FAS/src/fasatom.h

#ifndef FASATOM_H
#define FASATOM_H
#include <iostream>
#include <vector>
#include "fasbond.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<<8)
#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 ap4Ring = FAS_4RING_ATOM;
        const int ap3Ring = FAS_3RING_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 _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(int index);
                ~TFASAtom();
                
                //methods to set atomic information
                void SetIndex(unsigned int index)       {       _index = index;}
                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 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();}
                                
                //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:	66
Committed:	Tue Aug 13 16:02:26 2002 UTC (21 years, 10 months ago) by tim
Content type:	text/plain
File size:	7307 byte(s)
Log Message:	flexible atom selection
#	User	Rev	Content
1	tim	66	#ifndef FASATOM_H
2			#define FASATOM_H
3			#include <iostream>
4			#include <vector>
5			#include "fasbond.h"
6			using namespace std;
7
8			class TFASModel;
9			class TFASBond;
10			class TFASResidue;
11			class TFASMolecule;
12
13			//ATOM Property Macros
14			#define FAS_NORMAL_ATOM (1<<1)
15			#define FAS_PROTEINBACK_ATOM (1<<2)
16			#define FAS_NUCLEIC_ATOM (1<<3)
17			#define FAS_AROMATIC_ATOM (1<<4)
18			#define FAS_RING_ATOM (1<<5)
19			#define FAS_CSTEREO_ATOM (1<<6)
20			#define FAS_ACSTEREO_ATOM (1<<7)
21			#define FAS_DONOR_ATOM (1<<8)
22			#define FAS_ACCEPTOR_ATOM (1<<8)
23			#define FAS_CHIRAL_ATOM (1<<10)
24
25			namespace TAtomProp
26			{
27			const int apNormal = FAS_NORMAL_ATOM;
28			const int apProtein = FAS_PROTEINBACK_ATOM;
29			const int apNucleic = FAS_NUCLEIC_ATOM;
30			const int ap4Ring = FAS_4RING_ATOM;
31			const int ap3Ring = FAS_3RING_ATOM;
32			const int apAromatic = FAS_AROMATIC_ATOM;
33			const int apRing = FAS_RING_ATOM;
34			const int apCStereo = FAS_CSTEREO_ATOM;
35			const int apACStereo = FAS_ACSTEREO_ATOM;
36			const int apDonor = FAS_DONOR_ATOM;
37			const int apAcceptor = FAS_ACCEPTOR_ATOM;
38			const int apChiral = FAS_CHIRAL_ATOM;
39			};
40
41			class TFASAtom
42			{
43			protected:
44			unsigned int _index;
45			unsigned int _atomicNum;
46			unsigned int _nameIndex;
47			unsigned int _typeIndex;
48			unsigned int _resid;
49			unsigned int _residIndex;
50			unsigned int _resnameIndex;
51			unsigned int _chainIndex;
52			unsigned int _segnameIndex;
53			int _atomProp;
54
55			//actually we can put these properties on an element table, but we may want to change them sometime, who
56			//knows, anyway it is a trade off between space and speed
57			float _mass;
58			float _charge;
59			float _covRadius;
60			float _bondRadius;
61			float _vdwRadius;
62			float _maxBonds;
63			float _pcharge;
64			unsigned int _hyb;
65			unsigned int _impval;
66
67			TFASResidue *_residue;
68			TFASMolecule *_mol;
69			TFASModel * _model;
70			vector<TFASBond *> _bondList;
71			bool _pseudo;
72
73			void SetAtomProp(int atomProp) { _atomProp \|= atomProp;}
74			void Clear();
75			public:
76			TFASAtom(int index);
77			~TFASAtom();
78
79			//methods to set atomic information
80			void SetIndex(unsigned int index) { _index = index;}
81			void SetAtomicNum(unsigned int atomicNum) { _atomicNum = atomicNum;}
82			void SetNameIndex(unsigned int nameIndex) { _nameIndex = nameIndex;}
83			void SetTypeIndex(unsigned int typeIndex) { _typeIndex = typeIndex;}
84			void SetResid(unsigned int resid) { _resid=resid;}
85			void SetResidIndex(unsigned int residIndex) { _residIndex = residIndex;}
86			void SetResnameIndex(unsigned int resnameIndex) { _resnameIndex = resnameIndex;}
87			void SetChainIndex(unsigned int chainIndex) { _chainIndex = chainIndex;}
88			void SetSegnameIndex(unsigned int segnameIndex) { _segnameIndex = segnameIndex;}
89			void SetResidue(TFASResidue *residue) { _residue = residue;}
90			void SetMolecule(TFASMolecule *mol) { _mol = mol;}
91			void SetModel(TFASModel *model) { _model = model;}
92			void SetPseudo(bool pseudo) { _pseudo = pseudo;}
93			void SetMass(float mass) { _mass = mass;}
94			void SetCharge(float charge) { _charge = charge;}
95			void SetPartialCharge(float pcharge) { _pcharge = pcharge;}
96			void SetCovalentRadius(float covRadius) { _covRadius = covRadius;}
97			void SetBondRadius(float bondRadius) { _bondRadius = bondRadius;}
98			void SetVdwRadius(float vdwRadius) { _vdwRadius = vdwRadius;}
99			void SetMaxBonds(float maxBonds) { _maxBonds=maxBonds;}
100			void SetHyb(unsigned int hyb) { _hyb = hyb;}
101			void SetImplicitValence (unsigned int impval) { _impval = impval;}
102
103			//methods to get atomic information
104			unsigned int GetIndex() { return _index;}
105			unsigned int GetAtomicNum() { return _atomicNum;}
106			unsigned int GetNameIndex() { return _nameIndex;}
107			unsigned int GetTypeIndex() { return _typeIndex;}
108			unsigned int GetResid() { return _resid;}
109			unsigned int GetResidIndex() { return _residIndex;}
110			unsigned int GetResnameIndex() { return _resnameIndex;}
111			unsigned int GetChainIndex() { return _chainIndex;}
112			unsigned int GetSegnameIndex() { return _segnameIndex;}
113
114			TFASResidue *GetResidue() { return _residue;}
115			TFASMolecule *GetMolecule() { return _mol;}
116			TFASModel *GetModel() { return _model;}
117			bool IsPseudo() { return _pseudo;}
118
119			float GetMass() { return _mass;}
120			float GetCharge() { return _charge;}
121			float GetPartialCharge() { return _pcharge;}
122			float GetCovalentRadius() { return _covRadius;}
123			float GetBondRadius() { return _bondRadius;}
124			float GetVdwRadius() { return _vdwRadius;}
125			float GetMaxBonds() { return _maxBonds;}
126			unsigned int GetHyb() { return _hyb;}
127			unsigned int GetImplicitValence() { return _impval;}
128			unsigned int GetHvyValence();
129			unsigned int GetValence() {return (unsigned int)_bondList.size();}
130
131			//meothds to manipulate bond
132			void AddBond(TFASBond * bond);
133			void DeleteBond(TFASBond *bond);
134			TFASBond BeginBond(vector<TFASBond >::iterator &i);
135			TFASBond NextBond(vector<TFASBond >::iterator &i);
136			TFASBond GetBond(TFASAtom nbrAtom);
137			//methods to traverse neighbor atoms
138			TFASAtom BeginNbrAtom(vector<TFASBond >::iterator &i);
139			TFASAtom NextNbrAtom(vector<TFASBond >::iterator &i);
140
141			//
142
143			int GetAtomProp() { return _atomProp;}
144			bool HasAtomProp(int atomProp) { return _atomProp & atomProp;}
145			void SetAromatic() { SetAtomProp(TAtomProp::apAromatic);}
146			void UnSetAromatic() { _atomProp &= ~TAtomProp::apAromatic;}
147
148			void SetClockwiseStereo()
149			{
150			_atomProp &= ~TAtomProp::apACStereo;
151			SetAtomProp(TAtomProp::apCStereo\|TAtomProp::apChiral);
152			}
153
154			void SetAntiClockwiseStereo()
155			{
156			_atomProp &= ~TAtomProp::apCStereo;
157			SetAtomProp(TAtomProp::apACStereo\|TAtomProp::apChiral);
158			}
159
160			void UnSetStereo()
161			{
162			_atomProp &= ~TAtomProp::apCStereo;
163			_atomProp &= ~TAtomProp::apACStereo;
164			_atomProp &= ~TAtomProp::apChiral;
165			}
166
167			void SetNormal()
168			{
169			_atomProp &= ~TAtomProp::apProtein;
170			_atomProp &= ~TAtomProp::apNucleic;
171			}
172
173			void SetProtein()
174			{
175			_atomProp &= ~TAtomProp::apNormal;
176			_atomProp &= ~TAtomProp::apNucleic;
177
178			}
179
180			void SetNucleic()
181			{
182			_atomProp &= ~TAtomProp::apNormal;
183			_atomProp &= ~TAtomProp::apProtein;
184
185			}
186
187			bool HasResidue() { return(_residue != NULL);}
188			bool IsHydrogen() { return(_atomicNum == 1);}
189			bool IsCarbon() { return(_atomicNum == 6);}
190			bool IsNitrogen() { return(_atomicNum == 7);}
191			bool IsOxygen() { return(_atomicNum == 8);}
192			bool IsSulfur() { return(_atomicNum == 16);}
193			bool IsPhosphorus() { return(_atomicNum == 15);}
194			bool IsConnected(TFASAtom *atom);
195			bool IsOneThree(TFASAtom *atom);
196			bool IsOneFour(TFASAtom *atom);
197			bool IsCarboxylOxygen();
198			bool IsPhosphateOxygen();
199			bool IsSulfateOxygen();
200			bool IsNitroOxygen();
201			bool IsAmideNitrogen();
202			bool IsPolarHydrogen();
203			bool IsNonPolarHydrogen();
204			bool IsInRing();
205			bool IsInRingSize(int ringSize);
206			bool IsAromatic();
207			bool IsAromaticNOxide();
208			bool IsChiral();
209			bool IsAxial();
210			bool IsClockwise() { return HasAtomProp(TAtomProp::apCStereo);}
211			bool IsAntiClockwise() { return HasAtomProp(TAtomProp::apACStereo);}
212			bool HasChiralitySpecified() { return IsClockwise()\|IsAntiClockwise(); }
213			bool HasAlphaBetaUnsat(bool includePandS=true);
214			bool HasBondOfOrder(int order);
215			int CountBondsOfOrder(int order);
216			bool HasSingleBond() { return(HasBondOfOrder(1)); }
217			bool HasDoubleBond() { return(HasBondOfOrder(2)); }
218			bool HasAromaticBond() { return(HasBondOfOrder(4)); }
219			};
220			#endif