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Comparing trunk/FAS/src/fasatom.h (file contents):
Revision 66 by tim, Tue Aug 13 16:02:26 2002 UTC vs.
Revision 81 by tim, Thu Aug 15 22:14:31 2002 UTC

# Line 1 | Line 1
1 + /**********************************************************************
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   #ifndef FASATOM_H
21   #define FASATOM_H
22   #include <iostream>
23   #include <vector>
24   #include "fasbond.h"
25 + #include "fasmodel.h"
26   using namespace std;
27  
28   class TFASModel;
# Line 12 | Line 32 | class TFASMolecule;
32  
33   //ATOM Property Macros
34   #define FAS_NORMAL_ATOM                         (1<<1)
35 < #define FAS_PROTEINBACK_ATOM    (1<<2)
35 > #define FAS_PROTEINBACK_ATOM  (1<<2)
36   #define FAS_NUCLEIC_ATOM                        (1<<3)
37   #define FAS_AROMATIC_ATOM                       (1<<4)
38 < #define FAS_RING_ATOM                                   (1<<5)
38 > #define FAS_RING_ATOM                       (1<<5)
39   #define FAS_CSTEREO_ATOM                        (1<<6)
40   #define FAS_ACSTEREO_ATOM                       (1<<7)
41   #define FAS_DONOR_ATOM                          (1<<8)
42 < #define FAS_ACCEPTOR_ATOM                       (1<<8)
42 > #define FAS_ACCEPTOR_ATOM                       (1<<9)
43   #define FAS_CHIRAL_ATOM                         (1<<10)
44  
45   namespace TAtomProp
# Line 27 | Line 47 | namespace TAtomProp
47          const int apNormal = FAS_NORMAL_ATOM;
48          const int apProtein = FAS_PROTEINBACK_ATOM;
49          const int apNucleic = FAS_NUCLEIC_ATOM;
30 –        const int ap4Ring = FAS_4RING_ATOM;
31 –        const int ap3Ring = FAS_3RING_ATOM;
50          const int apAromatic = FAS_AROMATIC_ATOM;
51          const int apRing = FAS_RING_ATOM;
52          const int apCStereo = FAS_CSTEREO_ATOM;
53          const int apACStereo = FAS_ACSTEREO_ATOM;
54          const int apDonor = FAS_DONOR_ATOM;
55          const int apAcceptor = FAS_ACCEPTOR_ATOM;
56 <        const int apChiral = FAS_CHIRAL_ATOM;  
56 >        const int apChiral = FAS_CHIRAL_ATOM;
57   };
58  
59   class TFASAtom
60   {
61          protected:
62                  unsigned int _index;
63 +    unsigned int _frameIndex;
64                  unsigned int _atomicNum;
65                  unsigned int _nameIndex;
66                  unsigned int _typeIndex;
# Line 51 | Line 70 | class TFASAtom
70                  unsigned int _chainIndex;
71                  unsigned int _segnameIndex;
72                  int _atomProp;
73 <                
74 <                //actually we can put these properties on an element table, but we may want to change them sometime, who
73 >
74 >                //actually we can put these properties on an element table, but we may want to change them sometime, who
75                  //knows, anyway it is a trade off between space and speed
76                  float _mass;
77                  float _charge;
# Line 63 | Line 82 | class TFASAtom
82                  float _pcharge;
83                  unsigned int _hyb;
84                  unsigned int _impval;
85 <                
85 >
86                  TFASResidue *_residue;
87                  TFASMolecule *_mol;
88                  TFASModel * _model;
89                  vector<TFASBond *> _bondList;
90                  bool _pseudo;
91 <                
91 >
92                  void SetAtomProp(int atomProp)  {       _atomProp |= atomProp;}
93                  void Clear();
94          public:
95 +    TFASAtom();
96                  TFASAtom(int index);
97 +    TFASAtom(const TFASAtom & src);
98                  ~TFASAtom();
99 <                
99 >
100                  //methods to set atomic information
101 <                void SetIndex(unsigned int index)       {       _index = index;}
101 >                void SetIndex(unsigned int index)       {       _index = index, _frameIndex = 3*(index-1);}
102                  void SetAtomicNum(unsigned int atomicNum)       {       _atomicNum = atomicNum;}
103 <                void SetNameIndex(unsigned int nameIndex)       {       _nameIndex = nameIndex;}        
103 >                void SetNameIndex(unsigned int nameIndex)       {       _nameIndex = nameIndex;}
104                  void SetTypeIndex(unsigned int typeIndex)       {       _typeIndex = typeIndex;}
105                  void SetResid(unsigned int resid)       {       _resid=resid;}
106                  void SetResidIndex(unsigned int residIndex)     {       _residIndex = residIndex;}
107                  void SetResnameIndex(unsigned int resnameIndex) {       _resnameIndex = resnameIndex;}
108                  void SetChainIndex(unsigned int chainIndex)     {       _chainIndex = chainIndex;}
109 <                void SetSegnameIndex(unsigned int segnameIndex) {       _segnameIndex = segnameIndex;}          
109 >                void SetSegnameIndex(unsigned int segnameIndex) {       _segnameIndex = segnameIndex;}
110                  void SetResidue(TFASResidue *residue)   {       _residue = residue;}
111                  void SetMolecule(TFASMolecule *mol)     {       _mol = mol;}
112                  void SetModel(TFASModel *model) {       _model = model;}
# Line 99 | Line 120 | class TFASAtom
120                  void SetMaxBonds(float maxBonds)        {       _maxBonds=maxBonds;}
121                  void SetHyb(unsigned int hyb)   {       _hyb = hyb;}
122                  void SetImplicitValence (unsigned int impval)   {       _impval = impval;}
123 <                
123 >
124                  //methods to get atomic information
125                  unsigned int GetIndex() {       return _index;}
126 +    unsigned int GetFrameIndex()  { return _frameIndex;}
127                  unsigned int GetAtomicNum()     {       return _atomicNum;}
128                  unsigned int GetNameIndex()     { return _nameIndex;}
129                  unsigned int GetTypeIndex()     {       return _typeIndex;}
130 <                unsigned int GetResid()         {       return  _resid;}                
130 >                unsigned int GetResid()         {       return  _resid;}
131                  unsigned int GetResidIndex()    {       return _residIndex;}
132                  unsigned int GetResnameIndex()  {       return _resnameIndex;}
133                  unsigned int GetChainIndex()    {       return _chainIndex;}
134                  unsigned int GetSegnameIndex()  {       return _segnameIndex;}
135 <                
135 >
136                  TFASResidue *GetResidue()       {       return _residue;}
137                  TFASMolecule *GetMolecule()     {       return _mol;}
138                  TFASModel *GetModel()   {       return _model;}
139                  bool IsPseudo() {       return _pseudo;}
140 <                
140 >
141                  float GetMass() {       return _mass;}
142                  float GetCharge()       {       return _charge;}
143                  float GetPartialCharge()        {       return _pcharge;}
# Line 127 | Line 149 | class TFASAtom
149                  unsigned int GetImplicitValence()       {       return _impval;}
150                  unsigned int GetHvyValence();
151                  unsigned int GetValence()       {return (unsigned int)_bondList.size();}
152 <                                
152 >
153 >    //Get Coordinate and Velocity
154 > /*
155 >    float GetRX(int frameNum = -1);
156 >    float GetRY(int frameNum = -1);
157 >    float GetRZ(int frameNum = -1);
158 >    float GetVX(int frameNum = -1);
159 >    float GetVY(int frameNum = -1);
160 >    float GetVZ(int frameNum = -1);
161 > */
162                  //meothds to manipulate bond
163                  void AddBond(TFASBond * bond);
164                  void DeleteBond(TFASBond *bond);
165                  TFASBond *BeginBond(vector<TFASBond *>::iterator &i);
166                  TFASBond *NextBond(vector<TFASBond *>::iterator &i);
167 <                TFASBond *GetBond(TFASAtom *nbrAtom);          
167 >                TFASBond *GetBond(TFASAtom *nbrAtom);
168                  //methods to traverse neighbor atoms
169                  TFASAtom *BeginNbrAtom(vector<TFASBond *>::iterator &i);
170                  TFASAtom *NextNbrAtom(vector<TFASBond *>::iterator &i);
171 <                                
171 >
172                  //
173  
174                  int GetAtomProp() {     return _atomProp;}

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