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/********************************************************************** |
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ring.cpp - Deal with rings, find smallest set of smallest rings (SSSR). |
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|
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Copyright (C) 1998-2001 by OpenEye Scientific Software, Inc. |
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Some portions Copyright (C) 2001-2005 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 <deque> |
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|
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#include "obutil.hpp" |
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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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/*! \class OBRing |
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\brief Stores information on rings in a molecule from SSSR perception. |
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|
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Ring information beyond atom and bond membership is usually not |
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necessary, but more information can be had about the rings in a |
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molecule. The OBRing class is used to store the information from a |
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Smallest Set of Smallest Rings (SSSR) perception of a molecule. The |
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OBMol member function OBMol::GetSSSR() stores the information it perceives in |
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a vector<OBRing*> inside the molecule. Perception is only done once |
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for a molecule unless the connection table is modified. The following |
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code demonstrates how to extract the SSSR information: |
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\code |
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OBMol mol; |
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|
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vector<OBRing*> vr; |
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vr = mol.GetSSSR(); |
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\endcode |
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OBRings store the atom numbers of the atoms in each of the smallest |
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set of smallest rings in both a vector<int> and an OBBitVec. |
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An example of how to print out the atom numbers present in all SSSR |
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rings is show below: |
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\code |
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vector<OBRing*>::iterator i; |
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vector<int>::iterator j; |
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vector<OBRing*> *rlist = (vector<OBRing*>*)mol.GetData("RingList"); |
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for (i = rlist->begin();i != rlist->end();i++) |
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{ |
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for(j = (*i)->_path.begin();j != (*i)->_path.end();j++) |
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cout << *j << ` `; |
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cout << endl; |
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} |
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\endcode |
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will produce something like the following output for benzene: |
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\code |
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1 2 3 4 5 6 |
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\endcode |
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Ring information is automatically deleted from an OBMol when it goes |
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out of scope or the Clear() member function is called. |
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|
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Implements <a href="http://qsar.sourceforge.net/dicts/blue-obelisk/index.xhtml#findSmallestSetOfSmallestRings">blue-obelisk:findSmallestSetOfSmallestRings</a>. |
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*/ |
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|
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static int DetermineFRJ(OBMol &); |
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static void BuildOBRTreeVector(OBAtom*,OBRTree*,vector<OBRTree*>&,OBBitVec&); |
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|
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|
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void OBMol::FindSSSR() |
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{ |
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if (HasSSSRPerceived()) |
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return; |
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SetSSSRPerceived(); |
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obErrorLog.ThrowError(__FUNCTION__, |
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"Ran OpenBabel::FindSSSR", obAuditMsg); |
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|
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OBRing *ring; |
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vector<OBRing*>::iterator j; |
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|
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//get frerejaque taking int account multiple possible spanning graphs |
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int frj = DetermineFRJ(*this); |
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if (frj) |
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{ |
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vector<OBRing*> vr; |
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FindRingAtomsAndBonds(); |
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|
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OBBond *bond; |
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vector<OBEdgeBase*> cbonds; |
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vector<OBEdgeBase*>::iterator k; |
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|
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//restrict search for rings around closure bonds |
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for (bond = BeginBond(k);bond;bond = NextBond(k)) |
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if (bond->IsClosure()) |
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cbonds.push_back(bond); |
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|
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if (!cbonds.empty()) |
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{ |
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OBRingSearch rs; |
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//search for all rings about closures |
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vector<OBEdgeBase*>::iterator i; |
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|
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for (i = cbonds.begin();i != cbonds.end();i++) |
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rs.AddRingFromClosure(*this,(OBBond*)*i); |
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|
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rs.SortRings(); |
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rs.RemoveRedundant(frj); |
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//store the SSSR set |
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|
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for (j = rs.BeginRings();j != rs.EndRings();j++) |
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{ |
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ring = new OBRing ((*j)->_path,NumAtoms()+1); |
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ring->SetParent(this); |
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vr.push_back(ring); |
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} |
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//rs.WriteRings(); |
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} |
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|
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if (!HasData(OBGenericDataType::RingData)) |
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SetData(new OBRingData); |
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OBRingData *rd = (OBRingData*)GetData(OBGenericDataType::RingData); |
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rd->SetData(vr); |
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} |
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} |
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|
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static int DetermineFRJ(OBMol &mol) |
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{ |
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vector<vector<int> >::iterator i; |
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vector<vector<int> > cfl; |
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//find all continuous graphs in the mol area |
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mol.ContigFragList(cfl); |
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|
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if (cfl.empty()) |
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return(0); |
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if (cfl.size() == 1) |
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return(mol.NumBonds() - mol.NumAtoms() + 1); |
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|
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//count up the atoms and bonds belonging to each graph |
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OBBond *bond; |
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vector<OBEdgeBase*>::iterator j; |
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int numatoms,numbonds,frj=0; |
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OBBitVec frag; |
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for (i = cfl.begin();i != cfl.end();i++) |
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{ |
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frag.Clear(); |
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frag.FromVecInt(*i); |
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numatoms = (*i).size(); |
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numbonds=0; |
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for (bond = mol.BeginBond(j);bond;bond = mol.NextBond(j)) |
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if (frag.BitIsOn(bond->GetBeginAtomIdx()) && |
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frag.BitIsOn(bond->GetEndAtomIdx())) |
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numbonds++; |
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frj += numbonds - numatoms + 1; |
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} |
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|
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return(frj); |
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} |
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|
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void OBRingSearch::RemoveRedundant(int frj) |
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{ |
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OBBitVec tmp; |
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int i,j; |
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|
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//remove identical rings |
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for (i = _rlist.size()-1;i > 0;i--) |
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for (j = i-1;j >= 0;j--) |
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if ((_rlist[i])->_pathset == (_rlist[j])->_pathset) |
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{ |
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delete _rlist[i]; |
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_rlist.erase(_rlist.begin()+i); |
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break; |
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} |
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|
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//make sure tmp is the same size as the rings |
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for (j = 0;j < (signed)_rlist.size();j++) |
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tmp = (_rlist[j])->_pathset; |
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|
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//remove larger rings that cover the same atoms as smaller rings |
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for (i = _rlist.size()-1;i >= 0;i--) |
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{ |
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tmp.Clear(); |
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for (j = 0;j < (signed)_rlist.size();j++) |
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if ((_rlist[j])->_path.size() <= (_rlist[i])->_path.size() && i != j) |
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tmp |= (_rlist[j])->_pathset; |
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|
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tmp = tmp & (_rlist[i])->_pathset; |
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|
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if (tmp == (_rlist[i])->_pathset) |
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{ |
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delete _rlist[i]; |
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_rlist.erase(_rlist.begin()+i); |
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} |
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|
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if (_rlist.size() == (unsigned)frj) |
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break; |
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} |
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} |
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|
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|
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void OBRingSearch::AddRingFromClosure(OBMol &mol,OBBond *cbond) |
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{ |
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vector<OBRTree*> t1(mol.NumAtoms()+1,(OBRTree*)NULL); |
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vector<OBRTree*> t2(mol.NumAtoms()+1,(OBRTree*)NULL); |
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OBBitVec bv1,bv2; |
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|
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bv1.SetBitOn(cbond->GetEndAtomIdx()); |
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bv2.SetBitOn(cbond->GetBeginAtomIdx()); |
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BuildOBRTreeVector(cbond->GetBeginAtom(),NULL,t1,bv1); |
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BuildOBRTreeVector(cbond->GetEndAtom(),NULL,t2,bv2); |
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|
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bool pathok; |
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deque<int> p1,p2; |
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vector<OBNodeBase*> path1,path2; |
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vector<OBNodeBase*>::iterator m,n; |
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vector<OBRTree*>::iterator i; |
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|
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for (i = t1.begin();i != t1.end();i++) |
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if (*i) |
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{ |
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path1.clear(); |
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(*i)->PathToRoot(path1); |
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|
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if (t2[(*i)->GetAtomIdx()]) |
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{ |
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pathok = true; |
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path2.clear(); |
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t2[(*i)->GetAtomIdx()]->PathToRoot(path2); |
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|
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p1.clear(); |
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m = path1.begin(); |
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if (m != path1.end()) |
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p1.push_back((*m)->GetIdx()); |
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for (m = path1.begin(),m++;m != path1.end();m++) |
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{ |
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p1.push_back((*m)->GetIdx()); |
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p2.clear(); |
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for (n = path2.begin(),n++;n != path2.end();n++) |
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{ |
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p2.push_front((*n)->GetIdx()); |
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if (*n == *m)//don't traverse across identical atoms |
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{ |
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p2.pop_front(); |
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if (p1.size()+p2.size() > 2) |
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SaveUniqueRing(p1,p2); |
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pathok = false; |
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break; |
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} |
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if ((*n)->IsConnected(*m) && p1.size()+p2.size() > 2) |
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SaveUniqueRing(p1,p2); |
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} |
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if (!pathok) |
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break; |
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} |
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} |
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} |
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|
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//clean up OBRTree vectors |
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for (i = t1.begin();i != t1.end();i++) |
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if (*i) |
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delete *i; |
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|
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for (i = t2.begin();i != t2.end();i++) |
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if (*i) |
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delete *i; |
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} |
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|
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bool OBRingSearch::SaveUniqueRing(deque<int> &d1,deque<int> &d2) |
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{ |
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vector<int> path; |
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OBBitVec bv; |
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deque<int>::iterator i; |
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|
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for (i = d1.begin();i != d1.end();i++) |
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{ |
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bv.SetBitOn(*i); |
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path.push_back(*i); |
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} |
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|
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for (i = d2.begin();i != d2.end();i++) |
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{ |
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bv.SetBitOn(*i); |
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path.push_back(*i); |
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} |
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|
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vector<OBRing*>::iterator j; |
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for (j = _rlist.begin();j != _rlist.end();j++) |
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if (bv == (*j)->_pathset) |
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return(false); |
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|
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OBRing *ring = new OBRing; |
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ring->_path = path; |
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ring->_pathset = bv; |
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_rlist.push_back(ring); |
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|
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return(true); |
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} |
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|
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OBRingSearch::~OBRingSearch() |
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{ |
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vector<OBRing*>::iterator i; |
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for (i = _rlist.begin();i != _rlist.end();i++) |
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delete *i; |
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} |
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|
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bool CompareRingSize(const OBRing *a,const OBRing *b) |
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{ |
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return(a->PathSize() < b->PathSize()); |
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} |
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|
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void OBRingSearch::WriteRings() |
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{ |
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vector<OBRing*>::iterator i; |
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|
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for (i = _rlist.begin();i != _rlist.end();i++) |
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cout << (*i)->_pathset << endl; |
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} |
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|
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static void FindRings(OBMol &mol,vector<int> &path,OBBitVec &avisit, |
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OBBitVec &bvisit, int natom,int depth ); |
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|
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void OBMol::FindRingAtomsAndBonds() |
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{ |
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if (HasFlag(OB_RINGFLAGS_MOL)) |
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return; |
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SetFlag(OB_RINGFLAGS_MOL); |
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|
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obErrorLog.ThrowError(__FUNCTION__, |
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"Ran OpenBabel::FindRingAtomsAndBonds", obAuditMsg); |
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|
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OBBitVec avisit,bvisit; |
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avisit.Resize(NumAtoms()+1); |
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bvisit.Resize(NumAtoms()+1); |
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vector<int> path; |
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path.resize(NumAtoms()+1); |
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|
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for(unsigned int i=1; i<= NumAtoms(); i++ ) |
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if(!avisit[i]) |
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FindRings(*this,path,avisit,bvisit,i,0); |
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} |
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|
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static void FindRings(OBMol &mol,vector<int> &path,OBBitVec &avisit, |
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OBBitVec &bvisit, int natom,int depth ) |
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{ |
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OBAtom *atom; |
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OBBond *bond; |
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vector<OBEdgeBase*>::iterator k; |
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|
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if (avisit[natom]) |
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{ |
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int j = depth-1; |
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bond=mol.GetBond(path[j--]); |
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bond->SetInRing(); |
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while( j >= 0 ) |
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{ |
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bond=mol.GetBond(path[j--]); |
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bond->SetInRing(); |
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(bond->GetBeginAtom())->SetInRing(); |
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(bond->GetEndAtom())->SetInRing(); |
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if(bond->GetBeginAtomIdx()==static_cast<unsigned int>(natom) || bond-> |
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GetEndAtomIdx()==static_cast<unsigned int>(natom)) |
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break; |
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} |
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} |
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else |
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{ |
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avisit.SetBitOn(natom); |
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atom = mol.GetAtom(natom); |
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for(bond = atom->BeginBond(k);bond;bond=atom->NextBond(k)) |
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if( !bvisit[bond->GetIdx()]) |
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{ |
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path[depth] = bond->GetIdx(); |
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bvisit.SetBitOn(bond->GetIdx()); |
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FindRings(mol,path,avisit,bvisit,bond->GetNbrAtomIdx(atom), |
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depth+1); |
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} |
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} |
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} |
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|
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bool OBRing::IsAromatic() |
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{ |
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OBMol *mol = _parent; |
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vector<int>::iterator i; |
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for (i = _path.begin();i != _path.end();i++) |
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if (!(mol->GetAtom(*i))->IsAromatic()) |
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return(false); |
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|
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return(true); |
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} |
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|
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bool OBRing::IsMember(OBAtom *a) |
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{ |
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return(_pathset.BitIsOn(a->GetIdx())); |
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} |
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|
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bool OBRing::IsMember(OBBond *b) |
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{ |
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return((_pathset.BitIsOn(b->GetBeginAtomIdx()))&&(_pathset.BitIsOn(b->GetEndAtomIdx()))); |
| 404 |
} |
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|
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OBRing::OBRing(vector<int> &path,int size) |
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{ |
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_path = path; |
| 409 |
_pathset.FromVecInt(_path); |
| 410 |
_pathset.Resize(size); |
| 411 |
} |
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|
| 413 |
/*! |
| 414 |
**\brief OBRing copy constructor |
| 415 |
**\param src reference to original OBRing object (rhs) |
| 416 |
*/ |
| 417 |
OBRing::OBRing(const OBRing &src) |
| 418 |
//no base class |
| 419 |
: |
| 420 |
_path(src._path) |
| 421 |
, _pathset(src._pathset) //chain to member classes |
| 422 |
{ |
| 423 |
//member data |
| 424 |
_parent = src._parent; //this is messed up, but what can you do? |
| 425 |
} |
| 426 |
|
| 427 |
/*! |
| 428 |
**\brief OBRing assignment operator |
| 429 |
**\param src reference to original OBRing object (rhs) |
| 430 |
**\return reference to modified OBRing object (lhs) |
| 431 |
*/ |
| 432 |
OBRing& OBRing::operator =(const OBRing &src) |
| 433 |
{ |
| 434 |
//on identity, return |
| 435 |
if(this == &src) |
| 436 |
return(*this); |
| 437 |
|
| 438 |
//no base class |
| 439 |
|
| 440 |
//memeber classes & data |
| 441 |
_path = src._path; |
| 442 |
_pathset = src._pathset; |
| 443 |
_parent = src._parent; //note, this may not be what you want |
| 444 |
|
| 445 |
return(*this); |
| 446 |
} |
| 447 |
void BuildOBRTreeVector(OBAtom *atom,OBRTree *prv,vector<OBRTree*> &vt,OBBitVec &bv) |
| 448 |
{ |
| 449 |
vt[atom->GetIdx()] = new OBRTree (atom,prv); |
| 450 |
|
| 451 |
int i; |
| 452 |
OBAtom *nbr; |
| 453 |
OBMol *mol = (OBMol*)atom->GetParent(); |
| 454 |
OBBitVec curr,used,next; |
| 455 |
vector<OBEdgeBase*>::iterator j; |
| 456 |
curr |= atom->GetIdx(); |
| 457 |
used = bv|curr; |
| 458 |
|
| 459 |
#define OB_RTREE_CUTOFF 20 |
| 460 |
|
| 461 |
int level=0; |
| 462 |
for (;;) |
| 463 |
{ |
| 464 |
next.Clear(); |
| 465 |
for (i = curr.NextBit(0);i != bv.EndBit();i = curr.NextBit(i)) |
| 466 |
{ |
| 467 |
atom = mol->GetAtom(i); |
| 468 |
for (nbr = atom->BeginNbrAtom(j);nbr;nbr = atom->NextNbrAtom(j)) |
| 469 |
if (!used[nbr->GetIdx()]) |
| 470 |
{ |
| 471 |
next |= nbr->GetIdx(); |
| 472 |
used |= nbr->GetIdx(); |
| 473 |
vt[nbr->GetIdx()] = new OBRTree (nbr,vt[atom->GetIdx()]); |
| 474 |
} |
| 475 |
} |
| 476 |
|
| 477 |
if (next.Empty()) |
| 478 |
break; |
| 479 |
curr = next; |
| 480 |
level++; |
| 481 |
if (level > OB_RTREE_CUTOFF) |
| 482 |
break; |
| 483 |
} |
| 484 |
#undef OB_RTREE_CUTOFF |
| 485 |
} |
| 486 |
|
| 487 |
OBRTree::OBRTree(OBAtom *atom,OBRTree *prv) |
| 488 |
{ |
| 489 |
_atom = atom; |
| 490 |
_prv = prv; |
| 491 |
} |
| 492 |
|
| 493 |
//! The supplied path is built up of OBAtom nodes, with the root atom |
| 494 |
//! the last item in the vector. |
| 495 |
void OBRTree::PathToRoot(vector<OBNodeBase*> &path) |
| 496 |
{ |
| 497 |
path.push_back(_atom); |
| 498 |
if (_prv) |
| 499 |
_prv->PathToRoot(path); |
| 500 |
} |
| 501 |
|
| 502 |
int OBRTree::GetAtomIdx() |
| 503 |
{ |
| 504 |
return(_atom->GetIdx()); |
| 505 |
} |
| 506 |
|
| 507 |
bool OBRing::findCenterAndNormal(vector3 & center, vector3 &norm1, vector3 &norm2) |
| 508 |
{ |
| 509 |
OBMol *mol= this->_parent; |
| 510 |
int j= 0; |
| 511 |
const int nA= this->_path.size(); |
| 512 |
vector3 tmp; |
| 513 |
|
| 514 |
center.Set(0.0,0.0,0.0); |
| 515 |
norm1.Set(0.0,0.0,0.0); |
| 516 |
norm2.Set(0.0,0.0,0.0); |
| 517 |
for (j = 0; j != nA; j++) |
| 518 |
{ |
| 519 |
center += (mol->GetAtom(_path[j]))->GetVector(); |
| 520 |
} |
| 521 |
center/= double(nA); |
| 522 |
|
| 523 |
for (j = 0; j != nA; j++) |
| 524 |
{ |
| 525 |
vector3 v1= (mol->GetAtom(_path[j]))->GetVector() - center; |
| 526 |
vector3 v2= (mol->GetAtom(_path[j+1==nA?0:j+1]))->GetVector() - center; |
| 527 |
tmp= cross(v1,v2); |
| 528 |
norm1+= tmp; |
| 529 |
} |
| 530 |
norm1/= double(nA); |
| 531 |
norm1.normalize(); |
| 532 |
norm2= norm1; |
| 533 |
norm2 *= -1.0; |
| 534 |
return(true); |
| 535 |
} |
| 536 |
|
| 537 |
} // end namespace OpenBabel |
| 538 |
|
| 539 |
//! \file ring.cpp |
| 540 |
//! \brief Deal with rings, find smallest set of smallest rings (SSSR). |
