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/********************************************************************** |
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bond.cpp - Handle OBBond class |
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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 "typer.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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extern OBAromaticTyper aromtyper; |
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|
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/** \class OBBond |
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\brief Bond class |
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|
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The OBBond class is straightforward in its data access and |
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modification methods. OBBonds store pointers to the atoms on each end |
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of the bond. In storing pointers to atoms instead of integer indices, |
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the necessity of having to reorder bonds when atoms are shuffled, |
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added, or delete is obviated. |
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*/ |
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|
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// ******************************* |
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// *** OBBond member functions *** |
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// ******************************* |
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|
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OBBond::OBBond() |
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{ |
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_idx=0; |
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_order=0; |
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_flags=0; |
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_bgn=NULL; |
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_end=NULL; |
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_vdata.clear(); |
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} |
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|
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OBBond::~OBBond() |
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{ |
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if (!_vdata.empty()) |
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{ |
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vector<OBGenericData*>::iterator m; |
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for (m = _vdata.begin();m != _vdata.end();m++) |
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delete *m; |
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_vdata.clear(); |
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} |
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} |
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|
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void OBBond::Set(int idx,OBAtom *begin,OBAtom *end,int order,int flags) |
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{ |
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SetIdx(idx); |
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SetBegin(begin); |
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SetEnd(end); |
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SetBO(order); |
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SetFlag(flags); |
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} |
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|
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void OBBond::SetBO(int order) |
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{ |
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_order = (char)order; |
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if (order == 5) |
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{ |
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SetAromatic(); |
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if (_bgn) |
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_bgn->SetAromatic(); |
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if (_end) |
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_end->SetAromatic(); |
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} |
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else |
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{ |
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if (order == 1) |
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SetKSingle(); |
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else if (order == 2) |
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SetKDouble(); |
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else if (order == 3) |
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SetKTriple(); |
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|
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UnsetAromatic(); |
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} |
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} |
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|
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void OBBond::SetLength(OBAtom *fixed, double length) |
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{ |
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unsigned int i; |
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OBMol *mol = (OBMol*)fixed->GetParent(); |
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vector3 v1,v2,v3,v4,v5; |
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vector<int> children; |
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|
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obErrorLog.ThrowError(__FUNCTION__, |
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"Ran OpenBabel::SetBondLength", obAuditMsg); |
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|
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int a = fixed->GetIdx(); |
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int b = GetNbrAtom(fixed)->GetIdx(); |
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|
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mol->FindChildren(children,a,b); |
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children.push_back(b); |
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|
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v1 = GetNbrAtom(fixed)->GetVector(); |
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v2 = fixed->GetVector(); |
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v3 = v1 - v2; |
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v3.normalize(); |
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v3 *= length; |
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v3 += v2; |
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v4 = v3 - v1; |
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|
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for ( i = 0 ; i < children.size() ; i++ ) |
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{ |
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v1 = mol->GetAtom(children[i])->GetVector(); |
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v1 += v4; |
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mol->GetAtom(children[i])->SetVector(v1); |
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/* |
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idx = (children[i]-1) * 3; |
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c[idx] += x; |
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c[idx+1] += y; |
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c[idx+2] += z; |
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*/ |
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} |
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} |
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|
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bool OBBond::IsRotor() |
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{ |
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return(_bgn->GetHvyValence() > 1 && _end->GetHvyValence() > 1 && |
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_order == 1 && !IsInRing() && _bgn->GetHyb() != 1 && |
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_end->GetHyb() != 1); |
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} |
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|
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bool OBBond::IsAmide() |
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{ |
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OBAtom *a1,*a2; |
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a1 = a2 = NULL; |
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|
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if (_bgn->GetAtomicNum() == 6 && _end->GetAtomicNum() == 7) |
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{ |
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a1 = (OBAtom*)_bgn; |
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a2 = (OBAtom*)_end; |
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} |
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|
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if (_bgn->GetAtomicNum() == 7 && _end->GetAtomicNum() == 6) |
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{ |
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a1 = (OBAtom*)_end; |
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a2 = (OBAtom*)_bgn; |
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} |
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|
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if (!a1 || !a2) |
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return(false); |
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if (GetBO() != 1) |
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return(false); |
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|
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OBBond *bond; |
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vector<OBEdgeBase*>::iterator i; |
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for (bond = a1->BeginBond(i);bond;bond = a1->NextBond(i)) |
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if (bond->IsCarbonyl()) |
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return(true); |
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|
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return(false); |
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} |
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|
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bool OBBond::IsPrimaryAmide() |
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{ |
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OBAtom *a1,*a2; |
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a1 = a2 = NULL; |
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|
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if (_bgn->GetAtomicNum() == 6 && _end->GetAtomicNum() == 7) |
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{ |
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a1 = (OBAtom*)_bgn; |
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a2 = (OBAtom*)_end; |
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} |
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|
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if (_bgn->GetAtomicNum() == 7 && _end->GetAtomicNum() == 6) |
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{ |
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a1 = (OBAtom*)_end; |
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a2 = (OBAtom*)_bgn; |
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} |
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|
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if (!a1 || !a2) |
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return(false); |
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if (GetBO() != 1) |
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return(false); |
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|
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OBBond *bond; |
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vector<OBEdgeBase*>::iterator i; |
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for (bond = a1->BeginBond(i);bond;bond = a1->NextBond(i)) |
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if (bond->IsCarbonyl()) |
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if (a2->GetHvyValence() == 2) |
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return(true); |
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|
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return(false); |
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} |
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|
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//! \todo Implement this properly -- currently always returns false |
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bool OBBond::IsSecondaryAmide() |
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{ |
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return(false); |
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} |
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|
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bool OBBond::IsEster() |
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{ |
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OBAtom *a1,*a2; |
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a1 = a2 = NULL; |
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|
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if (_bgn->GetAtomicNum() == 6 && _end->GetAtomicNum() == 8) |
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{ |
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a1 = (OBAtom*)_bgn; |
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a2 = (OBAtom*)_end; |
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} |
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|
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if (_bgn->GetAtomicNum() == 8 && _end->GetAtomicNum() == 6) |
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{ |
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a1 = (OBAtom*)_end; |
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a2 = (OBAtom*)_bgn; |
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} |
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|
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if (!a1 || !a2) |
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return(false); |
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if (GetBO() != 1) |
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return(false); |
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|
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OBBond *bond; |
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vector<OBEdgeBase*>::iterator i; |
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for (bond = a1->BeginBond(i);bond;bond = a1->NextBond(i)) |
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if (bond->IsCarbonyl()) |
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return(true); |
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|
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return(false); |
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} |
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|
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bool OBBond::IsCarbonyl() |
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{ |
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if (GetBO() != 2) |
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return(false); |
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|
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if ((_bgn->GetAtomicNum() == 6 && _end->GetAtomicNum() == 8) || |
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(_bgn->GetAtomicNum() == 8 && _end->GetAtomicNum() == 6)) |
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return(true); |
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|
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return(false); |
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} |
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|
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bool OBBond::IsSingle() |
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{ |
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if (HasFlag(OB_AROMATIC_BOND)) |
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return(false); |
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|
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if (!((OBMol*)GetParent())->HasAromaticPerceived()) |
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{ |
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aromtyper.AssignAromaticFlags(*((OBMol*)GetParent())); |
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} |
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|
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if ((this->GetBondOrder()==1) && !(HasFlag(OB_AROMATIC_BOND))) |
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return(true); |
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|
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return(false); |
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} |
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|
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bool OBBond::IsDouble() |
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{ |
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if (HasFlag(OB_AROMATIC_BOND)) |
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return(false); |
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|
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if (!((OBMol*)GetParent())->HasAromaticPerceived()) |
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{ |
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aromtyper.AssignAromaticFlags(*((OBMol*)GetParent())); |
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} |
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|
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if ((this->GetBondOrder()==2) && !(HasFlag(OB_AROMATIC_BOND))) |
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return(true); |
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|
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return(false); |
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} |
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|
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bool OBBond::IsTriple() |
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{ |
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if (HasFlag(OB_AROMATIC_BOND)) |
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return(false); |
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|
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if (!((OBMol*)GetParent())->HasAromaticPerceived()) |
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{ |
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aromtyper.AssignAromaticFlags(*((OBMol*)GetParent())); |
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} |
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|
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if ((this->GetBondOrder()==3) && !(HasFlag(OB_AROMATIC_BOND))) |
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return(true); |
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|
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return(false); |
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} |
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|
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bool OBBond::IsAromatic() const |
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{ |
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if (((OBBond*)this)->HasFlag(OB_AROMATIC_BOND)) |
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return(true); |
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|
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OBMol *mol = (OBMol*)((OBBond*)this)->GetParent(); |
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if (!mol->HasAromaticPerceived()) |
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{ |
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aromtyper.AssignAromaticFlags(*mol); |
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if (((OBBond*)this)->HasFlag(OB_AROMATIC_BOND)) |
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return(true); |
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} |
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|
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return(false); |
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} |
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|
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/*! This method checks if the geometry around this bond looks unsaturated |
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by measuring the torsion angles formed by all connected atoms X-start=end-Y |
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and checking that they are close to 0 or 180 degrees */ |
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bool OBBond::IsDoubleBondGeometry() |
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{ |
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double torsion; |
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OBAtom *nbrStart,*nbrEnd; |
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vector<OBEdgeBase*>::iterator i,j; |
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// We concentrate on sp2 atoms with valence up to 3 and ignore the rest (like sp1 or S,P) |
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// As this is called from PerceiveBondOrders, GetHyb() may still be undefined. |
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if (_bgn->GetHyb()==1 || _bgn->GetValence()>3|| |
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_end->GetHyb()==1 || _end->GetValence()>3) |
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return(true); |
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|
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for (nbrStart = static_cast<OBAtom*>(_bgn)->BeginNbrAtom(i); nbrStart; |
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nbrStart = static_cast<OBAtom*>(_bgn)->NextNbrAtom(i)) |
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{ |
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if (nbrStart != _end) |
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{ |
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for (nbrEnd = static_cast<OBAtom*>(_end)->BeginNbrAtom(j); |
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nbrEnd; nbrEnd = static_cast<OBAtom*>(_end)->NextNbrAtom(j)) |
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{ |
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if (nbrEnd != _bgn) |
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{ |
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torsion=fabs(CalcTorsionAngle(nbrStart->GetVector(), |
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static_cast<OBAtom*>(_bgn)->GetVector(), |
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static_cast<OBAtom*>(_end)->GetVector(), |
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nbrEnd->GetVector())); |
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|
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// >12&&<168 not enough |
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if (torsion > 15.0f && torsion < 165.0f) |
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{ |
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// Geometry does not match a double bond |
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return(false); |
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} |
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|
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} |
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} // end loop for neighbors of end |
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} |
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} // end loop for neighbors of start |
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return(true); |
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} |
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|
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void OBBond::SetKSingle() |
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{ |
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_flags &= (~(OB_KSINGLE_BOND|OB_KDOUBLE_BOND|OB_KTRIPLE_BOND)); |
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_flags |= OB_KSINGLE_BOND; |
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} |
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|
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void OBBond::SetKDouble() |
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{ |
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_flags &= (~(OB_KSINGLE_BOND|OB_KDOUBLE_BOND|OB_KTRIPLE_BOND)); |
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_flags |= OB_KDOUBLE_BOND; |
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} |
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|
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void OBBond::SetKTriple() |
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{ |
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_flags &= (~(OB_KSINGLE_BOND|OB_KDOUBLE_BOND|OB_KTRIPLE_BOND)); |
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_flags |= OB_KTRIPLE_BOND; |
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} |
| 379 |
|
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bool OBBond::IsKSingle() |
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{ |
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if (_flags & OB_KSINGLE_BOND) |
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return(true); |
| 384 |
if (!((OBMol*)GetParent())->HasKekulePerceived()) |
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((OBMol*)GetParent())->NewPerceiveKekuleBonds(); |
| 386 |
|
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return((_flags & OB_KSINGLE_BOND) != 0) ? true : false; |
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} |
| 389 |
|
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bool OBBond::IsKDouble() |
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{ |
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if (_flags & OB_KDOUBLE_BOND) |
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return(true); |
| 394 |
if (!((OBMol*)GetParent())->HasKekulePerceived()) |
| 395 |
((OBMol*)GetParent())->NewPerceiveKekuleBonds(); |
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|
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return((_flags & OB_KDOUBLE_BOND) != 0) ? true : false; |
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} |
| 399 |
|
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bool OBBond::IsKTriple() |
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{ |
| 402 |
if (_flags & OB_KTRIPLE_BOND) |
| 403 |
return(true); |
| 404 |
if (!((OBMol*)GetParent())->HasKekulePerceived()) |
| 405 |
((OBMol*)GetParent())->NewPerceiveKekuleBonds(); |
| 406 |
|
| 407 |
return((_flags & OB_KTRIPLE_BOND) != 0) ? true : false; |
| 408 |
} |
| 409 |
|
| 410 |
bool OBBond::IsInRing() const |
| 411 |
{ |
| 412 |
if (((OBBond*)this)->HasFlag(OB_RING_BOND)) |
| 413 |
return(true); |
| 414 |
|
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OBMol *mol = (OBMol*)((OBBond*)this)->GetParent(); |
| 416 |
if (!mol->HasRingAtomsAndBondsPerceived()) |
| 417 |
{ |
| 418 |
mol->FindRingAtomsAndBonds(); |
| 419 |
if (((OBBond*)this)->HasFlag(OB_RING_BOND)) |
| 420 |
return(true); |
| 421 |
} |
| 422 |
|
| 423 |
return(false); |
| 424 |
} |
| 425 |
|
| 426 |
bool OBBond::IsClosure() |
| 427 |
{ |
| 428 |
OBMol *mol = (OBMol*)GetParent(); |
| 429 |
if (!mol) |
| 430 |
return(false); |
| 431 |
if (mol->HasClosureBondsPerceived()) |
| 432 |
return(HasFlag(OB_CLOSURE_BOND)); |
| 433 |
|
| 434 |
mol->SetClosureBondsPerceived(); |
| 435 |
|
| 436 |
obErrorLog.ThrowError(__FUNCTION__, |
| 437 |
"Ran OpenBabel::PerceiveClosureBonds", obAuditMsg); |
| 438 |
|
| 439 |
OBBond *bond; |
| 440 |
OBAtom *atom,*nbr; |
| 441 |
OBBitVec uatoms,ubonds; |
| 442 |
vector<OBNodeBase*> curr,next; |
| 443 |
vector<OBNodeBase*>::iterator i; |
| 444 |
vector<OBEdgeBase*>::iterator j; |
| 445 |
|
| 446 |
uatoms.Resize(mol->NumAtoms()+1); |
| 447 |
ubonds.Resize(mol->NumAtoms()+1); |
| 448 |
|
| 449 |
for (;uatoms.CountBits() < (signed)mol->NumAtoms();) |
| 450 |
{ |
| 451 |
if (curr.empty()) |
| 452 |
for (atom = mol->BeginAtom(i);atom;atom = mol->NextAtom(i)) |
| 453 |
if (!uatoms[atom->GetIdx()]) |
| 454 |
{ |
| 455 |
uatoms |= atom->GetIdx(); |
| 456 |
curr.push_back(atom); |
| 457 |
break; |
| 458 |
} |
| 459 |
|
| 460 |
for (;!curr.empty();) |
| 461 |
{ |
| 462 |
for (i = curr.begin();i != curr.end();i++) |
| 463 |
for (nbr = ((OBAtom*)*i)->BeginNbrAtom(j);nbr;nbr = ((OBAtom*)*i)->NextNbrAtom(j)) |
| 464 |
if (!uatoms[nbr->GetIdx()]) |
| 465 |
{ |
| 466 |
uatoms |= nbr->GetIdx(); |
| 467 |
ubonds |= (*j)->GetIdx(); |
| 468 |
next.push_back(nbr); |
| 469 |
} |
| 470 |
|
| 471 |
curr = next; |
| 472 |
next.clear(); |
| 473 |
} |
| 474 |
} |
| 475 |
|
| 476 |
for (bond = mol->BeginBond(j);bond;bond = mol->NextBond(j)) |
| 477 |
if (!ubonds[bond->GetIdx()]) |
| 478 |
bond->SetClosure(); |
| 479 |
|
| 480 |
return(HasFlag(OB_CLOSURE_BOND)); |
| 481 |
} |
| 482 |
|
| 483 |
double OBBond::GetEquibLength() |
| 484 |
{ |
| 485 |
double length; |
| 486 |
OBAtom *begin, *end; |
| 487 |
// CorrectedBondRad will always return a # now |
| 488 |
// if (!CorrectedBondRad(GetBeginAtom(),rad1)) return(0.0); |
| 489 |
// if (!CorrectedBondRad(GetEndAtom(),rad2)) return(0.0); |
| 490 |
|
| 491 |
begin = GetBeginAtom(); |
| 492 |
end = GetEndAtom(); |
| 493 |
length = etab.CorrectedBondRad(begin->GetAtomicNum(), begin->GetHyb()) |
| 494 |
+ etab.CorrectedBondRad(end->GetAtomicNum(), end->GetHyb()); |
| 495 |
|
| 496 |
if (IsAromatic()) |
| 497 |
length *= 0.93; |
| 498 |
else if (GetBO() == 2) |
| 499 |
length *= 0.91; |
| 500 |
else if (GetBO() == 3) |
| 501 |
length *= 0.87; |
| 502 |
return(length); |
| 503 |
} |
| 504 |
|
| 505 |
double OBBond::GetLength() |
| 506 |
{ |
| 507 |
double d2; |
| 508 |
OBAtom *begin, *end; |
| 509 |
begin = GetBeginAtom(); |
| 510 |
end = GetEndAtom(); |
| 511 |
|
| 512 |
d2 = SQUARE(begin->GetX() - end->GetX()); |
| 513 |
d2 += SQUARE(begin->GetY() - end->GetY()); |
| 514 |
d2 += SQUARE(begin->GetZ() - end->GetZ()); |
| 515 |
|
| 516 |
return(sqrt(d2)); |
| 517 |
} |
| 518 |
|
| 519 |
// OBGenericData methods |
| 520 |
bool OBBond::HasData(string &s) |
| 521 |
//returns true if the generic attribute/value pair exists |
| 522 |
{ |
| 523 |
if (_vdata.empty()) |
| 524 |
return(false); |
| 525 |
|
| 526 |
vector<OBGenericData*>::iterator i; |
| 527 |
|
| 528 |
for (i = _vdata.begin();i != _vdata.end();i++) |
| 529 |
if ((*i)->GetAttribute() == s) |
| 530 |
return(true); |
| 531 |
|
| 532 |
return(false); |
| 533 |
} |
| 534 |
|
| 535 |
bool OBBond::HasData(const char *s) |
| 536 |
//returns true if the generic attribute/value pair exists |
| 537 |
{ |
| 538 |
if (_vdata.empty()) |
| 539 |
return(false); |
| 540 |
|
| 541 |
vector<OBGenericData*>::iterator i; |
| 542 |
|
| 543 |
for (i = _vdata.begin();i != _vdata.end();i++) |
| 544 |
if ((*i)->GetAttribute() == s) |
| 545 |
return(true); |
| 546 |
|
| 547 |
return(false); |
| 548 |
} |
| 549 |
|
| 550 |
bool OBBond::HasData(unsigned int dt) |
| 551 |
//returns true if the generic attribute/value pair exists |
| 552 |
{ |
| 553 |
if (_vdata.empty()) |
| 554 |
return(false); |
| 555 |
|
| 556 |
vector<OBGenericData*>::iterator i; |
| 557 |
|
| 558 |
for (i = _vdata.begin();i != _vdata.end();i++) |
| 559 |
if ((*i)->GetDataType() == dt) |
| 560 |
return(true); |
| 561 |
|
| 562 |
return(false); |
| 563 |
} |
| 564 |
|
| 565 |
OBGenericData *OBBond::GetData(string &s) |
| 566 |
//returns the value given an attribute |
| 567 |
{ |
| 568 |
vector<OBGenericData*>::iterator i; |
| 569 |
|
| 570 |
for (i = _vdata.begin();i != _vdata.end();i++) |
| 571 |
if ((*i)->GetAttribute() == s) |
| 572 |
return(*i); |
| 573 |
|
| 574 |
return(NULL); |
| 575 |
} |
| 576 |
|
| 577 |
OBGenericData *OBBond::GetData(const char *s) |
| 578 |
//returns the value given an attribute |
| 579 |
{ |
| 580 |
vector<OBGenericData*>::iterator i; |
| 581 |
|
| 582 |
for (i = _vdata.begin();i != _vdata.end();i++) |
| 583 |
if ((*i)->GetAttribute() == s) |
| 584 |
return(*i); |
| 585 |
|
| 586 |
return(NULL); |
| 587 |
} |
| 588 |
|
| 589 |
OBGenericData *OBBond::GetData(unsigned int dt) |
| 590 |
{ |
| 591 |
vector<OBGenericData*>::iterator i; |
| 592 |
for (i = _vdata.begin();i != _vdata.end();i++) |
| 593 |
if ((*i)->GetDataType() == dt) |
| 594 |
return(*i); |
| 595 |
return(NULL); |
| 596 |
} |
| 597 |
|
| 598 |
void OBBond::DeleteData(unsigned int dt) |
| 599 |
{ |
| 600 |
vector<OBGenericData*> vdata; |
| 601 |
vector<OBGenericData*>::iterator i; |
| 602 |
for (i = _vdata.begin();i != _vdata.end();i++) |
| 603 |
if ((*i)->GetDataType() == dt) |
| 604 |
delete *i; |
| 605 |
else |
| 606 |
vdata.push_back(*i); |
| 607 |
_vdata = vdata; |
| 608 |
} |
| 609 |
|
| 610 |
void OBBond::DeleteData(vector<OBGenericData*> &vg) |
| 611 |
{ |
| 612 |
vector<OBGenericData*> vdata; |
| 613 |
vector<OBGenericData*>::iterator i,j; |
| 614 |
|
| 615 |
bool del; |
| 616 |
for (i = _vdata.begin();i != _vdata.end();i++) |
| 617 |
{ |
| 618 |
del = false; |
| 619 |
for (j = vg.begin();j != vg.end();j++) |
| 620 |
if (*i == *j) |
| 621 |
{ |
| 622 |
del = true; |
| 623 |
break; |
| 624 |
} |
| 625 |
if (del) |
| 626 |
delete *i; |
| 627 |
else |
| 628 |
vdata.push_back(*i); |
| 629 |
} |
| 630 |
_vdata = vdata; |
| 631 |
} |
| 632 |
|
| 633 |
void OBBond::DeleteData(OBGenericData *gd) |
| 634 |
{ |
| 635 |
vector<OBGenericData*>::iterator i; |
| 636 |
for (i = _vdata.begin();i != _vdata.end();i++) |
| 637 |
if (*i == gd) |
| 638 |
{ |
| 639 |
delete *i; |
| 640 |
_vdata.erase(i); |
| 641 |
} |
| 642 |
|
| 643 |
} |
| 644 |
|
| 645 |
} // end namespace OpenBabel |
| 646 |
|
| 647 |
//! \file bond.cpp |
| 648 |
//! \brief Handle OBBond class |
