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/********************************************************************** |
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* Copyright (C) 2002-2003 by Gezelter's Group
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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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*Author: Teng Lin Email: tlin@nd.edu |
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*Date: 08/13/2002 Version: 1.0 |
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* |
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************************************************************************ |
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*Description: |
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* |
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***********************************************************************/ |
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#include <iostream> |
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#include <vector> |
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#include "fasatom.h" |
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|
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using namespace std; |
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|
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/*********************************************************************** |
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* Class TFASAtom |
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***********************************************************************/ |
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void TFASAtom::Clear() |
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{ |
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_index = 0; |
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_frameIndex = 0; |
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_atomicNum = 0; |
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_nameIndex = 0; |
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_typeIndex = 0; |
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_resid = 0; |
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_residIndex = 0; |
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_resnameIndex = 0; |
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_chainIndex = 0; |
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_segnameIndex = 0; |
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_atomProp = TAtomProp::apNormal; |
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_mass = 0; |
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_charge = 0; |
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_covRadius = 0; |
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_vdwRadius = 0; |
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_maxBonds = 0; |
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_pcharge = 0; |
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_hyb = 0; |
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_impval = 0; |
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_pseudo = false; |
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_residue = NULL; |
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_mol = NULL; |
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_model = NULL; |
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_bondList.clear(); |
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|
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} |
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|
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TFASAtom::TFASAtom() |
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{ |
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Clear(); |
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} |
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|
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TFASAtom::TFASAtom(int index) |
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{ |
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Clear(); |
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_index = index; |
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_frameIndex = (index - 1) * 3; |
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} |
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|
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TFASAtom::TFASAtom(const TFASAtom &src) |
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{ |
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|
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} |
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|
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TFASAtom::~TFASAtom() |
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{ |
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Clear(); |
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} |
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|
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// |
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unsigned int TFASAtom::GetHvyValence() |
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{ |
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unsigned int count; |
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vector<TFASBond *>::iterator i; |
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TFASAtom *atom; |
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count=0; |
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|
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for(atom = BeginNbrAtom(i); atom != NULL; atom = NextNbrAtom(i)) |
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if(!atom->IsHydrogen()) count++; |
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|
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return count; |
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} |
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|
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//Get Coordinate & Velocity |
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/* |
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float TFASAtom::GetRX(int frameNum) |
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{ |
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if (_model != NULL) |
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{ |
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return _model->GetRX(_frameIndex, frameNum); |
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} |
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else |
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{ |
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|
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} |
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} |
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|
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float TFASAtom::GetRY(int frameNum) |
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{ |
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if (_model != NULL) |
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{ |
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return _model->GetRY(_frameIndex+1, frameNum); |
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} |
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else |
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{ |
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|
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} |
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|
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} |
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|
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float TFASAtom::GetRZ(int frameNum) |
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{ |
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if (_model != NULL) |
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{ |
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return _model->GetRZ(_frameIndex+2, frameNum); |
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} |
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else |
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{ |
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|
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} |
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|
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} |
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|
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float TFASAtom::GetVX(int frameNum) |
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{ |
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if (_model != NULL) |
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{ |
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return _model->GetVX(_frameIndex, frameNum); |
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} |
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else |
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{ |
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|
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} |
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|
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} |
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|
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float TFASAtom::GetVY(int frameNum) |
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{ |
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if (_model != NULL) |
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{ |
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return _model->GetVY(_frameIndex+1, frameNum); |
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} |
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else |
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{ |
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|
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} |
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|
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} |
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float TFASAtom::GetVZ(int frameNum) |
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{ |
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if (_model != NULL) |
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{ |
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return _model->GetVZ(_frameIndex+2, frameNum); |
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} |
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else |
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{ |
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|
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} |
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|
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} |
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*/ |
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void TFASAtom::AddBond(TFASBond * bond) |
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{ |
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if (bond==NULL) |
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{ |
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|
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} |
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else |
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{ |
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_bondList.push_back(bond); |
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} |
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} |
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|
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void TFASAtom::DeleteBond(TFASBond *bond) |
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{ |
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vector<TFASBond *>::iterator i; |
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i = find(_bondList.begin(), _bondList.end(), bond); |
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if (i != _bondList.end()) |
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{ |
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_bondList.erase(i); |
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} |
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else |
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{ |
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|
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} |
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} |
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TFASBond * TFASAtom::GetBond(TFASAtom *nbrAtom) |
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{ |
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TFASBond *bond; |
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vector<TFASBond *>::iterator i; |
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if(nbrAtom == NULL) |
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{ |
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|
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} |
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else |
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{ |
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for(bond = BeginBond(i); bond != NULL; bond = NextBond(i)) |
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{ |
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if (bond->GetNbrAtom(this) == nbrAtom) return bond; |
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} |
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return NULL; |
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} |
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} |
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|
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TFASBond * TFASAtom::BeginBond(vector<TFASBond *>::iterator &i) |
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{ |
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i = _bondList.begin(); |
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return (i == _bondList.end()) ? NULL : *i; |
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} |
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|
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TFASBond * TFASAtom::NextBond(vector<TFASBond *>::iterator &i) |
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{ |
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i++; |
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return (i == _bondList.end()) ? NULL : *i; |
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} |
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TFASAtom * TFASAtom::BeginNbrAtom(vector<TFASBond *>::iterator &i) |
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{ |
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TFASBond * bond = BeginBond(i); |
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|
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if(bond != NULL) |
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{ |
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return bond->GetNbrAtom(this); |
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} |
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else |
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{ |
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|
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} |
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} |
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TFASAtom * TFASAtom::NextNbrAtom(vector<TFASBond *>::iterator &i) |
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{ |
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TFASBond * bond = NextBond(i); |
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if(bond != NULL) |
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{ |
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return bond->GetNbrAtom(this); |
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} |
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else |
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{ |
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|
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} |
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} |
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bool TFASAtom::IsConnected(TFASAtom *atom) |
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{ |
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vector<TFASBond *>::iterator i; |
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TFASAtom *nbrAtom; |
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|
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for(nbrAtom = BeginNbrAtom(i); nbrAtom != NULL; nbrAtom = NextNbrAtom(i)) |
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{ |
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if (atom == nbrAtom) |
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{ |
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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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bool TFASAtom::IsOneThree(TFASAtom *atom) |
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{ |
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TFASAtom *thisNbr; |
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TFASAtom *atomNbr; |
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vector<TFASBond *>::iterator i; |
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vector<TFASBond *>::iterator j; |
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for(thisNbr = this->BeginNbrAtom(i); thisNbr != NULL; thisNbr = this->NextNbrAtom(i)) |
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for(atomNbr = atom->BeginNbrAtom(j); thisNbr != NULL; atomNbr = atom->NextNbrAtom(j)) |
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if (atomNbr == thisNbr) return true; |
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return false; |
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|
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} |
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bool TFASAtom::IsOneFour(TFASAtom *atom) |
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{ |
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TFASAtom *thisNbr; |
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TFASAtom *atomNbr; |
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vector<TFASBond *>::iterator i; |
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vector<TFASBond *>::iterator j; |
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for(thisNbr = this->BeginNbrAtom(i); thisNbr != NULL; thisNbr = this->NextNbrAtom(i)) |
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for(atomNbr = atom->BeginNbrAtom(j); atomNbr != NULL; atomNbr = atom->NextNbrAtom(j)) |
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if (thisNbr->IsConnected(atomNbr)) return true; |
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return false; |
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|
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} |
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bool TFASAtom::IsCarboxylOxygen() |
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{ |
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if (!IsOxygen()) return false; |
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if (GetHvyValence() != 1) return false; |
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|
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TFASAtom *atom; |
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vector<TFASBond *>::iterator i; |
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for(atom=BeginNbrAtom(i); atom != NULL; atom = NextNbrAtom(i)) |
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if (atom->IsCarbon()) break; |
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if (atom == NULL) return false; |
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|
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} |
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bool TFASAtom::IsPhosphateOxygen() |
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{ |
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if (!IsOxygen()) return false; |
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} |
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bool TFASAtom::IsSulfateOxygen() |
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{ |
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} |
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bool TFASAtom::IsNitroOxygen() |
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{ |
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} |
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bool TFASAtom::IsAmideNitrogen() |
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{ |
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} |
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bool TFASAtom::IsPolarHydrogen() |
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{ |
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} |
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bool TFASAtom::IsNonPolarHydrogen() |
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{ |
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} |
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bool TFASAtom::IsInRing() |
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{ |
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} |
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bool TFASAtom::IsInRingSize(int ringSize) |
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{ |
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} |
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bool TFASAtom::IsAromatic() |
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{ |
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} |
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bool TFASAtom::IsAromaticNOxide() |
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{ |
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} |
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bool TFASAtom::IsChiral() |
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{ |
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} |
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bool TFASAtom::IsAxial() |
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{ |
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} |
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bool TFASAtom::HasAlphaBetaUnsat(bool includePandS) |
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{ |
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} |
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bool TFASAtom::HasBondOfOrder(int order) |
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{ |
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} |
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int TFASAtom::CountBondsOfOrder(int order) |
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{ |
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|
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} |
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|
