDErrorHandling()\n";
BOOST_LOG(rdErrorLog) << "-----------------------------------------\n\n";
BOOST_LOG(rdErrorLog) << "-----------------------------------------\n";
testIssue381();
BOOST_LOG(rdErrorLog) << "Finished: testIssue381()\n";
BOOST_LOG(rdErrorLog) << "-----------------------------------------\n\n";
BOOST_LOG(rdErrorLog) << "-----------------------------------------\n";
testSetStreamIndices();
BOOST_LOG(rdErrorLog) << "Finished: testSetStreamIndices()\n";
BOOST_LOG(rdErrorLog) << "-----------------------------------------\n\n";
BOOST_LOG(rdErrorLog) << "-----------------------------------------\n";
testMixIterAndRandom();
BOOST_LOG(rdErrorLog) << "Finished: testMixIterAndRandom()\n";
BOOST_LOG(rdErrorLog) << "-----------------------------------------\n\n";
BOOST_LOG(rdErrorLog) << "-----------------------------------------\n";
testRemoveHs();
BOOST_LOG(rdErrorLog) << "Finished: testRemoveHs()\n";
BOOST_LOG(rdErrorLog) << "-----------------------------------------\n\n";
BOOST_LOG(rdErrorLog) << "-----------------------------------------\n";
testGetItemText();
BOOST_LOG(rdErrorLog) << "Finished: testGetItemText()\n";
BOOST_LOG(rdErrorLog) << "-----------------------------------------\n\n";
BOOST_LOG(rdErrorLog) << "-----------------------------------------\n";
testForwardSDSupplier();
BOOST_LOG(rdErrorLog) << "Finished: testForwardSDSupplier()\n";
BOOST_LOG(rdErrorLog) << "-----------------------------------------\n\n";
BOOST_LOG(rdErrorLog) << "-----------------------------------------\n";
testMissingCRSDSupplier();
BOOST_LOG(rdErrorLog) << "Finished: testMissingCRSDSupplier()\n";
BOOST_LOG(rdErrorLog) << "-----------------------------------------\n\n";
BOOST_LOG(rdErrorLog) << "-----------------------------------------\n";
testIssue3482695();
BOOST_LOG(rdErrorLog) << "Finished: testIssue3482695()\n";
BOOST_LOG(rdErrorLog) << "-----------------------------------------\n\n";
#endif
BOOST_LOG(rdErrorLog) << "-----------------------------------------\n";
testIssue3525673();
BOOST_LOG(rdErrorLog) << "Finished: testIssue3525673()\n";
BOOST_LOG(rdErrorLog) << "-----------------------------------------\n\n";
BOOST_LOG(rdErrorLog) << "-----------------------------------------\n";
testBlankLinesInProps();
BOOST_LOG(rdErrorLog) << "Finished: testBlankLinesInProps()\n";
BOOST_LOG(rdErrorLog) << "-----------------------------------------\n\n";
BOOST_LOG(rdErrorLog) << "-----------------------------------------\n";
testSkipLines();
BOOST_LOG(rdErrorLog) << "Finished: testSkipLines()\n";
BOOST_LOG(rdErrorLog) << "-----------------------------------------\n\n";
BOOST_LOG(rdErrorLog) << "-----------------------------------------\n";
testGitHub23();
BOOST_LOG(rdErrorLog) << "Finished: testGitHub23()\n";
BOOST_LOG(rdErrorLog) << "-----------------------------------------\n\n";
BOOST_LOG(rdErrorLog) << "-----------------------------------------\n";
testGitHub88();
BOOST_LOG(rdErrorLog) << "Finished: testGitHub88()\n";
BOOST_LOG(rdErrorLog) << "-----------------------------------------\n\n";
BOOST_LOG(rdErrorLog) << "-----------------------------------------\n";
testGitHub2285();
BOOST_LOG(rdErrorLog) << "Finished: testGitHub2285()\n";
BOOST_LOG(rdErrorLog) << "-----------------------------------------\n\n";
return 0;
}
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