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/**********************************************************************
gziptest.cpp - Test handling of gzipped files.
Copyright (C) 2015 David R. Koes
This file is part of the Open Babel project.
For more information, see <http://openbabel.org/>
This program is free software; you can redistribute it and/or modify
it under the terms of the GNU General Public License as published by
the Free Software Foundation version 2 of the License.
This program is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
GNU General Public License for more details.
***********************************************************************/
// used to set import/export for Cygwin DLLs
#ifdef WIN32
#define USING_OBDLL
#endif
#include <cstdlib>
#include <openbabel/babelconfig.h>
#include <openbabel/mol.h>
#include <openbabel/obconversion.h>
#include <stdio.h>
#include <iostream>
#include <fstream>
using namespace std;
using namespace OpenBabel;
//reads molecule(s) from file and compares to results
//outputs error and terminates if not consistent
void checkResults(const string& file, const vector<string>& correctResults)
{
if(correctResults.size() == 0)
return;
OBMol mol;
OBConversion conv(file);
conv.SetOutFormat(conv.GetInFormat(), conv.GetInGzipped());
vector<string> results;
while(conv.Read(&mol))
{
OBConversion strconv;
string cansmi;
if (conv.GetInFormat() == conv.FindFormat("mol2")) {
// Don't test roundtripping for mol2 as the atom types are changed by the reader (TODO: Fix this)
strconv.SetOutFormat("can");
strconv.SetOptions("n", conv.OUTOPTIONS);
cansmi = strconv.WriteString(&mol, true);
}
else {
// Testing roundtrip through gz with Read/WriteString
OBMol mol2;
string gzippedstr = conv.WriteString(&mol);
strconv.SetInAndOutFormats(conv.GetInFormat(), conv.FindFormat("CAN"), conv.GetInGzipped());
strconv.SetOptions("n", OBConversion::OUTOPTIONS);
strconv.ReadString(&mol2, gzippedstr);
cansmi = strconv.WriteString(&mol2, true);
}
results.push_back(cansmi);
}
if(results.size() != correctResults.size())
{
cout << "Incorrect number of outputs (" << results.size() << " vs " << correctResults.size() << ") for " << file << "\n";
exit(-1);
}
for(unsigned i = 0, n = results.size(); i < n; i ++)
{
if(results[i] != correctResults[i])
{
cout << file << " match failure: " << results[i] << " != " << correctResults[i] << "\n";
exit(-1);
}
}
}
// 1
// reads gzip.infiles, which has a file name on each line,
// converts each molecule into a gzipped string, converts that
// string into a molecule, converts that molecule into canonical smiles
// and compares to gzip.out
int gziptest(int argc, char* argv[])
{
int choice = 1;
if (argc > 1) {
if(sscanf(argv[1], "%d", &choice) != 1) {
printf("Couldn't parse that input as a number\n");
return -1;
}
}
if(choice != 1) //eh, not bothering to split this up
{
cout << "Test number " << choice << " does not exist!\n";
return -1;
}
cout << endl << "# Testing gzip handling... " << endl;
#ifdef TESTDATADIR
string testdatadir(TESTDATADIR);
string gzipin = testdatadir + "gzip.in";
#else
string gzipin = "files/gzip.in";
#endif
#ifdef FORMATDIR
char env[BUFF_SIZE];
snprintf(env, BUFF_SIZE, "BABEL_LIBDIR=%s", FORMATDIR);
putenv(env);
#endif
ifstream ifs(gzipin.c_str());
if (!ifs)
{
cout << "Bail out! Cannot read gzip.in!" << endl;
return(-1);
}
//gzip.in specifies what files to read and their canonical smiles
string line;
string filepath;
vector<string> correctResults; //read from file
OBConversion conv;
conv.SetInAndOutFormats("smi", "can");
conv.SetOptions("n", conv.OUTOPTIONS);
OBMol mol;
while(getline(ifs, line))
{
if(line.length() == 0)
continue; //ignore blank lines
if(line[0] == '#')
{
checkResults(filepath, correctResults);
correctResults.clear();
//next token should be file name
stringstream str(line);
string fname;
str >> fname; //# character
if(fname.length() == 1)
{
str >> fname; // actual file name
}
else
{
fname = fname.substr(1); //strip #
}
#ifdef TESTDATADIR
filepath = testdatadir + fname;
#else
filepath = "files/" + fname;
#endif
}
else
{
conv.ReadString(&mol, line);
std::string can = conv.WriteString(&mol, true);
correctResults.push_back(can);
}
}
checkResults(filepath, correctResults);
return(0);
}
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