FAS/src/fasatom.h

/**********************************************************************
*           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:
*
***********************************************************************/
#ifndef FASATOM_H
#define FASATOM_H
#include <iostream>
#include <vector>
#include "fasbond.h"
#include "fasmodel.h"
using namespace std;

class TFASModel;
class TFASBond;
class TFASResidue;
class TFASMolecule;

//ATOM Property Macros
#define FAS_NORMAL_ATOM                         (1<<1)
#define FAS_PROTEINBACK_ATOM  (1<<2)
#define FAS_NUCLEIC_ATOM                        (1<<3)
#define FAS_AROMATIC_ATOM                       (1<<4)
#define FAS_RING_ATOM                       (1<<5)
#define FAS_CSTEREO_ATOM                        (1<<6)
#define FAS_ACSTEREO_ATOM                       (1<<7)
#define FAS_DONOR_ATOM                          (1<<8)
#define FAS_ACCEPTOR_ATOM                       (1<<9)
#define FAS_CHIRAL_ATOM                         (1<<10)

namespace TAtomProp
{
        const int apNormal = FAS_NORMAL_ATOM;
        const int apProtein = FAS_PROTEINBACK_ATOM;
        const int apNucleic = FAS_NUCLEIC_ATOM;
        const int apAromatic = FAS_AROMATIC_ATOM;
        const int apRing = FAS_RING_ATOM;
        const int apCStereo = FAS_CSTEREO_ATOM;
        const int apACStereo = FAS_ACSTEREO_ATOM;
        const int apDonor = FAS_DONOR_ATOM;
        const int apAcceptor = FAS_ACCEPTOR_ATOM;
        const int apChiral = FAS_CHIRAL_ATOM;
};

class TFASAtom
{
        protected:
                unsigned int _index;
    unsigned int _frameIndex;
                unsigned int _atomicNum;
                unsigned int _nameIndex;
                unsigned int _typeIndex;
                unsigned int _resid;
                unsigned int _residIndex;
                unsigned int _resnameIndex;
                unsigned int _chainIndex;
                unsigned int _segnameIndex;
                int _atomProp;

                //actually we can put these properties on an element table, but we may want to change them sometime, who
                //knows, anyway it is a trade off between space and speed
                float _mass;
                float _charge;
                float _covRadius;
                float _bondRadius;
                float _vdwRadius;
                float _maxBonds;
                float _pcharge;
                unsigned int _hyb;
                unsigned int _impval;

                TFASResidue *_residue;
                TFASMolecule *_mol;
                TFASModel * _model;
                vector<TFASBond *> _bondList;
                bool _pseudo;

                void SetAtomProp(int atomProp)  {       _atomProp |= atomProp;}
                void Clear();
        public:
    TFASAtom();
                TFASAtom(int index);
    TFASAtom(const TFASAtom & src);
                ~TFASAtom();

                //methods to set atomic information
                void SetIndex(unsigned int index)       {       _index = index, _frameIndex = 3*(index-1);}
                void SetAtomicNum(unsigned int atomicNum)       {       _atomicNum = atomicNum;}
                void SetNameIndex(unsigned int nameIndex)       {       _nameIndex = nameIndex;}
                void SetTypeIndex(unsigned int typeIndex)       {       _typeIndex = typeIndex;}
                void SetResid(unsigned int resid)       {       _resid=resid;}
                void SetResidIndex(unsigned int residIndex)     {       _residIndex = residIndex;}
                void SetResnameIndex(unsigned int resnameIndex) {       _resnameIndex = resnameIndex;}
                void SetChainIndex(unsigned int chainIndex)     {       _chainIndex = chainIndex;}
                void SetSegnameIndex(unsigned int segnameIndex) {       _segnameIndex = segnameIndex;}
                void SetResidue(TFASResidue *residue)   {       _residue = residue;}
                void SetMolecule(TFASMolecule *mol)     {       _mol = mol;}
                void SetModel(TFASModel *model) {       _model = model;}
                void SetPseudo(bool pseudo)     {       _pseudo = pseudo;}
                void SetMass(float mass)        {       _mass = mass;}
                void SetCharge(float charge)    {       _charge = charge;}
                void SetPartialCharge(float pcharge)    {       _pcharge = pcharge;}
                void SetCovalentRadius(float covRadius) {       _covRadius = covRadius;}
                void SetBondRadius(float bondRadius)    {       _bondRadius = bondRadius;}
                void SetVdwRadius(float vdwRadius)      {       _vdwRadius = vdwRadius;}
                void SetMaxBonds(float maxBonds)        {       _maxBonds=maxBonds;}
                void SetHyb(unsigned int hyb)   {       _hyb = hyb;}
                void SetImplicitValence (unsigned int impval)   {       _impval = impval;}

                //methods to get atomic information
                unsigned int GetIndex() {       return _index;}
    unsigned int GetFrameIndex()  { return _frameIndex;}
                unsigned int GetAtomicNum()     {       return _atomicNum;}
                unsigned int GetNameIndex()     { return _nameIndex;}
                unsigned int GetTypeIndex()     {       return _typeIndex;}
                unsigned int GetResid()         {       return  _resid;}
                unsigned int GetResidIndex()    {       return _residIndex;}
                unsigned int GetResnameIndex()  {       return _resnameIndex;}
                unsigned int GetChainIndex()    {       return _chainIndex;}
                unsigned int GetSegnameIndex()  {       return _segnameIndex;}

                TFASResidue *GetResidue()       {       return _residue;}
                TFASMolecule *GetMolecule()     {       return _mol;}
                TFASModel *GetModel()   {       return _model;}
                bool IsPseudo() {       return _pseudo;}

                float GetMass() {       return _mass;}
                float GetCharge()       {       return _charge;}
                float GetPartialCharge()        {       return _pcharge;}
                float GetCovalentRadius()       {       return _covRadius;}
                float GetBondRadius()   {       return _bondRadius;}
                float GetVdwRadius()    {       return _vdwRadius;}
                float GetMaxBonds()     {       return _maxBonds;}
                unsigned int GetHyb()   {       return _hyb;}
                unsigned int GetImplicitValence()       {       return _impval;}
                unsigned int GetHvyValence();
                unsigned int GetValence()       {return (unsigned int)_bondList.size();}

    //Get Coordinate and Velocity
/*
    float GetRX(int frameNum = -1);
    float GetRY(int frameNum = -1);
    float GetRZ(int frameNum = -1);
    float GetVX(int frameNum = -1);
    float GetVY(int frameNum = -1);
    float GetVZ(int frameNum = -1);
*/
                //meothds to manipulate bond
                void AddBond(TFASBond * bond);
                void DeleteBond(TFASBond *bond);
                TFASBond *BeginBond(vector<TFASBond *>::iterator &i);
                TFASBond *NextBond(vector<TFASBond *>::iterator &i);
                TFASBond *GetBond(TFASAtom *nbrAtom);
                //methods to traverse neighbor atoms
                TFASAtom *BeginNbrAtom(vector<TFASBond *>::iterator &i);
                TFASAtom *NextNbrAtom(vector<TFASBond *>::iterator &i);

                //

                int GetAtomProp() {     return _atomProp;}
                bool HasAtomProp(int atomProp)  {       return _atomProp & atomProp;}
                void SetAromatic()      {       SetAtomProp(TAtomProp::apAromatic);}
                void UnSetAromatic()    {       _atomProp &= ~TAtomProp::apAromatic;}           
                
                void SetClockwiseStereo()       
                {
                        _atomProp &= ~TAtomProp::apACStereo;
                        SetAtomProp(TAtomProp::apCStereo|TAtomProp::apChiral);
                }
                
                void SetAntiClockwiseStereo()
                {
                        _atomProp &= ~TAtomProp::apCStereo;
                        SetAtomProp(TAtomProp::apACStereo|TAtomProp::apChiral);
                }
                
                void UnSetStereo()
                {
                        _atomProp &= ~TAtomProp::apCStereo;
                        _atomProp &= ~TAtomProp::apACStereo;
                        _atomProp &= ~TAtomProp::apChiral;
                }
                
                void SetNormal()
                {
                        _atomProp &= ~TAtomProp::apProtein;
                        _atomProp &= ~TAtomProp::apNucleic;             
                }
                
                void SetProtein()
                {
                        _atomProp &= ~TAtomProp::apNormal;
                        _atomProp &= ~TAtomProp::apNucleic;
                        
                }
                
                void SetNucleic()
                {
                        _atomProp &= ~TAtomProp::apNormal;
                        _atomProp &= ~TAtomProp::apProtein;
                        
                }
                
                bool HasResidue()       { return(_residue != NULL);}
                bool IsHydrogen()       { return(_atomicNum == 1);}
                bool IsCarbon() { return(_atomicNum == 6);}
                bool IsNitrogen()       { return(_atomicNum == 7);}
                bool IsOxygen() { return(_atomicNum == 8);}
                bool IsSulfur() { return(_atomicNum == 16);}
                bool IsPhosphorus()     { return(_atomicNum == 15);}
                bool IsConnected(TFASAtom *atom);
                bool IsOneThree(TFASAtom *atom);
                bool IsOneFour(TFASAtom *atom);
                bool IsCarboxylOxygen();
                bool IsPhosphateOxygen();
                bool IsSulfateOxygen();
                bool IsNitroOxygen();
                bool IsAmideNitrogen();
                bool IsPolarHydrogen();
                bool IsNonPolarHydrogen();
                bool IsInRing();
                bool IsInRingSize(int ringSize);
                bool IsAromatic();
                bool IsAromaticNOxide();
                bool IsChiral();
                bool IsAxial();
                bool IsClockwise()      { return HasAtomProp(TAtomProp::apCStereo);}
                bool IsAntiClockwise()  { return HasAtomProp(TAtomProp::apACStereo);}
                bool HasChiralitySpecified()    { return IsClockwise()|IsAntiClockwise(); }
                bool HasAlphaBetaUnsat(bool includePandS=true);
                bool HasBondOfOrder(int order);
                int  CountBondsOfOrder(int order);
                bool HasSingleBond()               { return(HasBondOfOrder(1)); }
                bool HasDoubleBond()               { return(HasBondOfOrder(2)); }
                bool HasAromaticBond()             { return(HasBondOfOrder(4)); }               
};
#endif
Revision:	81
Committed:	Thu Aug 15 22:14:31 2002 UTC (21 years, 10 months ago) by tim
Content type:	text/plain
File size:	8558 byte(s)
Log Message:	* empty log message *
#	Content
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;
29	class TFASBond;
30	class TFASResidue;
31	class TFASMolecule;
32
33	//ATOM Property Macros
34	#define FAS_NORMAL_ATOM (1<<1)
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)
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<<9)
43	#define FAS_CHIRAL_ATOM (1<<10)
44
45	namespace TAtomProp
46	{
47	const int apNormal = FAS_NORMAL_ATOM;
48	const int apProtein = FAS_PROTEINBACK_ATOM;
49	const int apNucleic = FAS_NUCLEIC_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;
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;
67	unsigned int _resid;
68	unsigned int _residIndex;
69	unsigned int _resnameIndex;
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
75	//knows, anyway it is a trade off between space and speed
76	float _mass;
77	float _charge;
78	float _covRadius;
79	float _bondRadius;
80	float _vdwRadius;
81	float _maxBonds;
82	float _pcharge;
83	unsigned int _hyb;
84	unsigned int _impval;
85
86	TFASResidue *_residue;
87	TFASMolecule *_mol;
88	TFASModel * _model;
89	vector<TFASBond *> _bondList;
90	bool _pseudo;
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
100	//methods to set atomic information
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;}
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;}
110	void SetResidue(TFASResidue *residue) { _residue = residue;}
111	void SetMolecule(TFASMolecule *mol) { _mol = mol;}
112	void SetModel(TFASModel *model) { _model = model;}
113	void SetPseudo(bool pseudo) { _pseudo = pseudo;}
114	void SetMass(float mass) { _mass = mass;}
115	void SetCharge(float charge) { _charge = charge;}
116	void SetPartialCharge(float pcharge) { _pcharge = pcharge;}
117	void SetCovalentRadius(float covRadius) { _covRadius = covRadius;}
118	void SetBondRadius(float bondRadius) { _bondRadius = bondRadius;}
119	void SetVdwRadius(float vdwRadius) { _vdwRadius = vdwRadius;}
120	void SetMaxBonds(float maxBonds) { _maxBonds=maxBonds;}
121	void SetHyb(unsigned int hyb) { _hyb = hyb;}
122	void SetImplicitValence (unsigned int impval) { _impval = impval;}
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;}
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
136	TFASResidue *GetResidue() { return _residue;}
137	TFASMolecule *GetMolecule() { return _mol;}
138	TFASModel *GetModel() { return _model;}
139	bool IsPseudo() { return _pseudo;}
140
141	float GetMass() { return _mass;}
142	float GetCharge() { return _charge;}
143	float GetPartialCharge() { return _pcharge;}
144	float GetCovalentRadius() { return _covRadius;}
145	float GetBondRadius() { return _bondRadius;}
146	float GetVdwRadius() { return _vdwRadius;}
147	float GetMaxBonds() { return _maxBonds;}
148	unsigned int GetHyb() { return _hyb;}
149	unsigned int GetImplicitValence() { return _impval;}
150	unsigned int GetHvyValence();
151	unsigned int GetValence() {return (unsigned int)_bondList.size();}
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);
168	//methods to traverse neighbor atoms
169	TFASAtom BeginNbrAtom(vector<TFASBond >::iterator &i);
170	TFASAtom NextNbrAtom(vector<TFASBond >::iterator &i);
171
172	//
173
174	int GetAtomProp() { return _atomProp;}
175	bool HasAtomProp(int atomProp) { return _atomProp & atomProp;}
176	void SetAromatic() { SetAtomProp(TAtomProp::apAromatic);}
177	void UnSetAromatic() { _atomProp &= ~TAtomProp::apAromatic;}
178
179	void SetClockwiseStereo()
180	{
181	_atomProp &= ~TAtomProp::apACStereo;
182	SetAtomProp(TAtomProp::apCStereo\|TAtomProp::apChiral);
183	}
184
185	void SetAntiClockwiseStereo()
186	{
187	_atomProp &= ~TAtomProp::apCStereo;
188	SetAtomProp(TAtomProp::apACStereo\|TAtomProp::apChiral);
189	}
190
191	void UnSetStereo()
192	{
193	_atomProp &= ~TAtomProp::apCStereo;
194	_atomProp &= ~TAtomProp::apACStereo;
195	_atomProp &= ~TAtomProp::apChiral;
196	}
197
198	void SetNormal()
199	{
200	_atomProp &= ~TAtomProp::apProtein;
201	_atomProp &= ~TAtomProp::apNucleic;
202	}
203
204	void SetProtein()
205	{
206	_atomProp &= ~TAtomProp::apNormal;
207	_atomProp &= ~TAtomProp::apNucleic;
208
209	}
210
211	void SetNucleic()
212	{
213	_atomProp &= ~TAtomProp::apNormal;
214	_atomProp &= ~TAtomProp::apProtein;
215
216	}
217
218	bool HasResidue() { return(_residue != NULL);}
219	bool IsHydrogen() { return(_atomicNum == 1);}
220	bool IsCarbon() { return(_atomicNum == 6);}
221	bool IsNitrogen() { return(_atomicNum == 7);}
222	bool IsOxygen() { return(_atomicNum == 8);}
223	bool IsSulfur() { return(_atomicNum == 16);}
224	bool IsPhosphorus() { return(_atomicNum == 15);}
225	bool IsConnected(TFASAtom *atom);
226	bool IsOneThree(TFASAtom *atom);
227	bool IsOneFour(TFASAtom *atom);
228	bool IsCarboxylOxygen();
229	bool IsPhosphateOxygen();
230	bool IsSulfateOxygen();
231	bool IsNitroOxygen();
232	bool IsAmideNitrogen();
233	bool IsPolarHydrogen();
234	bool IsNonPolarHydrogen();
235	bool IsInRing();
236	bool IsInRingSize(int ringSize);
237	bool IsAromatic();
238	bool IsAromaticNOxide();
239	bool IsChiral();
240	bool IsAxial();
241	bool IsClockwise() { return HasAtomProp(TAtomProp::apCStereo);}
242	bool IsAntiClockwise() { return HasAtomProp(TAtomProp::apACStereo);}
243	bool HasChiralitySpecified() { return IsClockwise()\|IsAntiClockwise(); }
244	bool HasAlphaBetaUnsat(bool includePandS=true);
245	bool HasBondOfOrder(int order);
246	int CountBondsOfOrder(int order);
247	bool HasSingleBond() { return(HasBondOfOrder(1)); }
248	bool HasDoubleBond() { return(HasBondOfOrder(2)); }
249	bool HasAromaticBond() { return(HasBondOfOrder(4)); }
250	};
251	#endif