--- trunk/FAS/src/fasatom.cpp	2002/08/13 16:02:26	66
+++ trunk/FAS/src/fasatom.cpp	2002/08/15 22:14:31	81
@@ -1,12 +1,35 @@
+/**********************************************************************
+*           Copyright (C) 2002-2003 by Gezelter's Group
+*This program is free software; you can redistribute it and/or modify
+*it under the terms of the GNU General Public License as published by
+*the Free Software Foundation version 2 of the License.
+*
+*This program is distributed in the hope that it will be useful,
+*but WITHOUT ANY WARRANTY; without even the implied warranty of
+*MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+*GNU General Public License for more details.
+*
+************************************************************************
+*Author: Teng Lin               Email:  tlin@nd.edu
+*Date: 08/13/2002               Version: 1.0
+*
+************************************************************************
+*Description:
+*
+***********************************************************************/
 #include <iostream>
 #include <vector>
 #include "fasatom.h"
 
 using namespace std;
 
+/***********************************************************************
+* Class TFASAtom
+***********************************************************************/
 void TFASAtom::Clear()
 {
 	_index = 0;
+  _frameIndex = 0;
 	_atomicNum = 0;
 	_nameIndex = 0;
 	_typeIndex = 0;
@@ -28,44 +51,134 @@ void TFASAtom::Clear()
 	_residue = NULL;
 	_mol = NULL;
 	_model = NULL;
-	_bondList.clear();	
-	
+	_bondList.clear();
+
 }
 
+TFASAtom::TFASAtom()
+{
+  Clear();
+}
+
 TFASAtom::TFASAtom(int index)
 {
 	Clear();
 	_index = index;
+  _frameIndex = (index - 1) * 3;
 }
 
+TFASAtom::TFASAtom(const TFASAtom &src)
+{
+
+}
+
 TFASAtom::~TFASAtom()
 {
-	
+  Clear();
 }
 
+//
 unsigned int TFASAtom::GetHvyValence()
 {
 	unsigned int count;
 	vector<TFASBond *>::iterator i;
 	TFASAtom *atom;
 	count=0;
-	
+
 	for(atom = BeginNbrAtom(i); atom != NULL; atom = NextNbrAtom(i))
 		if(!atom->IsHydrogen()) count++;
-	
+
 	return count;
 }
 
+//Get Coordinate & Velocity
+/*
+float TFASAtom::GetRX(int frameNum)
+{
+  if (_model != NULL)
+  {
+    return _model->GetRX(_frameIndex, frameNum);
+  }
+  else
+  {
+
+  }
+}
+
+float TFASAtom::GetRY(int frameNum)
+{
+  if (_model != NULL)
+  {
+    return _model->GetRY(_frameIndex+1, frameNum);
+  }
+  else
+  {
+
+  }
+
+}
+
+float TFASAtom::GetRZ(int frameNum)
+{
+  if (_model != NULL)
+  {
+    return _model->GetRZ(_frameIndex+2, frameNum);
+  }
+  else
+  {
+
+  }
+
+}
+
+float TFASAtom::GetVX(int frameNum)
+{
+  if (_model != NULL)
+  {
+    return _model->GetVX(_frameIndex, frameNum);
+  }
+  else
+  {
+
+  }
+
+}
+
+float TFASAtom::GetVY(int frameNum)
+{
+  if (_model != NULL)
+  {
+    return _model->GetVY(_frameIndex+1, frameNum);
+  }
+  else
+  {
+
+  }
+
+}
+
+float TFASAtom::GetVZ(int frameNum)
+{
+  if (_model != NULL)
+  {
+    return _model->GetVZ(_frameIndex+2, frameNum);
+  }
+  else
+  {
+
+  }
+
+}
+*/
 void TFASAtom::AddBond(TFASBond * bond)
 {
 	if (bond==NULL)
 	{
-		
+
 	}
 	else
 	{
 		_bondList.push_back(bond);
-		back(bond);
 	}
 }
 
@@ -206,7 +319,9 @@ bool TFASAtom::IsPhosphateOxygen()
 
 bool TFASAtom::IsPhosphateOxygen()
 {
+  if (!IsOxygen()) return false;
 
+
 }
 
 bool TFASAtom::IsSulfateOxygen()
@@ -264,7 +379,7 @@ bool TFASAtom::IsAxial()
 
 }
 
-bool TFASAtom::HasAlphaBetaUnsat(bool includePandS=true)
+bool TFASAtom::HasAlphaBetaUnsat(bool includePandS)
 {
 
 }