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rdkit/Code/GraphMol/FileParsers/testMolSupplier.cpp
Greg Landrum 8c70417690 Fixes #88
2013-08-21 20:45:54 +02:00

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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 <GraphMol/RDKitBase.h>
#include <string>
#include <iostream>
#include <fstream>
#include <map>
#include "MolSupplier.h"
#include "MolWriters.h"
#include "FileParsers.h"
#include <RDGeneral/FileParseException.h>
#include <RDGeneral/BadFileException.h>
#include <RDGeneral/RDLog.h>
#include <GraphMol/SmilesParse/SmilesWrite.h>
#include <GraphMol/SmilesParse/SmilesParse.h>
#include <GraphMol/Depictor/RDDepictor.h>
#ifdef TEST_GZIP_SD
#include <boost/iostreams/device/file.hpp>
#include <boost/iostreams/filtering_stream.hpp>
#include <boost/iostreams/filter/gzip.hpp>
namespace io=boost::iostreams;
#endif
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("_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("_Name"));
TEST_ASSERT(nmol->hasProp("NCI_AIDS_Antiviral_Screen_Conclusion"));
delete nmol;
}
}
// test issue 3524949:
TEST_ASSERT(sdsup.atEnd());
bool ok=false;
try{
ROMol *mol = 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("_Name"));
TEST_ASSERT(nmol->hasProp("NCI_AIDS_Antiviral_Screen_Conclusion"));
delete nmol;
}
i++;
}
TEST_ASSERT(i==16);
}
{
std::ifstream *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("_Name"));
TEST_ASSERT(nmol->hasProp("NCI_AIDS_Antiviral_Screen_Conclusion"));
delete nmol;
}
i++;
}
TEST_ASSERT(i==16);
}
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("_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("_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("_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("_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("_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("_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()){
mol=nSup->next();
TEST_ASSERT(mol);
delete mol;
nRead++;
}
TEST_ASSERT(nSup->length() == 10);
TEST_ASSERT(nRead == 10);
delete nSup;
}
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();
TEST_ASSERT(nAts==2);
mol = nSup2[3];
nAts = mol->getNumAtoms();
TEST_ASSERT(nAts==6);
TEST_ASSERT(nSup2.length()==4);
failed=false;
try {
mol = nSup2[4];
} catch (FileParseException &) {
failed=true;
}
TEST_ASSERT(failed);
mol = nSup2[2];
nAts = mol->getNumAtoms();
TEST_ASSERT(nAts==4);
TEST_ASSERT(mol->hasProp("_Name"));
mol->getProp("_Name",mname);
TEST_ASSERT(mname=="2");
}
{
nSup2.setData(text," ",0,-1,false,true);
mol = nSup2[2];
TEST_ASSERT(mol);
nAts = mol->getNumAtoms();
TEST_ASSERT(nAts==4);
TEST_ASSERT(mol->hasProp("_Name"));
mol->getProp("_Name",mname);
TEST_ASSERT(mname=="2");
mol = nSup2[3];
TEST_ASSERT(mol);
nAts = mol->getNumAtoms();
TEST_ASSERT(nAts==6);
TEST_ASSERT(mol->hasProp("_Name"));
mol->getProp("_Name",mname);
TEST_ASSERT(mname=="3");
}
{
nSup2.setData(text," ",0,-1,false,true);
mol = nSup2[3];
TEST_ASSERT(mol);
nAts = mol->getNumAtoms();
TEST_ASSERT(nAts==6);
TEST_ASSERT(mol->hasProp("_Name"));
mol->getProp("_Name",mname);
TEST_ASSERT(mname=="3");
mol = nSup2[2];
TEST_ASSERT(mol);
nAts = mol->getNumAtoms();
TEST_ASSERT(nAts==4);
TEST_ASSERT(mol->hasProp("_Name"));
mol->getProp("_Name",mname);
TEST_ASSERT(mname=="2");
}
// --------------
// 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("_Name",mname);
TEST_ASSERT(mname=="mol-4");
mol->getProp("Column_2",mname);
TEST_ASSERT(mname=="16.0");
// 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("_Name",mname);
TEST_ASSERT(mname=="mol-3");
mol->getProp("Column_2",mname);
TEST_ASSERT(mname=="9.0");
// 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("_Name",mname);
TEST_ASSERT(mname=="mol-4");
mol->getProp("Column_2",mname);
TEST_ASSERT(mname=="16.0");
// failures should give null molecules:
mol = nSup2[2];
TEST_ASSERT(!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("_Name",mname);
TEST_ASSERT(mname=="mol-4");
mol->getProp("Column_2",mname);
TEST_ASSERT(mname=="16.0");
TEST_ASSERT(nSup2.atEnd());
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("_Name",mname);
TEST_ASSERT(mname=="mol-4");
mol->getProp("Column_2",mname);
TEST_ASSERT(mname=="16.0");
TEST_ASSERT(nSup2.atEnd());
try {
mol = nSup2[3];
} 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("_Name",mname);
TEST_ASSERT(mname=="mol-4");
mol->getProp("Column_2",mname);
TEST_ASSERT(mname=="16.0");
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);
// 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;
nSup2.next();
mol = nSup2[3];
TEST_ASSERT(nSup2.length()==4);
failed=false;
try {
mol = nSup2[4];
} 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];
} 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("_Name",mname);
TEST_ASSERT(mname=="mol-3");
mol->getProp("Column_2",mname);
TEST_ASSERT(mname=="9.0");
mol = nSup2[1];
mol->getProp("_Name",mname);
TEST_ASSERT(mname=="mol-2");
mol->getProp("Column_2",mname);
TEST_ASSERT(mname=="4.0");
// 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.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("_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 writer;
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("_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;
}
}
}
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.sdf";
SDWriter *writer = new SDWriter(ofile);
STR_VECT names;
while (!sdsup.atEnd()) {
ROMol *mol = sdsup.next();
std::string mname;
mol->getProp("_Name", mname);
names.push_back(mname);
writer->write(*mol);
delete mol;
}
writer->flush();
CHECK_INVARIANT(writer->numMols() == 16, "");
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("_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("_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("_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.sdf";
SDWriter writer(ofile);
while(!smiSup.atEnd()){
ROMol *mol = smiSup.next();
TEST_ASSERT(mol);
RDDepict::compute2DCoords(*mol);
writer.write(*mol);
delete mol;
}
// do the round test
// parse the sd file and write it out to smiles
SDMolSupplier *reader;
try{
reader = new SDMolSupplier("cisTrans.sdf");
} catch (FileParseException &) {
reader=0;
}
TEST_ASSERT(reader);
while (!reader->atEnd()) {
ROMol *mol = reader->next();
std::string mname;
mol->getProp("_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=0;
}
TEST_ASSERT(smiSup)
std::map<std::string, std::string> nameSmi;
std::string ofile = rdbase + "/Code/GraphMol/FileParsers/test_data/cdk2_stereo.sdf";
SDWriter* writer = new SDWriter(ofile);
int count = 0;
while(!smiSup->atEnd()) {
ROMol *mol = smiSup->next();
//mol->debugMol(std::cout);
std::string mname;
mol->getProp("_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";
}
}
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=0;
}
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("_Name", mname);
if (nameSmi[mname] != smiles) {
BOOST_LOG(rdInfoLog) << mname << " " << nameSmi[mname] << " " << smiles << "\n";
}
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"));
}
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("_Name"));
TEST_ASSERT(nmol->hasProp("MFCD"));
nmol->getProp("PN",prop1);
nmol->getProp("_Name",prop2);
TEST_ASSERT(prop1==prop2);
// we didn't ask for 2D conformers, so there should be a property 2D:
TEST_ASSERT(nmol->hasProp("2D"));
// and no conformer:
TEST_ASSERT(!nmol->getNumConformers());
delete nmol;
i++;
}
}
TEST_ASSERT(i==10);
}
{
std::ifstream strm(fname.c_str());
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("_Name"));
TEST_ASSERT(nmol->hasProp("MFCD"));
nmol->getProp("PN",prop1);
nmol->getProp("_Name",prop2);
TEST_ASSERT(prop1==prop2);
// we didn't ask for 2D conformers, so there should be a property 2D:
TEST_ASSERT(nmol->hasProp("2D"));
// 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("_Name"));
TEST_ASSERT(nmol->hasProp("MFCD"));
nmol->getProp("PN",prop1);
nmol->getProp("_Name",prop2);
TEST_ASSERT(prop1==prop2);
// we asked for 2D conformers, so there should be no property 2D:
TEST_ASSERT(!nmol->hasProp("2D"));
// 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("_Name"));
nmol->getProp("CAS",prop1);
nmol->getProp("_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("_Name"));
nmol->getProp("CAS",prop1);
nmol->getProp("_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("_Name"));
TEST_ASSERT(mol->hasProp("ID"));
i++;
delete mol;
}
TEST_ASSERT(i==2);
}
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=0;
// 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;
// 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;
// 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;
// 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;
}
void testIssue381() {
std::string rdbase = getenv("RDBASE");
std::string fname = rdbase + "/Code/GraphMol/FileParsers/test_data/Issue381.sdf";
SDMolSupplier *sdsup;
ROMol *nmol=0;
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";
int tmpIndices[16]={0, 2136, 6198, 8520, 11070, 12292, 14025, 15313, 17313, 20125, 22231,
23729, 26147, 28331, 32541, 33991};
std::vector<std::streampos> indices(tmpIndices,tmpIndices+16);
SDMolSupplier *sdsup;
ROMol *nmol=0;
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=0;
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);
mol=tSup->next();
TEST_ASSERT(mol);
mol=tSup->next();
TEST_ASSERT(mol);
TEST_ASSERT(mol->getNumAtoms()==10);
delete tSup;
delete mol;
tSup = new TDTMolSupplier(fname);
TEST_ASSERT(tSup);
mol=0;
try {
mol=(*tSup)[20];
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("_Name"));
TEST_ASSERT(nmol->hasProp("NCI_AIDS_Antiviral_Screen_Conclusion"));
delete nmol;
i++;
}
}
TEST_ASSERT(i==16);
}
#ifdef TEST_GZIP_SD
// 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);
++i;
if(i>1000) break;
}
TEST_ASSERT(i==998);
}
{
io::filtering_istream strm;
strm.push(io::gzip_decompressor());
strm.push(io::file_source(fname2));
unsigned int i = 0;
while (!strm.eof()) {
std::string line;
std::getline(strm,line);
++i;
if(i>1000) break;
}
TEST_ASSERT(i==998);
}
// looks good, now do a supplier:
{
io::filtering_istream strm;
strm.push(io::gzip_decompressor());
strm.push(io::file_source(fname2));
ForwardSDMolSupplier sdsup(&strm,false);
unsigned int i = 0;
while (!sdsup.atEnd()) {
ROMol *nmol = sdsup.next();
if (nmol) {
TEST_ASSERT(nmol->hasProp("_Name"));
TEST_ASSERT(nmol->hasProp("NCI_AIDS_Antiviral_Screen_Conclusion"));
delete nmol;
i++;
}
}
TEST_ASSERT(i==16);
}
#endif
return 1;
}
void testMissingCRSDSupplier() {
std::string rdbase = getenv("RDBASE");
std::string infile = rdbase + "/Code/GraphMol/FileParsers/test_data/missingCR.sdf";
SDMolSupplier reader(infile);
reader.next();
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);
nmol = reader.next();
TEST_ASSERT(nmol);
TEST_ASSERT(nmol->getNumAtoms()==37);
delete nmol;
nmol = reader.next();
TEST_ASSERT(!nmol);
nmol = reader.next();
TEST_ASSERT(!nmol);
nmol = reader.next();
TEST_ASSERT(nmol);
TEST_ASSERT(nmol->getNumAtoms()==58);
delete nmol;
nmol = reader.next();
TEST_ASSERT(!nmol);
nmol = reader.next();
TEST_ASSERT(!nmol);
nmol = reader.next();
TEST_ASSERT(nmol);
TEST_ASSERT(nmol->getNumAtoms()==58);
delete nmol;
nmol = reader.next();
TEST_ASSERT(!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.sdf";
SDWriter *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->flush();
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;
}
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";
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";
return 0;
}
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