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/**********************************************************************
obsort -- sort the fragment database
Copyright (C) 2007 Geoffrey R. Hutchison
This file is part of the Open Babel project.
For more information, see <http://openbabel.sourceforge.net/>
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 <openbabel/babelconfig.h>
#include <openbabel/mol.h>
#include <openbabel/obconversion.h>
#if !HAVE_STRNCASECMP
extern "C" int strncasecmp(const char *s1, const char *s2, size_t n);
#endif
#include <stdio.h>
#include <iostream>
#include <fstream>
#include <algorithm>
using namespace std;
using namespace OpenBabel;
bool CompareSMILES(const string &a, const string &b)
{
// Originally a.length() > b.length()
// Now it uses the actual number of atoms and number of bonds
vector<string> va;
tokenize(va, a.c_str());
vector<string> vb;
tokenize(vb, b.c_str());
// Sort based on the number of atoms, then the number of bonds, then the length
if (atoi(va[1].c_str()) > atoi(vb[1].c_str()))
return true;
else if (atoi(va[1].c_str()) == atoi(vb[1].c_str())) {
if (atoi(va[2].c_str()) > atoi(vb[2].c_str()))
return true;
else if (atoi(va[2].c_str()) == atoi(vb[2].c_str()))
return a.length() > b.length();
}
else
return false;
}
int main(int argc,char *argv[])
{
// turn off slow sync with C-style output (we don't use it anyway).
std::ios::sync_with_stdio(false);
if (argc != 3) {
cout << "Usage: obsort <fragments> <freq>" << endl;
return(-1);
}
ifstream ifs(argv[1]);
if (!ifs) {
cout << "Bail out! Cannot read input file!" << endl;
return(-1);
}
OBConversion conv(&ifs, &cout);
OBFormat* pFormat;
pFormat = conv.FormatFromExt(argv[1]);
if ( pFormat == nullptr ) {
cout << "Bail out! Cannot read file format!" << endl;
return(-1);
}
if (! conv.SetInAndOutFormats(pFormat, pFormat)) {
cout << "Bail out! File format isn't loaded" << endl;
return (-1);
}
ifstream freq(argv[2]);
if (!freq) {
cout << "Bail out! Cannot read list of frequencies!" << endl;
}
OBMol *mol;
OBAtom *atom;
OBSmartsPattern sp;
map<string, OBMol*> molIndex; // index of molecules
// First read in the molecules and hash them
int molCount = 0;
string temp, title;
vector<string> vs;
while(ifs.peek() != EOF && ifs.good()) {
mol = new OBMol;
conv.Read(mol);
/*if (!mol->Has3D())
continue; // invalid coordinates*/
temp = std::string(mol->GetTitle());
//cout << "Title" << temp << endl;
OBMol clone;
clone = OBMol(*mol);
temp = Trim(temp);
if (!sp.Init(temp)) // not a valid SMARTS pattern
continue;
tokenize(vs, temp);
title = vs[0] + "\t" + vs[1] + "\t" + vs[2];
molIndex[title] = mol;
// Give some progress
molCount++;
if (molCount % 500 == 0)
cerr << "Count: " << molCount << endl;
} // while reading molecules
// Now read in the list of frequencies and SMILES
// (We sort the SMILES by length -- it's already sorted by frequency)
vector<string> smilesIndex;
string line;
char buffer[BUFF_SIZE];
do {
getline(freq, line); // Count INDEX CanSMI
tokenize(vs, line);
string title = vs[2] + "\t" + vs[3] + "\t" + vs[4];
if (molIndex.find(title) == molIndex.end())
continue;
smilesIndex.push_back(title);
} while (freq.peek() != EOF && freq.good());
sort(smilesIndex.begin(), smilesIndex.end(), CompareSMILES);
// Finally, we loop through the index of SMILES and write the molecules
for (vector<string>::iterator j = smilesIndex.begin(); j != smilesIndex.end(); ++j) {
mol = molIndex[(*j)];
if (!mol) // Shouldn't happen, but it's good defensive programming
continue;
mol->Center();
// cout << mol->NumAtoms() << "\n";
tokenize(vs, *j);
cout << vs[0] << "\n";
for(unsigned int i = 1;i <= mol->NumAtoms(); i++)
{
atom = mol->GetAtom(i);
snprintf(buffer, BUFF_SIZE, "%7.3f%7.3f%7.3f\n",
atom->x(), atom->y(), atom->z());
cout << buffer;
}
// delete(mol);
mol = nullptr;
}
return(0);
}
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