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/**********************************************************************
obfragment - Generate coordinate database of ring fragments
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/atom.h>
#include <openbabel/bond.h>
#include <openbabel/generic.h>
#include <openbabel/mol.h>
#include <openbabel/obconversion.h>
#include <openbabel/graphsym.h>
#include <openbabel/builder.h>
#include <openbabel/parsmart.h>
#include <openbabel/data.h>
#include <openbabel/math/align.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 <sstream>
#include <iterator>
#include <algorithm>
#include <queue>
#include <map>
using namespace std;
using namespace OpenBabel;
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);
OBConversion conv;
conv.SetOptions("O", conv.OUTOPTIONS);
OBFormat *inFormat, *canFormat;
ifstream ifs;
OBMol mol;
OBAtom *atom;
OBBond *bond;
char buffer[BUFF_SIZE];
map<std::string, vector<OBMol> > fragment_list;
map<std::string, int> fragment_count;
vector<pair<int, std::string> > fragment_size;
canFormat = conv.FindFormat("can"); // Canonical SMILES format
conv.SetOutFormat(canFormat);
if (argc < 2)
{
cerr << "Usage: obfragment <file>" << endl;
return(-1);
}
for (int i = 1; i < argc; ++i) {
cerr << " Reading file " << argv[i] << endl;
inFormat = conv.FormatFromExt(argv[i]);
if(inFormat==nullptr || !conv.SetInFormat(inFormat))
{
cerr << " Cannot read file format for " << argv[i] << endl;
continue; // try next file
}
ifs.open(argv[i]);
if (!ifs)
{
cerr << "Cannot read input file: " << argv[i] << endl;
continue;
}
while(ifs.peek() != EOF && ifs.good())
{
conv.Read(&mol, &ifs);
mol.DeleteHydrogens();
unsigned int size = mol.NumAtoms();
OBBitVec atomsToCopy(size+1);
for (unsigned int i = 1; i <= size; ++i) {
atom = mol.GetAtom(i);
atomsToCopy.SetBitOn(atom->GetIdx());
}
size = mol.NumBonds();
OBBitVec bondsToExclude(size);
for (unsigned int i = 0; i < size; ++i) {
bond = mol.GetBond(i);
if (bond->IsRotor()) {
bondsToExclude.SetBitOn(bond->GetIdx());
}
}
OBMol mol_copy;
mol.CopySubstructure(mol_copy, &atomsToCopy, &bondsToExclude);
vector<OBMol> fragments = mol_copy.Separate(); // Copies each disconnected fragment as a separate
for (unsigned int i = 0; i < fragments.size(); ++i) {
if (fragments[i].NumAtoms() < 5) // too small to care
continue;
if (!fragments[i].HasNonZeroCoords())
continue;
string smiles = conv.WriteString(&fragments[i], true);
if (fragment_count.count(smiles) == 0) {
vector<OBMol> v;
v.push_back(fragments[i]);
fragment_list[smiles] = v;
fragment_count[smiles] = 1;
} else {
fragment_count[smiles]++;
vector<OBMol> &f = fragment_list[smiles];
bool isDifferent = true;
for (vector<OBMol>::iterator j = f.begin(); j != f.end(); ++j) {
OBAlign aln(fragments[i], *j, false, false);
aln.Align();
if (aln.GetRMSD() < 5.0) {
isDifferent = false;
break;
}
}
if(isDifferent)
fragment_list[smiles].push_back(fragments[i]);
}
}
} // while reading molecules (in this file)
ifs.close();
ifs.clear();
} // // while reading files
// sort fragments by the number of molecules
for (map<std::string, vector<OBMol> >::iterator i = fragment_list.begin(); i != fragment_list.end(); ++i) {
std::string smiles = i->first;
fragment_size.push_back(std::make_pair<int, std::string>(i->second[0].NumAtoms(), smiles.c_str()));
}
sort(fragment_size.rbegin(), fragment_size.rend());
for (vector<pair<int, string> >::iterator i = fragment_size.begin(); i != fragment_size.end(); ++i) {
if (fragment_count[i->second] < 3) continue;
// OK, now retrieve the canonical SMILES ordering for the fragment
vector<OBMol>& fragments = fragment_list[i->second];
vector<OBMol> t;
for (size_t idx = 0; idx < fragments.size(); ++idx) {
if (!fragments[idx].HasNonZeroCoords())
continue;
t.push_back(fragments[idx]);
OBPairData *pd = dynamic_cast<OBPairData*>(fragments[idx].GetData("SMILES Atom Order"));
istringstream iss(pd->GetValue());
vector<unsigned int> canonical_order;
canonical_order.clear();
copy(istream_iterator<unsigned int>(iss),
istream_iterator<unsigned int>(),
back_inserter<vector<unsigned int> >(canonical_order));
// Write out an XYZ-style file with the CANSMI as the title
cout << i->second << '\n'; // endl causes a flush
unsigned int order;
OBAtom *atom;
fragments[idx].Center(); // Translate to the center of all coordinates
fragments[idx].ToInertialFrame(); // Translate all conformers to the inertial frame-of-reference.
for (unsigned int index = 0; index < canonical_order.size(); ++index) {
order = canonical_order[index];
atom = fragments[idx].GetAtom(order);
snprintf(buffer, BUFF_SIZE, "%d %9.3f %9.3f %9.3f\n",
atom->GetAtomicNum(),
atom->x(), atom->y(), atom->z());
cout << buffer;
}
}
}
}
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