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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 <algorithm> |
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#include "fasresidue.h" |
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#include "fasatom.h" |
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#include "fasbond.h" |
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#include "bitvector.h" |
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|
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//constuctor/destructor |
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TFASResidue::TFASResidue() |
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{ |
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Clear(); |
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} |
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|
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TFASResidue::TFASResidue(const unsigned int index) |
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{ |
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Clear(); |
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_index = index; |
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} |
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|
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TFASResidue::TFASResidue(const TFASResidue &residue) |
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{ |
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_index = residue._index; |
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_resid = residue._resid; |
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_model = residue._model; |
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_mol = residue._mol; |
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_atomList = residue._atomList; |
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|
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} |
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|
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TFASResidue::~TFASResidue() |
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{ |
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Clear(); |
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} |
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|
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void TFASResidue::Clear() |
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{ |
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vector<TFASAtom *>::iterator i; |
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TFASAtom *atom; |
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for (atom=BeginAtom(i); atom!=NULL;atom=NextAtom(i)) |
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{ |
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atom->SetResidue(NULL); |
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} |
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|
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_index = -1; |
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_resid = -1; |
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_mol = NULL; |
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_model = NULL; |
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_atomList.clear(); |
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} |
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|
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//overload operator = |
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TFASResidue &TFASResidue::operator =(const TFASResidue &residue) |
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{ |
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if (this != &residue) |
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{ |
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_index = residue._index; |
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_resid = residue._resid; |
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_model = residue._model; |
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_mol = residue._mol; |
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_atomList = residue._atomList; |
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} |
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|
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return *this; |
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} |
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//method to traverse atoms |
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TFASAtom *TFASResidue::BeginAtom(vector<TFASAtom *>::iterator &i) |
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{ |
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i = _atomList.begin(); |
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if (i != _atomList.end()) |
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{ |
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return *i; |
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} |
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else |
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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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|
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TFASAtom *TFASResidue::NextAtom(vector<TFASAtom *>::iterator &i) |
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{ |
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i++; |
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if (i != _atomList.end()) |
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{ |
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return *i; |
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} |
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else |
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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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void TFASResidue::AddAtom(TFASAtom *atom) |
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{ |
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if (atom != NULL) |
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{ |
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_atomList.push_back(atom); |
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atom->SetResidue(this); |
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} |
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|
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} |
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void TFASResidue::DeleteAtom(TFASAtom *atom) |
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{ |
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vector<TFASAtom *>::iterator i; |
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i = find(_atomList.begin(), _atomList.end(), atom); |
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if (i != _atomList.end()) |
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{ |
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_atomList.erase(i); |
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} |
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|
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} |
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vector<TFASBond *> TFASResidue::GetBonds(bool exterior) |
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{ |
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vector<TFASAtom *>::iterator i; |
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vector<TFASBond *>::iterator j; |
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TFASAtom * atom; |
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TFASBond * bond; |
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vector<TFASBond *> bondList; |
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TBitVector bondIndexs; |
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|
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for (atom=BeginAtom(i); atom!=NULL; atom=NextAtom(i)) |
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{ |
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for (bond=atom->BeginBond(j); bond!=NULL; bond=atom->NextBond(j)) |
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{ |
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if (bondIndexs.IsBitOn(bond->GetIndex())) |
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{ |
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if (!exterior) |
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{ |
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if ((bond->GetNbrAtom(atom))->GetResidue() == this) |
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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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else |
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bondList.push_back(bond); |
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bondIndexs.SetBitOn(bond->GetIndex()); |
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} |
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} |
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} |
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return bondList; |
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} |
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vector<TFASBond *> TFASResidue::GetBondsByType(int bondType) |
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{ |
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vector<TFASAtom *>::iterator i; |
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vector<TFASBond *>::iterator j; |
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TFASAtom * atom; |
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TFASBond * bond; |
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vector<TFASBond *> bondList; |
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TBitVector bondIndexs; |
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|
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for (atom=BeginAtom(i); atom!=NULL; atom=NextAtom(i)) |
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{ |
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for (bond=atom->BeginBond(j); bond!=NULL; bond=atom->NextBond(j)) |
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{ |
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if (bondIndexs.IsBitOn(bond->GetIndex())) |
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{ |
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if (bond->HasBondType(bondType)) |
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bondList.push_back(bond); |
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bondIndexs.SetBitOn(bond->GetIndex()); |
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} |
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} |
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} |
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return bondList; |
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} |
