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/********************************************************************** |
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kekulize.cpp - Alternate algorithm to kekulize a molecule. |
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|
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Copyright (C) 2004-2005 by Fabien Fontaine |
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Some portions Copyright (C) 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 "oberror.hpp" |
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|
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#ifdef HAVE_SSTREAM |
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#include <sstream> |
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#else |
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#include <strstream> |
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#endif |
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|
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#define SINGLE 1 |
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#define DOUBLE 2 |
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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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//! \brief Kekulize aromatic rings without using implicit valence |
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|
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//! This new perceive kekule bonds function has been especifically designed to |
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//! handle molecule files without explicit hydrogens such as pdb or xyz. |
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//! The function does not rely on GetImplicitValence function |
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//! The function looks for groups of aromatic cycle |
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//! For each group it tries to guess the number of electrons given by each atom |
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//! in order to satisfy the huckel (4n+2) rule |
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//! If the huckel rule cannot be satisfied the algorithm try with its best alternative guess |
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//! Then it recursively walk on the atoms of the cycle and assign single and double bonds |
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void OBMol::NewPerceiveKekuleBonds() |
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{ |
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|
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if (HasKekulePerceived()) return; |
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SetKekulePerceived(); |
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|
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OBAtom *atom; |
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int n, de, minde; |
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std::vector<OBAtom*> cycle; |
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OBBitVec avisit,cvisit; |
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avisit.Resize(NumAtoms()+1); |
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cvisit.Resize(NumAtoms()+1); |
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OBBond *bond; |
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std::vector<OBEdgeBase*>::iterator bi; |
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std::vector<int> electron; |
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int sume, orden, bestatom; |
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int bestorden = 99; |
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// Init the kekulized bonds |
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unsigned i; |
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FOR_BONDS_OF_MOL(bond, *this) |
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{ |
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switch (bond->GetBO()) |
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{ |
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case 1: bond->SetKSingle(); break; |
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case 2: bond->SetKDouble(); break; |
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case 3: bond->SetKTriple(); break; |
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} |
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} |
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|
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// Find all the groups of aromatic cycle |
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for(i=1; i<= NumAtoms(); i++ ) { |
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atom = GetAtom(i); |
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if (atom->HasAromaticBond() && !cvisit[i]) { // is new aromatic atom of an aromatic cycle ? |
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|
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avisit.Clear(); |
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electron.clear(); |
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cycle.clear(); |
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|
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avisit.SetBitOn(i); |
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expandcycle (atom, avisit); |
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//store the atoms of the cycle(s) |
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unsigned int j; |
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for(j=1; j<= NumAtoms(); j++) { |
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if ( avisit[j] ) { |
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atom = GetAtom(j); |
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cycle.push_back(atom); |
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} |
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} |
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// At the begining each atom give one electron to the cycle |
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for(j=0; j< cycle.size(); j++) { |
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electron.push_back(1); |
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} |
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|
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// remove one electron if the atom make a double bond out of the cycle |
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sume =0; |
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for(j=0; j< cycle.size(); j++) { |
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atom = cycle[j]; |
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for(bond = atom->BeginBond(bi); bond; bond = atom->NextBond(bi)) { |
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if ( bond->IsDouble() ) { |
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OBAtom *atom2 = bond->GetNbrAtom(atom); |
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int fcharge = atom->GetFormalCharge(); |
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int fcharge2 = atom2->GetFormalCharge(); |
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if(atom->IsNitrogen() && atom2->IsOxygen() |
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&& fcharge == 0 && fcharge2 == 0) { //n=O to [n+][O-] |
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atom->SetFormalCharge(1); |
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atom2->SetFormalCharge(-1); |
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bond->SetKSingle(); |
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bond->SetBO(1); |
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} |
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else { |
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electron[j] = 0; |
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} |
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} |
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} |
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// count the number of electrons |
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sume += electron[j]; |
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} |
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|
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|
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// Save the electron state in case huckel rule is not satisfied |
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vector<int> previousElectron = electron; |
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|
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// find the ideal number of electrons according to the huckel 4n+2 rule |
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minde=99; |
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for (i=1; 1; i++) { |
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n = 4 *i +2; |
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de = n - sume; |
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if ( de < minde ) |
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minde=de; |
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else if ( minde < 0 ) |
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minde=de; |
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else |
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break; |
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} |
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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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|
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//cout << "minde before:" << minde << endl; |
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// if huckel rule not satisfied some atoms must give more electrons |
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//cout << "minde " << minde << endl; |
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while ( minde != 0 ) { |
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bestorden=99; |
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for(j=0; j< cycle.size(); j++) { |
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if (electron[j] == 1) { |
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orden = getorden(cycle[j]); |
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if (orden < bestorden) { |
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bestorden = orden; |
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bestatom = j; |
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} |
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} |
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} |
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if (bestorden==99) { // no electron giving atom found |
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errorMsg << "Kekulize: Huckel rule not satisfied for molecule " << GetTitle() << endl; |
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obErrorLog.ThrowError(__func__, errorMsg.str(), obInfo); |
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break; // Huckel rule cannot be satisfied |
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} // try to kekulize anyway |
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else { |
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electron[bestatom] += 1; |
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minde--; |
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} |
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} |
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|
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if (bestorden == 99) { // Huckel rule not satisfied, just try to get an even number of electron before kekulizing |
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|
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electron = previousElectron; // restore electon's state |
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|
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int odd = sume % 2; |
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//cout << "odd:" << odd << endl; |
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if(odd) { // odd number of electrons try to add an electron to the best possible atom |
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for(j=0; j< cycle.size(); j++) { |
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if (electron[j] == 1) { |
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orden = getorden(cycle[j]); |
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if (orden < bestorden) { |
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bestorden = orden; |
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bestatom = j; |
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} |
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} |
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} |
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if (bestorden==99) { // no electron giving atom found |
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errorMsg << "Kekulize: Cannot get an even number of electron for molecule " << GetTitle() << "\n"; |
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obErrorLog.ThrowError(__func__, errorMsg.str(), obInfo); |
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break; // impossible to choose an atom to obtain an even number of electron |
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} // try to kekulize anyway |
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else { |
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electron[bestatom] += 1; |
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} |
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} |
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} |
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|
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//cout << "minde after:" << minde <<endl; |
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//for(j=0; j < cycle.size(); j++) { |
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//OBAtom *cycleAtom = cycle[j]; |
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//cout << "\t" << cycleAtom->GetIdx(); |
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//} |
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//cout << endl; |
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|
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//for(j=0; j < electron.size(); j++) { |
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//cout << "\t" << electron[j]; |
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//} |
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//cout << endl; |
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|
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// kekulize the cycle(s) |
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start_kekulize(cycle,electron); |
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|
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// Set the kekulized cycle(s) as visited |
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for(j=1; j<= NumAtoms(); j++) { |
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if (avisit[j]) |
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cvisit.SetBitOn(j); |
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} |
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|
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} |
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} |
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// Double bond have been assigned, set the remaining aromatic bonds to single |
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//std::cout << "Set not assigned single bonds\n"; |
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for(i=0;i <NumBonds(); i++) { |
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bond = GetBond(i); |
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//std::cout << "bond " << bond->GetBeginAtomIdx() << " " << bond->GetEndAtomIdx() << " "; |
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if (bond->GetBO()==5 ) { |
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bond->SetKSingle(); |
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bond->SetBO(1); |
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//std::cout << "single\n"; |
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} |
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//else |
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// std::cout << "double\n"; |
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} |
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|
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return; |
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} |
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|
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/////////////////////////////////////////////////////////////////////////////////////// |
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//! \brief Start kekulizing one or a fused set of aromatic ring(s) |
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|
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//! The initial electronic state indicates if an atoms must make a double bond or not |
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//! Kekulizing is attempted recursively for all the atoms bonded to the first atom |
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//! of the cycle. |
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void OBMol::start_kekulize( std::vector <OBAtom*> &cycle, std::vector<int> &electron) { |
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|
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std::vector<int> initState; |
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std::vector<int> currentState; |
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std::vector<int> binitState; |
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std::vector<int> bcurrentState; |
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std::vector<bool> mark; |
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unsigned int Idx; |
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OBAtom *atom, *atom2; |
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OBBond *bond; |
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|
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//init the atom arrays |
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unsigned i; |
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for(i=0;i <NumAtoms()+1; i++) { |
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initState.push_back(-1); |
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currentState.push_back(-1); |
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mark.push_back(false); |
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} |
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|
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//init the bond arrays with single bonds |
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for(i=0;i <NumBonds(); i++) { |
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binitState.push_back(SINGLE); |
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bcurrentState.push_back(SINGLE); |
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} |
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|
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//set the electron number |
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for(i=0; i< cycle.size(); i++) { |
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atom = cycle[i]; |
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Idx = atom->GetIdx(); |
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if ( electron[i] == 1) |
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initState[Idx] = 1; // make 1 double bond |
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else |
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initState[Idx] = 2; // make 2 single bonds |
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|
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currentState[Idx] = initState[Idx]; |
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} |
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|
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std::vector<OBEdgeBase*>::iterator b; |
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OBAtom *nbr; |
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|
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bool second_pass=false; |
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// for( i=1; i<= NumAtoms(); i++) { |
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// if(currentState[i] == 1) { // the atom can make a double bond |
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// atom = GetAtom(i); |
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// //find a neighbour that can make a double bond |
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// // and start kekulize |
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// for (nbr = atom->BeginNbrAtom(b);nbr;nbr = atom->NextNbrAtom(b)) { |
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// if(currentState[nbr->GetIdx()]==1){ |
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// if(!expand_kekulize(atom,nbr,currentState,initState, bcurrentState,binitState, mark)) { |
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// second_pass=true; |
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// } |
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|
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// } |
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// } |
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// } |
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// } |
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bool expand_successful; |
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atom = cycle[0]; |
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for (nbr = atom->BeginNbrAtom(b);nbr;nbr = atom->NextNbrAtom(b)) { |
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if(initState[nbr->GetIdx()] == -1) //neighbor atom not in the cycle, try next one |
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continue; |
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//std::cout << "Expand kekulize\n"; |
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expand_kekulize(atom,nbr,currentState,initState, bcurrentState,binitState, mark) ; |
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//Control that all the electron have been given to the cycle(s) |
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expand_successful = true; |
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for(unsigned i=0; i< cycle.size(); i++) { |
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atom2 = cycle[i]; |
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Idx = atom2->GetIdx(); |
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//cout << "\t" << currentState[Idx]; |
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if (currentState[Idx] == 1) |
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expand_successful=false; |
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} |
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//cout << endl; |
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if (expand_successful) |
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break; |
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else { |
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unsigned i; |
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for(i=0;i <NumAtoms()+1; i++) { |
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currentState[i]=initState[i]; |
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mark[i]=false; |
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} |
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for(i=0;i <NumBonds(); i++) { |
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bcurrentState[i]=binitState[i]; |
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} |
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} |
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} |
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if (!expand_successful) |
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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 << "Kekulize Error for molecule " << GetTitle() << endl; |
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obErrorLog.ThrowError(__func__, errorMsg.str(), obInfo); |
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} |
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|
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// Set the double bonds |
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// std::cout << "Set double bonds\n"; |
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for(i=0;i <NumBonds(); i++) { |
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bond = GetBond(i); |
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// std::cout << "bond " << bond->GetBeginAtomIdx() << " " << bond->GetEndAtomIdx() << " "; |
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if (bond->GetBO()==5 && bcurrentState[i] == DOUBLE) { |
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if ( (bond->GetBeginAtom())->IsSulfur() |
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&& bond->GetEndAtom()->IsSulfur() ) { |
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// no double bonds between aromatic sulfur atoms -- PR#1504089 |
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continue; |
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} |
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|
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bond->SetKDouble(); |
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bond->SetBO(2); |
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//std::cout << "double\n"; |
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} |
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//else |
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//std::cout << "single\n"; |
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//else if (bond->IsAromatic() && bond->GetBO() != 2) |
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// bond->SetBO(1); |
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} |
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|
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return; |
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} |
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|
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|
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///////////////////////////////////////////////////////////////////////////////////////// |
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//! \brief recursively assign single and double bonds according to the electronical state |
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//! of the atoms of the current bond |
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int OBMol::expand_kekulize(OBAtom *atom1, OBAtom *atom2, std::vector<int> ¤tState, std::vector<int> &initState, std::vector<int> &bcurrentState, std::vector<int> &binitState, std::vector<bool> &mark) |
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{ |
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int done; |
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int Idx1=atom1->GetIdx(), Idx2=atom2->GetIdx(); |
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OBBond *bond; |
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std::vector<OBEdgeBase*>::iterator i; |
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OBAtom *nbr; |
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int natom; |
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|
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mark[Idx1]= true; |
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bond = atom1->GetBond(atom2); |
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int bIdx = bond->GetIdx(); |
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|
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//cout << "assign bond state for atoms " << Idx1 << " and " << Idx2 << endl; |
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if (currentState[Idx1] == 1 && currentState[Idx2] == 1) { |
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currentState[Idx1]=0; |
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currentState[Idx2]=0; |
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// set bond to double |
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//std::cout << "bond " << Idx1 << " " << Idx2 << " double\n"; |
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bcurrentState[bIdx]=DOUBLE; |
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} |
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else if (currentState[Idx1] == 0 && currentState[Idx2] == 1 || |
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currentState[Idx1] == 2 && currentState[Idx2] == 1 || |
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currentState[Idx1] == 2 && currentState[Idx2] == 2) { |
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//std::cout << "bond " << Idx1 << " " << Idx2 << " single\n"; |
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// leave bond to single |
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} |
| 399 |
else if (currentState[Idx1] == 1 && currentState[Idx2] == 0 || |
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currentState[Idx1] == 1 && currentState[Idx2] == 2) { |
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mark[Idx1]=false; |
| 402 |
//std::cout << "bond " << Idx1 << " " << Idx2 << " error\n"; |
| 403 |
return (0); // error |
| 404 |
} |
| 405 |
else if (currentState[Idx1] == 0 && currentState[Idx2] == 0 |
| 406 |
|| currentState[Idx1] == 2 && currentState[Idx2] == 0) { |
| 407 |
//std::cout << "bond " << Idx1 << " " << Idx2 << " done\n"; |
| 408 |
mark[Idx2]=true; |
| 409 |
return (1); //done |
| 410 |
} |
| 411 |
else if (currentState[Idx1] == 0 && currentState[Idx2] == 2) { |
| 412 |
currentState[Idx2]=0; |
| 413 |
//std::cout << "bond " << Idx1 << " " << Idx2 << " leave single\n"; |
| 414 |
// leave bond to single |
| 415 |
} |
| 416 |
else { |
| 417 |
|
| 418 |
#ifdef HAVE_SSTREAM |
| 419 |
stringstream errorMsg; |
| 420 |
#else |
| 421 |
strstream errorMsg; |
| 422 |
#endif |
| 423 |
|
| 424 |
errorMsg << "unexpected state:" << "atom " << Idx1 << " " << currentState[Idx1] |
| 425 |
<< " atom " << Idx2 << " " << currentState[Idx2] << endl; |
| 426 |
obErrorLog.ThrowError(__func__, errorMsg.str(), obDebug); |
| 427 |
return(false); |
| 428 |
} |
| 429 |
|
| 430 |
//int c; |
| 431 |
//for(c=1; c < currentState.size(); c++) { |
| 432 |
//cout << c << "\t"; |
| 433 |
//} |
| 434 |
//cout << endl; |
| 435 |
//for(c=1; c < currentState.size(); c++) { |
| 436 |
//cout << currentState[c] << "\t"; |
| 437 |
//} |
| 438 |
//cout << endl; |
| 439 |
|
| 440 |
vector<int> previousState = currentState; // Backup the atom |
| 441 |
vector<int> bpreviousState = bcurrentState; // and the bond states before expanding again |
| 442 |
|
| 443 |
bool return_false=false; |
| 444 |
// for each neighbor of atom 2 not already kekulized |
| 445 |
for (nbr = atom2->BeginNbrAtom(i);nbr;nbr = atom2->NextNbrAtom(i)) |
| 446 |
{ |
| 447 |
natom = nbr->GetIdx(); |
| 448 |
if(initState[natom] == -1) //neighbor atom not in the cycle, try next one |
| 449 |
continue; |
| 450 |
if ( !mark[natom] ) { |
| 451 |
done = expand_kekulize(atom2, nbr, currentState, initState, bcurrentState, binitState, mark); |
| 452 |
if ( !done ) // kekulize failed |
| 453 |
return_false =true; |
| 454 |
else |
| 455 |
return_false =false; |
| 456 |
} |
| 457 |
|
| 458 |
} |
| 459 |
if (return_false) { // no good solution found |
| 460 |
//cout << "return_false:no good solution\n" << endl; |
| 461 |
//cout << "reset state of " << Idx1 << " and " << Idx2 << " from " << currentState[Idx1] |
| 462 |
//<< " " << currentState[Idx2] << " to "; |
| 463 |
|
| 464 |
// retrieve the states that might have been changed during kekulize expansion |
| 465 |
currentState = previousState; |
| 466 |
|
| 467 |
|
| 468 |
bcurrentState = bpreviousState; |
| 469 |
|
| 470 |
|
| 471 |
// reset the bond and the atom states |
| 472 |
if (bcurrentState[bIdx] == DOUBLE) |
| 473 |
currentState[Idx1]=initState[Idx1]; |
| 474 |
|
| 475 |
currentState[Idx2]=initState[Idx2]; |
| 476 |
bcurrentState[bIdx]=binitState[bIdx]; // should be always single |
| 477 |
mark[Idx2]=false; |
| 478 |
|
| 479 |
//cout << currentState[Idx1] << " " << currentState[Idx2] << endl; |
| 480 |
return (false); |
| 481 |
} |
| 482 |
// atom 2 cannot make any bond, should not have 1 electron |
| 483 |
if (currentState[Idx2] == 1) { |
| 484 |
// currentState[Idx1]=initState[Idx1]; |
| 485 |
//cout << "return true but " << Idx2 << " state = 1\n"; |
| 486 |
mark[Idx1]=false; |
| 487 |
return (false); |
| 488 |
} |
| 489 |
else { |
| 490 |
// if we found a good solution, then the state of Idx2 may have shifted from 1 to 0 during the kekulization |
| 491 |
// If it is the case, we should check if there is a remaining unmarked neighbor because it is possible |
| 492 |
// that kekulizing from this neigbor failed just because Idx2 was equal to 1 |
| 493 |
|
| 494 |
if(previousState[Idx2] == 1) { |
| 495 |
// Since now Idx2 is equal to 0 because it kekulized well the kekulizing of the failed neigbor could be successfull |
| 496 |
// If there is still an unmarked neigbor try to kekulize it again |
| 497 |
//mark[Idx2]=true; |
| 498 |
return_false=false; |
| 499 |
//cout << "retry kekulizing from " << Idx2 << endl; |
| 500 |
|
| 501 |
for (nbr = atom2->BeginNbrAtom(i);nbr;nbr = atom2->NextNbrAtom(i)) |
| 502 |
{ |
| 503 |
natom = nbr->GetIdx(); |
| 504 |
if(initState[natom] == -1) //neighbor atom not in the cycle, try next one |
| 505 |
continue; |
| 506 |
if ( !mark[natom] ) { |
| 507 |
//cout << "atom " << natom << " not marked, expand again" << endl; |
| 508 |
done = expand_kekulize(atom2, nbr, currentState, initState, bcurrentState, binitState, mark); |
| 509 |
if ( !done ) // kekulize failed |
| 510 |
return_false =true; |
| 511 |
else |
| 512 |
return_false =false; |
| 513 |
} |
| 514 |
|
| 515 |
} |
| 516 |
|
| 517 |
// if we cannot kekulize the remaining neigbor again then we have to return false |
| 518 |
// we do not have to reset the states because the kekulize will fail anyway |
| 519 |
if(return_false) { |
| 520 |
//cout << "rekekulize failed" << endl; |
| 521 |
return(false); |
| 522 |
} |
| 523 |
else { |
| 524 |
//cout << "rekekulized successfull" << endl; |
| 525 |
return (true); |
| 526 |
} |
| 527 |
|
| 528 |
} |
| 529 |
|
| 530 |
|
| 531 |
//cout << "return_true: good solution" << endl; |
| 532 |
return (true); |
| 533 |
} |
| 534 |
} |
| 535 |
|
| 536 |
//! Give the priority to give two electrons instead of 1 |
| 537 |
int OBMol::getorden( OBAtom *atom) |
| 538 |
{ |
| 539 |
if ( atom->IsSulfur() ) return 1; |
| 540 |
if ( atom->IsOxygen() ) return 2; |
| 541 |
if ( atom->GetAtomicNum() == 34 ) return 3; |
| 542 |
if ( atom->IsNitrogen() && atom->GetFormalCharge() == 0 && atom->GetValence() == 3) return 5; |
| 543 |
if ( atom->IsAmideNitrogen() ) return 4; |
| 544 |
if ( atom->IsNitrogen() && atom->GetFormalCharge() == -1) return 6; |
| 545 |
if ( atom->IsNitrogen() && atom->GetFormalCharge() == 0 && atom->IsInRingSize(5) ) return 7; |
| 546 |
if ( atom->IsNitrogen() && atom->GetFormalCharge() == 0 ) return 8; |
| 547 |
if ( atom->IsCarbon() && atom->GetFormalCharge() == -1) return 9; |
| 548 |
//if ( atom->IsCarbon() ) return 9; |
| 549 |
|
| 550 |
return (100); //no atom found |
| 551 |
} |
| 552 |
|
| 553 |
//! Recursively find the aromatic atoms with an aromatic bond to the current atom |
| 554 |
void OBMol::expandcycle (OBAtom *atom, OBBitVec &avisit) |
| 555 |
{ |
| 556 |
OBAtom *nbr; |
| 557 |
// OBBond *bond; |
| 558 |
std::vector<OBEdgeBase*>::iterator i; |
| 559 |
int natom; |
| 560 |
//for each neighbour atom test if it is in the aromatic ring |
| 561 |
for (nbr = atom->BeginNbrAtom(i);nbr;nbr = atom->NextNbrAtom(i)) |
| 562 |
{ |
| 563 |
natom = nbr->GetIdx(); |
| 564 |
// if (!avisit[natom] && nbr->IsAromatic() && ((OBBond*) *i)->IsAromatic()) { |
| 565 |
if (!avisit[natom] && ((OBBond*) *i)->GetBO()==5) { |
| 566 |
avisit.SetBitOn(natom); |
| 567 |
expandcycle(nbr, avisit); |
| 568 |
} |
| 569 |
} |
| 570 |
} |
| 571 |
|
| 572 |
} // end namespace OpenBabel |
| 573 |
|
| 574 |
//! \file kekulize.cpp |
| 575 |
//! \brief Alternate algorithm to kekulize a molecule (OBMol::NewPerceiveKekuleBonds()). |
