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/********************************************************************** |
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bondtyper.cpp - Bond typer to perceive connectivity and bond orders/types. |
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Copyright (C) 2003-2005 by Geoffrey R. Hutchison |
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|
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This file is part of the Open Babel project. |
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For more information, see <http://openbabel.sourceforge.net/> |
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|
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This program is free software; you can redistribute it and/or modify |
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it under the terms of the GNU General Public License as published by |
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the Free Software Foundation version 2 of the License. |
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|
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This program is distributed in the hope that it will be useful, |
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but WITHOUT ANY WARRANTY; without even the implied warranty of |
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MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the |
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GNU General Public License for more details. |
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***********************************************************************/ |
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|
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#include "mol.hpp" |
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#include "bondtyper.hpp" |
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#include "bondtyp.hpp" |
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|
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#ifdef WIN32 |
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#pragma warning (disable : 4786) |
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#endif |
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|
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using namespace std; |
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|
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namespace OpenBabel |
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{ |
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|
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//! Global OBBondTyper for perception of bond order assignment. |
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OBBondTyper bondtyper; |
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|
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/*! \class OBBondTyper |
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\brief Assigns bond types for file formats without bond information |
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|
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The OBBondTyper class is designed to read in a list of bond typing |
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rules and apply them to molecules. |
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*/ |
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OBBondTyper::OBBondTyper() |
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{ |
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_init = false; |
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STR_DEFINE(_dir, FRC_PATH ); |
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_envvar = "FORCE_PARAM_PATH"; |
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_filename = "bondtyp.txt"; |
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_subdir = "data"; |
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_dataptr = BondTypeData; |
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} |
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|
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void OBBondTyper::ParseLine(const char *buffer) |
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{ |
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vector<string> vs; |
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vector<int> bovector; |
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OBSmartsPattern *sp; |
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|
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if (buffer[0] != '#') |
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{ |
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tokenize(vs,buffer); |
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// Make sure we actually have a SMARTS pattern plus at least one triple |
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// and make sure we have the correct number of integers |
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if (vs.empty() || vs.size() < 4) |
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return; // just ignore empty (or short lines) |
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else if (!vs.empty() && vs.size() >= 4 && (vs.size() % 3 != 1)) |
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{ |
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#ifdef HAVE_SSTREAM |
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stringstream errorMsg; |
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#else |
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strstream errorMsg; |
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#endif |
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errorMsg << " Error in OBBondTyper. Pattern is incorrect, found " |
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<< vs.size() << " tokens." << endl; |
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errorMsg << " Buffer is: " << buffer << endl; |
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obErrorLog.ThrowError(__FUNCTION__, errorMsg.str(), obInfo); |
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return; |
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} |
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|
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sp = new OBSmartsPattern; |
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if (sp->Init(vs[0])) |
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{ |
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for (unsigned int i = 1; i < vs.size() ; i++) |
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{ |
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bovector.push_back( atoi((char *)vs[i].c_str()) ); |
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} |
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_fgbonds.push_back(pair<OBSmartsPattern*,vector<int> > |
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(sp, bovector)); |
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} |
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else |
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{ |
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delete sp; |
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sp = NULL; |
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} |
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} |
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} |
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|
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OBBondTyper::~OBBondTyper() |
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{ |
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vector<pair<OBSmartsPattern*, vector<int> > >::iterator i; |
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for (i = _fgbonds.begin();i != _fgbonds.end();i++) |
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{ |
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delete i->first; |
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i->first = NULL; |
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} |
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} |
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|
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void OBBondTyper::AssignFunctionalGroupBonds(OBMol &mol) |
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{ |
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if (!_init) |
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Init(); |
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|
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OBSmartsPattern *currentPattern; |
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OBBond *b1, *b2; |
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OBAtom *a1,*a2, *a3; |
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double angle, dist1, dist2; |
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vector<int> assignments; |
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vector<vector<int> > mlist; |
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vector<vector<int> >::iterator matches, l; |
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vector<pair<OBSmartsPattern*, vector<int> > >::iterator i; |
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unsigned int j; |
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|
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// Loop through for all the functional groups and assign bond orders |
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for (i = _fgbonds.begin();i != _fgbonds.end();i++) |
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{ |
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currentPattern = i->first; |
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assignments = i->second; |
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|
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if (currentPattern && currentPattern->Match(mol)) |
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{ |
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mlist = currentPattern->GetUMapList(); |
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for (matches = mlist.begin(); matches != mlist.end(); matches++) |
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{ |
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// Now loop through the bonds to assign from _fgbonds |
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for (j = 0; j < assignments.size(); j += 3) |
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{ |
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// along the assignments vector: atomID1 atomID2 bondOrder |
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a1 = mol.GetAtom((*matches)[ assignments[j] ]); |
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a2 = mol.GetAtom((*matches)[ assignments[j+1 ] ]); |
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if (!a1 || !a2) continue; |
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|
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b1 = a1->GetBond(a2); |
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|
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if (!b1) continue; |
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b1->SetBO(assignments[j+2]); |
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} // bond order assignments |
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} // each match |
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} // current pattern matches |
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|
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} // for(functional groups) |
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|
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// FG with distance and/or bond criteria |
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// Carbonyl oxygen C=O |
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OBSmartsPattern carbo; carbo.Init("[#8D1][#6](*)(*)"); |
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|
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if (carbo.Match(mol)) |
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{ |
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mlist = carbo.GetUMapList(); |
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for (l = mlist.begin(); l != mlist.end(); l++) |
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{ |
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a1 = mol.GetAtom((*l)[0]); |
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a2 = mol.GetAtom((*l)[1]); |
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|
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angle = a2->AverageBondAngle(); |
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dist1 = a1->GetDistance(a2); |
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|
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// carbonyl geometries ? |
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if (angle > 115 && angle < 150 && dist1 < 1.28) { |
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|
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if ( !a1->HasDoubleBond() ) {// no double bond already assigned |
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b1 = a1->GetBond(a2); |
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|
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if (!b1 ) continue; |
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b1->SetBO(2); |
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} |
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} |
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} |
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} // Carbonyl oxygen |
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|
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// thione C=S |
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OBSmartsPattern thione; thione.Init("[#16D1][#6](*)(*)"); |
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|
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if (thione.Match(mol)) |
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{ |
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mlist = thione.GetUMapList(); |
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for (l = mlist.begin(); l != mlist.end(); l++) |
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{ |
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a1 = mol.GetAtom((*l)[0]); |
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a2 = mol.GetAtom((*l)[1]); |
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|
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angle = a2->AverageBondAngle(); |
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dist1 = a1->GetDistance(a2); |
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|
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// thione geometries ? |
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if (angle > 115 && angle < 150 && dist1 < 1.72) { |
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|
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if ( !a1->HasDoubleBond() ) {// no double bond already assigned |
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b1 = a1->GetBond(a2); |
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|
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if (!b1 ) continue; |
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b1->SetBO(2); |
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} |
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} |
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} |
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} // thione |
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|
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// Isocyanate N=C=O or Isothiocyanate |
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bool dist1OK; |
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OBSmartsPattern isocyanate; isocyanate.Init("[#8,#16;D1][#6D2][#7D2]"); |
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if (isocyanate.Match(mol)) |
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{ |
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mlist = isocyanate.GetUMapList(); |
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for (l = mlist.begin(); l != mlist.end(); l++) |
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{ |
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a1 = mol.GetAtom((*l)[0]); |
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a2 = mol.GetAtom((*l)[1]); |
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a3 = mol.GetAtom((*l)[2]); |
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|
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angle = a2->AverageBondAngle(); |
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dist1 = a1->GetDistance(a2); |
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dist2 = a2->GetDistance(a3); |
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|
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// isocyanate geometry or Isotiocyanate geometry ? |
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if (a1->IsOxygen()) |
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dist1OK = dist1 < 1.28; |
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else |
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dist1OK = dist1 < 1.72; |
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if (angle > 150 && dist1OK && dist2 < 1.34) { |
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b1 = a1->GetBond(a2); |
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b2 = a2->GetBond(a3); |
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if (!b1 || !b2) continue; |
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b1->SetBO(2); |
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b2->SetBO(2); |
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|
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} |
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|
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} |
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} // Isocyanate |
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|
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} |
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|
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} //namespace OpenBabel; |
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|
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//! \file bondtyper.cpp |
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//! \brief Bond typer to perceive connectivity and bond orders/types. |
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//! \todo Needs to add aromatic ring bond order assignment. |
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//! Eventually need to migrate OBMol::PerceiveBondOrders(), |
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//! OBMol::ConnectTheDots(), and possibly some of the Kekulize routines |
