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 *
#	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	#ifndef FASATOM_H
21			#define FASATOM_H
22			#include <iostream>
23			#include <vector>
24			#include "fasbond.h"
25	tim	81	#include "fasmodel.h"
26	tim	66	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	tim	77	#define FAS_PROTEINBACK_ATOM (1<<2)
36	tim	66	#define FAS_NUCLEIC_ATOM (1<<3)
37			#define FAS_AROMATIC_ATOM (1<<4)
38	tim	77	#define FAS_RING_ATOM (1<<5)
39	tim	66	#define FAS_CSTEREO_ATOM (1<<6)
40			#define FAS_ACSTEREO_ATOM (1<<7)
41			#define FAS_DONOR_ATOM (1<<8)
42	tim	77	#define FAS_ACCEPTOR_ATOM (1<<9)
43	tim	66	#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	tim	77	const int apChiral = FAS_CHIRAL_ATOM;
57	tim	66	};
58
59			class TFASAtom
60			{
61			protected:
62			unsigned int _index;
63	tim	81	unsigned int _frameIndex;
64	tim	66	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	tim	81
74			//actually we can put these properties on an element table, but we may want to change them sometime, who
75	tim	66	//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	tim	81
86	tim	66	TFASResidue *_residue;
87			TFASMolecule *_mol;
88			TFASModel * _model;
89			vector<TFASBond *> _bondList;
90			bool _pseudo;
91	tim	81
92	tim	66	void SetAtomProp(int atomProp) { _atomProp \|= atomProp;}
93			void Clear();
94			public:
95	tim	81	TFASAtom();
96	tim	66	TFASAtom(int index);
97	tim	81	TFASAtom(const TFASAtom & src);
98	tim	66	~TFASAtom();
99	tim	81
100	tim	66	//methods to set atomic information
101	tim	81	void SetIndex(unsigned int index) { _index = index, _frameIndex = 3*(index-1);}
102	tim	66	void SetAtomicNum(unsigned int atomicNum) { _atomicNum = atomicNum;}
103	tim	81	void SetNameIndex(unsigned int nameIndex) { _nameIndex = nameIndex;}
104	tim	66	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	tim	81	void SetSegnameIndex(unsigned int segnameIndex) { _segnameIndex = segnameIndex;}
110	tim	66	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	tim	81
124	tim	66	//methods to get atomic information
125			unsigned int GetIndex() { return _index;}
126	tim	81	unsigned int GetFrameIndex() { return _frameIndex;}
127	tim	66	unsigned int GetAtomicNum() { return _atomicNum;}
128			unsigned int GetNameIndex() { return _nameIndex;}
129			unsigned int GetTypeIndex() { return _typeIndex;}
130	tim	81	unsigned int GetResid() { return _resid;}
131	tim	66	unsigned int GetResidIndex() { return _residIndex;}
132			unsigned int GetResnameIndex() { return _resnameIndex;}
133			unsigned int GetChainIndex() { return _chainIndex;}
134			unsigned int GetSegnameIndex() { return _segnameIndex;}
135	tim	81
136	tim	66	TFASResidue *GetResidue() { return _residue;}
137			TFASMolecule *GetMolecule() { return _mol;}
138			TFASModel *GetModel() { return _model;}
139			bool IsPseudo() { return _pseudo;}
140	tim	81
141	tim	66	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	tim	81
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	tim	66	//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	tim	81	TFASBond GetBond(TFASAtom nbrAtom);
168	tim	66	//methods to traverse neighbor atoms
169			TFASAtom BeginNbrAtom(vector<TFASBond >::iterator &i);
170			TFASAtom NextNbrAtom(vector<TFASBond >::iterator &i);
171	tim	81
172	tim	66	//
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