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/********************************************************************** |
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molchrg.cpp - Assign Gasteiger partial charges. |
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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 "molchrg.hpp" |
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|
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using namespace std; |
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namespace OpenBabel |
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{ |
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|
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/*! \class OBGastChrg |
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\brief Assigns Gasteiger partial charges |
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|
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The OBGastChrg class is responsible for the assignment of partial |
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charges to a molecule according to the Gasteiger charge model (sigma). When |
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the partial charge of an atom is requested and partial charges do not |
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yet exist for the molecule the OBGastChrg class will automatically be |
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called to assign charges for the molecule. If charges have been read |
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in for a molecule the following code shows how to force the |
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recalculation of partial charges: |
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\code |
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OBMol mol; |
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|
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mol.UnsetPartialChargesPerceived(); |
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FOR_ATOMS_IN_MOL(atom, mol) |
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{ |
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cout << "atom number = " << atom->GetIdx(); |
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cout << " charge = " << atom->GetPartialCharge() << endl; |
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} |
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\endcode |
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Formal charges are used as seed values of the initial charge of atoms, |
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and the partial charge is propagated to neighboring atoms. For |
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example, quaternary amines would have a +1 charge, and the effect of |
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the positive charge would be felt by neighboring atoms according to |
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the Gasteiger model (sigma). |
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|
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For more information, see: |
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J. Gasteiger & M. Marsili, "A New Model for Calculating Atomic Charges in Molecules" Tetrahedron Lett., (1978) 3181-3184. |
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*/ |
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|
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bool OBGastChrg::AssignPartialCharges(OBMol &mol) |
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{ |
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//InitialPartialCharges(mol); |
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obErrorLog.ThrowError(__FUNCTION__, |
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"Ran OpenBabel::AssignPartialCharges", obAuditMsg); |
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|
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OBAtom *atom; |
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vector<OBNodeBase*>::iterator i; |
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|
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GSVResize(mol.NumAtoms()+1); |
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double a,b,c; |
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for (atom = mol.BeginAtom(i);atom;atom = mol.NextAtom(i)) |
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{ |
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if (!GasteigerSigmaChi(atom,a,b,c)) |
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return(false); |
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_gsv[atom->GetIdx()]->SetValues(a,b,c,atom->GetPartialCharge()); |
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} |
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|
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double alpha,charge,denom; |
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unsigned j; |
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int iter; |
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OBBond *bond; |
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OBAtom *src,*dst; |
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vector<OBEdgeBase*>::iterator k; |
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alpha = 1.0; |
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for(iter = 0;iter < OB_GASTEIGER_ITERS;iter++) |
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{ |
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alpha *= OB_GASTEIGER_DAMP; |
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|
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for( j=1;j < _gsv.size();j++) |
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{ |
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charge = _gsv[j]->q; |
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_gsv[j]->chi = (_gsv[j]->c*charge+_gsv[j]->b)*charge+_gsv[j]->a; |
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} |
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|
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for (bond = mol.BeginBond(k);bond;bond = mol.NextBond(k)) |
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{ |
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src = bond->GetBeginAtom(); |
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dst = bond->GetEndAtom(); |
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|
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if (_gsv[src->GetIdx()]->chi >= _gsv[dst->GetIdx()]->chi) |
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{ |
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if (dst->IsHydrogen()) |
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denom = double(OB_GASTEIGER_DENOM); |
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else |
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denom = _gsv[dst->GetIdx()]->denom; |
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} |
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else |
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{ |
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if (src->IsHydrogen()) |
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denom = double(OB_GASTEIGER_DENOM); |
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else |
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denom = _gsv[src->GetIdx()]->denom; |
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} |
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|
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charge = (_gsv[src->GetIdx()]->chi - _gsv[dst->GetIdx()]->chi)/denom; |
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_gsv[src->GetIdx()]->q -= alpha*charge; |
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_gsv[dst->GetIdx()]->q += alpha*charge; |
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} |
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} |
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|
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for (atom = mol.BeginAtom(i);atom;atom = mol.NextAtom(i)) |
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atom->SetPartialCharge(_gsv[atom->GetIdx()]->q); |
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|
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return(true); |
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} |
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|
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void OBGastChrg::InitialPartialCharges(OBMol &mol) |
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{ |
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OBAtom *atom; |
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vector<OBNodeBase*>::iterator i; |
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|
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for (atom = mol.BeginAtom(i);atom;atom = mol.NextAtom(i)) |
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{ |
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if (atom->IsCarboxylOxygen()) |
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atom->SetPartialCharge(-0.500); |
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else if (atom->IsPhosphateOxygen() && |
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atom->GetHvyValence() == 1) |
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atom->SetPartialCharge(-0.666); |
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else if (atom->IsSulfateOxygen()) |
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atom->SetPartialCharge(-0.500); |
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else |
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atom->SetPartialCharge((double)atom->GetFormalCharge()); |
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} |
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} |
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|
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bool OBGastChrg::GasteigerSigmaChi(OBAtom *atom,double &a,double &b,double &c ) |
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{ |
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int count; |
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double val[3] = {0.0,0.0,0.0}; |
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|
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switch(atom->GetAtomicNum()) |
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{ |
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case 1: //H |
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val[0] = 0.37; |
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val[1] = 7.17; |
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val[2] = 12.85; |
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break; |
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case 6: //C |
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if (atom->GetHyb() == 3) |
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{ |
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val[0] = 0.68; |
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val[1] = 7.98; |
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val[2] = 19.04; |
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} |
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if (atom->GetHyb() == 2) |
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{ |
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val[0] = 0.98; |
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val[1] = 8.79; |
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val[2] = 19.62; |
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} |
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if (atom->GetHyb() == 1) |
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{ |
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val[0] = 1.67; |
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val[1] = 10.39; |
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val[2] = 20.57; |
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} |
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break; |
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case 7: //N |
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if (atom->GetHyb() == 3) |
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{ |
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if (atom->GetValence() == 4 || atom->GetFormalCharge()) |
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{ |
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val[0] = 0.0; |
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val[1] = 0.0; |
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val[2] = 23.72; |
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} |
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else |
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{ |
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val[0] = 2.08; |
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val[1] = 11.54; |
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val[2] = 23.72; |
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} |
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} |
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|
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if (atom->GetHyb() == 2) |
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{ |
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if (EQ(atom->GetType(),"Npl") || EQ(atom->GetType(),"Nam")) |
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{ |
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val[0] = 2.46; |
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val[1] = 12.32; |
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val[2] = 24.86; |
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} |
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else |
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{ |
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val[0] = 2.57; |
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val[1] = 12.87; |
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val[2] = 24.87; |
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} |
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} |
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|
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if (atom->GetHyb() == 1) |
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{ |
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val[0] = 3.71; |
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val[1] = 15.68; |
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val[2] = 27.11; |
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} |
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break; |
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case 8: //O |
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if (atom->GetHyb() == 3) |
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{ |
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val[0] = 2.65; |
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val[1] = 14.18; |
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val[2] = 28.49; |
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} |
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if (atom->GetHyb() == 2) |
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{ |
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val[0] = 3.75; |
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val[1] = 17.07; |
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val[2] = 31.33; |
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} |
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break; |
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case 9: //F |
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val[0] = 3.12; |
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val[1] = 14.66; |
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val[2] = 30.82; |
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break; |
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case 15: //P |
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val[0] = 1.62; |
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val[1] = 8.90; |
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val[2] = 18.10; |
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break; |
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case 16: //S |
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count = atom->CountFreeOxygens(); |
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if (count == 0 || count == 1) |
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{ |
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val[0] = 2.39; |
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val[1] = 10.14; |
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val[2] = 20.65; |
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} |
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if (count > 1) |
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{ |
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val[0] = 2.39; |
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val[1] = 12.00; |
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val[2] = 24.00; |
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} |
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/*S2? if (count == 0) {val[0] = 2.72;val[1] = 10.88;val[2] = 21.69;}*/ |
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break; |
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case 17: //Cl |
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val[0] = 2.66; |
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val[1] = 11.00; |
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val[2] = 22.04; |
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break; |
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case 35: //Br |
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val[0] = 2.77; |
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val[1] = 10.08; |
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val[2] = 19.71; |
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break; |
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case 53: //I |
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val[0] = 2.90; |
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val[1] = 9.90; |
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val[2] = 18.82; |
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break; |
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case 13: //Al |
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val[0] = 1.06; |
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val[1] = 5.47; |
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val[2] = 11.65; |
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break; |
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} |
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|
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if (!IsNearZero(val[2])) |
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{ |
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a = val[1]; |
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b = (val[2]-val[0])/2; |
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c = (val[2]+val[0])/2 - val[1]; |
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} |
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else |
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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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void OBGastChrg::GSVResize(int size) |
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{ |
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vector <GasteigerState*>::iterator i; |
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for (i = _gsv.begin();i != _gsv.end();i++) |
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delete *i; |
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_gsv.clear(); |
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|
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for (int j = 0;j < size;j++) |
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_gsv.push_back(new GasteigerState); |
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} |
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|
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OBGastChrg::~OBGastChrg() |
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{ |
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vector <GasteigerState*>::iterator i; |
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for (i = _gsv.begin();i != _gsv.end();i++) |
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delete *i; |
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} |
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|
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GasteigerState::GasteigerState() |
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{ |
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a = 0.0; |
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b = 0.0; |
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c = 0.0; |
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denom = 0.0; |
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chi = 0.0; |
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q = 0.0; |
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} |
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|
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} // end namespace OpenBabel |
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|
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//! \file molchrg.cpp |
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//! \brief Assign Gasteiger partial charges. |
