FAS/src/fasatom.cpp

/**********************************************************************
*           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;
        _resid = 0;
        _residIndex = 0;
        _resnameIndex = 0;
        _chainIndex = 0;
        _segnameIndex = 0;
        _atomProp = TAtomProp::apNormal;
        _mass = 0;
        _charge = 0;
        _covRadius = 0;
        _vdwRadius = 0;
        _maxBonds = 0;
        _pcharge = 0;
        _hyb = 0;
        _impval = 0;
        _pseudo = false;
        _residue = NULL;
        _mol = NULL;
        _model = NULL;
        _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);
        }
}

void TFASAtom::DeleteBond(TFASBond *bond)
{
        vector<TFASBond *>::iterator i;
        i = find(_bondList.begin(), _bondList.end(), bond);
        if (i != _bondList.end())
        {
                _bondList.erase(i);
        }
        else
        {
        
        }
}

TFASBond * TFASAtom::GetBond(TFASAtom *nbrAtom)
{
        TFASBond *bond;
        vector<TFASBond *>::iterator i;
        if(nbrAtom == NULL)
        {
        
        }
        else 
        {
        
                for(bond = BeginBond(i); bond != NULL; bond = NextBond(i))
                {
                        if (bond->GetNbrAtom(this) == nbrAtom) return bond;
                }
                return NULL;
        }
}

TFASBond * TFASAtom::BeginBond(vector<TFASBond *>::iterator &i)
{
        i = _bondList.begin();
        return (i == _bondList.end()) ? NULL : *i;
}

TFASBond * TFASAtom::NextBond(vector<TFASBond *>::iterator &i)
{
        i++;
        return (i == _bondList.end()) ? NULL : *i;
}

TFASAtom * TFASAtom::BeginNbrAtom(vector<TFASBond *>::iterator &i)
{
        TFASBond * bond = BeginBond(i);
        
        if(bond != NULL)
        {
                return bond->GetNbrAtom(this);
        }
        else
        {
        
        }
}

TFASAtom * TFASAtom::NextNbrAtom(vector<TFASBond *>::iterator &i)
{
        TFASBond * bond = NextBond(i);
        
        if(bond != NULL)
        {
                return bond->GetNbrAtom(this);
        }
        else
        {
        
        }
}

bool TFASAtom::IsConnected(TFASAtom *atom)
{
        vector<TFASBond *>::iterator i;
        TFASAtom *nbrAtom;
        
        for(nbrAtom = BeginNbrAtom(i); nbrAtom != NULL; nbrAtom = NextNbrAtom(i))
        {
                if (atom == nbrAtom)
                {
                        return true;
                }               
        }
        
        return false;
}

bool TFASAtom::IsOneThree(TFASAtom *atom)
{
        TFASAtom *thisNbr;
        TFASAtom *atomNbr;
        vector<TFASBond *>::iterator i;
        vector<TFASBond *>::iterator j;
        
        for(thisNbr = this->BeginNbrAtom(i); thisNbr != NULL; thisNbr = this->NextNbrAtom(i))
                for(atomNbr = atom->BeginNbrAtom(j); thisNbr != NULL; atomNbr = atom->NextNbrAtom(j))
                        if (atomNbr == thisNbr) return true;
                
        return false;
                
}

bool TFASAtom::IsOneFour(TFASAtom *atom)
{
        TFASAtom *thisNbr;
        TFASAtom *atomNbr;
        vector<TFASBond *>::iterator i;
        vector<TFASBond *>::iterator j;
        
        for(thisNbr = this->BeginNbrAtom(i); thisNbr != NULL; thisNbr = this->NextNbrAtom(i))
                for(atomNbr = atom->BeginNbrAtom(j); atomNbr != NULL; atomNbr = atom->NextNbrAtom(j))
                        if (thisNbr->IsConnected(atomNbr)) return true;
                
        return false;

}

bool TFASAtom::IsCarboxylOxygen()
{
        if (!IsOxygen())        return false;
        if (GetHvyValence() != 1) return false;
        
        TFASAtom *atom;
        vector<TFASBond *>::iterator i;
        
        for(atom=BeginNbrAtom(i); atom != NULL; atom = NextNbrAtom(i))
                if (atom->IsCarbon()) break;
        
        if (atom == NULL) return false;
        
                                
}

bool TFASAtom::IsPhosphateOxygen()
{
  if (!IsOxygen()) return false;


}

bool TFASAtom::IsSulfateOxygen()
{

}

bool TFASAtom::IsNitroOxygen()
{

}

bool TFASAtom::IsAmideNitrogen()
{

}

bool TFASAtom::IsPolarHydrogen()
{

}

bool TFASAtom::IsNonPolarHydrogen()
{

}

bool TFASAtom::IsInRing()
{

}

bool TFASAtom::IsInRingSize(int ringSize)
{

}

bool TFASAtom::IsAromatic()
{

}

bool TFASAtom::IsAromaticNOxide()
{

}

bool TFASAtom::IsChiral()
{

}

bool TFASAtom::IsAxial()
{

}

bool TFASAtom::HasAlphaBetaUnsat(bool includePandS)
{

}

bool TFASAtom::HasBondOfOrder(int order)
{

}

int TFASAtom::CountBondsOfOrder(int order)
{

}

Revision:	81
Committed:	Thu Aug 15 22:14:31 2002 UTC (21 years, 10 months ago) by tim
File size:	6108 byte(s)
Log Message:	* empty log message *
#	User	Rev	Content
1	tim	77	/**********************************************************************
2			* Copyright (C) 2002-2003 by Gezelter's Group
3			*This program is free software; you can redistribute it and/or modify
4			*it under the terms of the GNU General Public License as published by
5			*the Free Software Foundation version 2 of the License.
6			*
7			*This program is distributed in the hope that it will be useful,
8			*but WITHOUT ANY WARRANTY; without even the implied warranty of
9			*MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
10			*GNU General Public License for more details.
11			*
12			************************************************************************
13			*Author: Teng Lin Email: tlin@nd.edu
14			*Date: 08/13/2002 Version: 1.0
15			*
16			************************************************************************
17			*Description:
18			*
19			***********************************************************************/
20	tim	66	#include <iostream>
21			#include <vector>
22			#include "fasatom.h"
23
24			using namespace std;
25
26	tim	81	/***********************************************************************
27			* Class TFASAtom
28			***********************************************************************/
29	tim	66	void TFASAtom::Clear()
30			{
31			_index = 0;
32	tim	81	_frameIndex = 0;
33	tim	66	_atomicNum = 0;
34			_nameIndex = 0;
35			_typeIndex = 0;
36			_resid = 0;
37			_residIndex = 0;
38			_resnameIndex = 0;
39			_chainIndex = 0;
40			_segnameIndex = 0;
41			_atomProp = TAtomProp::apNormal;
42			_mass = 0;
43			_charge = 0;
44			_covRadius = 0;
45			_vdwRadius = 0;
46			_maxBonds = 0;
47			_pcharge = 0;
48			_hyb = 0;
49			_impval = 0;
50			_pseudo = false;
51			_residue = NULL;
52			_mol = NULL;
53			_model = NULL;
54	tim	81	_bondList.clear();
55
56	tim	66	}
57
58	tim	81	TFASAtom::TFASAtom()
59			{
60			Clear();
61			}
62
63	tim	66	TFASAtom::TFASAtom(int index)
64			{
65			Clear();
66			_index = index;
67	tim	81	_frameIndex = (index - 1) * 3;
68	tim	66	}
69
70	tim	81	TFASAtom::TFASAtom(const TFASAtom &src)
71			{
72
73			}
74
75	tim	66	TFASAtom::~TFASAtom()
76			{
77	tim	81	Clear();
78	tim	66	}
79
80	tim	81	//
81	tim	66	unsigned int TFASAtom::GetHvyValence()
82			{
83			unsigned int count;
84			vector<TFASBond *>::iterator i;
85			TFASAtom *atom;
86			count=0;
87	tim	81
88	tim	66	for(atom = BeginNbrAtom(i); atom != NULL; atom = NextNbrAtom(i))
89			if(!atom->IsHydrogen()) count++;
90	tim	81
91	tim	66	return count;
92			}
93
94	tim	81	//Get Coordinate & Velocity
95			/*
96			float TFASAtom::GetRX(int frameNum)
97			{
98			if (_model != NULL)
99			{
100			return _model->GetRX(_frameIndex, frameNum);
101			}
102			else
103			{
104
105			}
106			}
107
108			float TFASAtom::GetRY(int frameNum)
109			{
110			if (_model != NULL)
111			{
112			return _model->GetRY(_frameIndex+1, frameNum);
113			}
114			else
115			{
116
117			}
118
119			}
120
121			float TFASAtom::GetRZ(int frameNum)
122			{
123			if (_model != NULL)
124			{
125			return _model->GetRZ(_frameIndex+2, frameNum);
126			}
127			else
128			{
129
130			}
131
132			}
133
134			float TFASAtom::GetVX(int frameNum)
135			{
136			if (_model != NULL)
137			{
138			return _model->GetVX(_frameIndex, frameNum);
139			}
140			else
141			{
142
143			}
144
145			}
146
147			float TFASAtom::GetVY(int frameNum)
148			{
149			if (_model != NULL)
150			{
151			return _model->GetVY(_frameIndex+1, frameNum);
152			}
153			else
154			{
155
156			}
157
158			}
159
160			float TFASAtom::GetVZ(int frameNum)
161			{
162			if (_model != NULL)
163			{
164			return _model->GetVZ(_frameIndex+2, frameNum);
165			}
166			else
167			{
168
169			}
170
171			}
172			*/
173	tim	66	void TFASAtom::AddBond(TFASBond * bond)
174			{
175			if (bond==NULL)
176			{
177	tim	81
178	tim	66	}
179			else
180			{
181			_bondList.push_back(bond);
182			}
183			}
184
185			void TFASAtom::DeleteBond(TFASBond *bond)
186			{
187			vector<TFASBond *>::iterator i;
188			i = find(_bondList.begin(), _bondList.end(), bond);
189			if (i != _bondList.end())
190			{
191			_bondList.erase(i);
192			}
193			else
194			{
195
196			}
197			}
198
199			TFASBond * TFASAtom::GetBond(TFASAtom *nbrAtom)
200			{
201			TFASBond *bond;
202			vector<TFASBond *>::iterator i;
203			if(nbrAtom == NULL)
204			{
205
206			}
207			else
208			{
209
210			for(bond = BeginBond(i); bond != NULL; bond = NextBond(i))
211			{
212			if (bond->GetNbrAtom(this) == nbrAtom) return bond;
213			}
214			return NULL;
215			}
216			}
217
218			TFASBond * TFASAtom::BeginBond(vector<TFASBond *>::iterator &i)
219			{
220			i = _bondList.begin();
221			return (i == _bondList.end()) ? NULL : *i;
222			}
223
224			TFASBond * TFASAtom::NextBond(vector<TFASBond *>::iterator &i)
225			{
226			i++;
227			return (i == _bondList.end()) ? NULL : *i;
228			}
229
230			TFASAtom * TFASAtom::BeginNbrAtom(vector<TFASBond *>::iterator &i)
231			{
232			TFASBond * bond = BeginBond(i);
233
234			if(bond != NULL)
235			{
236			return bond->GetNbrAtom(this);
237			}
238			else
239			{
240
241			}
242			}
243
244			TFASAtom * TFASAtom::NextNbrAtom(vector<TFASBond *>::iterator &i)
245			{
246			TFASBond * bond = NextBond(i);
247
248			if(bond != NULL)
249			{
250			return bond->GetNbrAtom(this);
251			}
252			else
253			{
254
255			}
256			}
257
258			bool TFASAtom::IsConnected(TFASAtom *atom)
259			{
260			vector<TFASBond *>::iterator i;
261			TFASAtom *nbrAtom;
262
263			for(nbrAtom = BeginNbrAtom(i); nbrAtom != NULL; nbrAtom = NextNbrAtom(i))
264			{
265			if (atom == nbrAtom)
266			{
267			return true;
268			}
269			}
270
271			return false;
272			}
273
274			bool TFASAtom::IsOneThree(TFASAtom *atom)
275			{
276			TFASAtom *thisNbr;
277			TFASAtom *atomNbr;
278			vector<TFASBond *>::iterator i;
279			vector<TFASBond *>::iterator j;
280
281			for(thisNbr = this->BeginNbrAtom(i); thisNbr != NULL; thisNbr = this->NextNbrAtom(i))
282			for(atomNbr = atom->BeginNbrAtom(j); thisNbr != NULL; atomNbr = atom->NextNbrAtom(j))
283			if (atomNbr == thisNbr) return true;
284
285			return false;
286
287			}
288
289			bool TFASAtom::IsOneFour(TFASAtom *atom)
290			{
291			TFASAtom *thisNbr;
292			TFASAtom *atomNbr;
293			vector<TFASBond *>::iterator i;
294			vector<TFASBond *>::iterator j;
295
296			for(thisNbr = this->BeginNbrAtom(i); thisNbr != NULL; thisNbr = this->NextNbrAtom(i))
297			for(atomNbr = atom->BeginNbrAtom(j); atomNbr != NULL; atomNbr = atom->NextNbrAtom(j))
298			if (thisNbr->IsConnected(atomNbr)) return true;
299
300			return false;
301
302			}
303
304			bool TFASAtom::IsCarboxylOxygen()
305			{
306			if (!IsOxygen()) return false;
307			if (GetHvyValence() != 1) return false;
308
309			TFASAtom *atom;
310			vector<TFASBond *>::iterator i;
311
312			for(atom=BeginNbrAtom(i); atom != NULL; atom = NextNbrAtom(i))
313			if (atom->IsCarbon()) break;
314
315			if (atom == NULL) return false;
316
317
318			}
319
320			bool TFASAtom::IsPhosphateOxygen()
321			{
322	tim	81	if (!IsOxygen()) return false;
323	tim	66
324	tim	81
325	tim	66	}
326
327			bool TFASAtom::IsSulfateOxygen()
328			{
329
330			}
331
332			bool TFASAtom::IsNitroOxygen()
333			{
334
335			}
336
337			bool TFASAtom::IsAmideNitrogen()
338			{
339
340			}
341
342			bool TFASAtom::IsPolarHydrogen()
343			{
344
345			}
346
347			bool TFASAtom::IsNonPolarHydrogen()
348			{
349
350			}
351
352			bool TFASAtom::IsInRing()
353			{
354
355			}
356
357			bool TFASAtom::IsInRingSize(int ringSize)
358			{
359
360			}
361
362			bool TFASAtom::IsAromatic()
363			{
364
365			}
366
367			bool TFASAtom::IsAromaticNOxide()
368			{
369
370			}
371
372			bool TFASAtom::IsChiral()
373			{
374
375			}
376
377			bool TFASAtom::IsAxial()
378			{
379
380			}
381
382	tim	77	bool TFASAtom::HasAlphaBetaUnsat(bool includePandS)
383	tim	66	{
384
385			}
386
387			bool TFASAtom::HasBondOfOrder(int order)
388			{
389
390			}
391
392			int TFASAtom::CountBondsOfOrder(int order)
393			{
394
395			}
396