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/**********************************************************************
bondtyper.cpp - Bond typer to perceive connectivity and bond orders/types.
Copyright (C) 2003-2006 by 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.
***********************************************************************/
#include <openbabel/babelconfig.h>
#include <openbabel/mol.h>
#include <openbabel/bondtyper.h>
// data header with default parameters
#include "bondtyp.h"
using namespace std;
namespace OpenBabel
{
//! Global OBBondTyper for perception of bond order assignment.
OBBondTyper bondtyper;
/*! \class OBBondTyper bondtyper.h <openbabel/bondtyper.cpp>
\brief Assigns bond types for file formats without bond information
The OBBondTyper class is designed to read in a list of bond typing
rules and apply them to molecules. It is called from the
OBMol::PerceiveBondOrders() method.
*/
OBBondTyper::OBBondTyper()
{
_init = false;
_dir = BABEL_DATADIR;
_envvar = "BABEL_DATADIR";
_filename = "bondtyp.txt";
_subdir = "data";
_dataptr = BondTypeData;
}
void OBBondTyper::ParseLine(const char *buffer)
{
vector<string> vs;
vector<int> bovector;
OBSmartsPattern *sp;
if (buffer[0] != '#')
{
tokenize(vs,buffer);
// Make sure we actually have a SMARTS pattern plus at least one triple
// and make sure we have the correct number of integers
if (vs.empty() || vs.size() < 4)
return; // just ignore empty (or short lines)
else if (!vs.empty() && vs.size() >= 4 && (vs.size() % 3 != 1))
{
stringstream errorMsg;
errorMsg << " Error in OBBondTyper. Pattern is incorrect, found "
<< vs.size() << " tokens." << endl;
errorMsg << " Buffer is: " << buffer << endl;
obErrorLog.ThrowError(__FUNCTION__, errorMsg.str(), obInfo);
return;
}
sp = new OBSmartsPattern;
if (sp->Init(vs[0]))
{
for (unsigned int i = 1; i < vs.size() ; ++i)
{
bovector.push_back( atoi((char *)vs[i].c_str()) );
}
_fgbonds.push_back(pair<OBSmartsPattern*,vector<int> >
(sp, bovector));
}
else
{
delete sp;
sp = NULL;
}
}
}
OBBondTyper::~OBBondTyper()
{
vector<pair<OBSmartsPattern*, vector<int> > >::iterator i;
for (i = _fgbonds.begin();i != _fgbonds.end();++i)
{
delete i->first;
i->first = NULL;
}
}
void OBBondTyper::AssignFunctionalGroupBonds(OBMol &mol)
{
if (!_init)
Init();
OBSmartsPattern *currentPattern;
OBBond *b1, *b2;
OBAtom *a1,*a2, *a3;
double angle, dist1, dist2;
vector<int> assignments;
vector<vector<int> > mlist;
vector<vector<int> >::iterator matches, l;
vector<pair<OBSmartsPattern*, vector<int> > >::iterator i;
unsigned int j;
// Loop through for all the functional groups and assign bond orders
for (i = _fgbonds.begin();i != _fgbonds.end();++i)
{
currentPattern = i->first;
assignments = i->second;
if (currentPattern && currentPattern->Match(mol))
{
mlist = currentPattern->GetUMapList();
for (matches = mlist.begin(); matches != mlist.end(); ++matches)
{
// Now loop through the bonds to assign from _fgbonds
for (j = 0; j < assignments.size(); j += 3)
{
// along the assignments vector: atomID1 atomID2 bondOrder
a1 = mol.GetAtom((*matches)[ assignments[j] ]);
a2 = mol.GetAtom((*matches)[ assignments[j+1 ] ]);
if (!a1 || !a2) continue;
b1 = a1->GetBond(a2);
if (!b1) continue;
b1->SetBO(assignments[j+2]);
} // bond order assignments
} // each match
} // current pattern matches
} // for(functional groups)
// FG with distance and/or bond criteria
// Carbonyl oxygen C=O
OBSmartsPattern carbo; carbo.Init("[#8D1][#6](*)(*)");
if (carbo.Match(mol))
{
mlist = carbo.GetUMapList();
for (l = mlist.begin(); l != mlist.end(); ++l)
{
a1 = mol.GetAtom((*l)[0]);
a2 = mol.GetAtom((*l)[1]);
angle = a2->AverageBondAngle();
dist1 = a1->GetDistance(a2);
// carbonyl geometries ?
if (angle > 115 && angle < 150 && dist1 < 1.28) {
if ( !a1->HasDoubleBond() ) {// no double bond already assigned
b1 = a1->GetBond(a2);
if (!b1 ) continue;
b1->SetBO(2);
}
}
}
} // Carbonyl oxygen
// thione C=S
OBSmartsPattern thione; thione.Init("[#16D1][#6](*)(*)");
if (thione.Match(mol))
{
mlist = thione.GetUMapList();
for (l = mlist.begin(); l != mlist.end(); ++l)
{
a1 = mol.GetAtom((*l)[0]);
a2 = mol.GetAtom((*l)[1]);
angle = a2->AverageBondAngle();
dist1 = a1->GetDistance(a2);
// thione geometries ?
if (angle > 115 && angle < 150 && dist1 < 1.72) {
if ( !a1->HasDoubleBond() ) {// no double bond already assigned
b1 = a1->GetBond(a2);
if (!b1 ) continue;
b1->SetBO(2);
}
}
}
} // thione
// Isocyanate N=C=O or Isothiocyanate
bool dist1OK;
OBSmartsPattern isocyanate; isocyanate.Init("[#8,#16;D1][#6D2][#7D2]");
if (isocyanate.Match(mol))
{
mlist = isocyanate.GetUMapList();
for (l = mlist.begin(); l != mlist.end(); ++l)
{
a1 = mol.GetAtom((*l)[0]);
a2 = mol.GetAtom((*l)[1]);
a3 = mol.GetAtom((*l)[2]);
angle = a2->AverageBondAngle();
dist1 = a1->GetDistance(a2);
dist2 = a2->GetDistance(a3);
// isocyanate geometry or Isotiocyanate geometry ?
if (a1->IsOxygen())
dist1OK = dist1 < 1.28;
else
dist1OK = dist1 < 1.72;
if (angle > 150 && dist1OK && dist2 < 1.34) {
b1 = a1->GetBond(a2);
b2 = a2->GetBond(a3);
if (!b1 || !b2) continue;
b1->SetBO(2);
b2->SetBO(2);
}
}
} // Isocyanate
}
} //namespace OpenBabel;
//! \file bondtyper.cpp
//! \brief Bond typer to perceive connectivity and bond orders/types.
//! \todo Needs to add aromatic ring bond order assignment.
//! Eventually need to migrate OBMol::PerceiveBondOrders(),
//! OBMol::ConnectTheDots(), and possibly some of the Kekulize routines
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