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"
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 _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:	77
Committed:	Wed Aug 14 23:27:28 2002 UTC (22 years ago) by tim
Content type:	text/plain
File size:	8144 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			using namespace std;
26
27			class TFASModel;
28			class TFASBond;
29			class TFASResidue;
30			class TFASMolecule;
31
32			//ATOM Property Macros
33			#define FAS_NORMAL_ATOM (1<<1)
34	tim	77	#define FAS_PROTEINBACK_ATOM (1<<2)
35	tim	66	#define FAS_NUCLEIC_ATOM (1<<3)
36			#define FAS_AROMATIC_ATOM (1<<4)
37	tim	77	#define FAS_RING_ATOM (1<<5)
38	tim	66	#define FAS_CSTEREO_ATOM (1<<6)
39			#define FAS_ACSTEREO_ATOM (1<<7)
40			#define FAS_DONOR_ATOM (1<<8)
41	tim	77	#define FAS_ACCEPTOR_ATOM (1<<9)
42	tim	66	#define FAS_CHIRAL_ATOM (1<<10)
43
44			namespace TAtomProp
45			{
46			const int apNormal = FAS_NORMAL_ATOM;
47			const int apProtein = FAS_PROTEINBACK_ATOM;
48			const int apNucleic = FAS_NUCLEIC_ATOM;
49			const int apAromatic = FAS_AROMATIC_ATOM;
50			const int apRing = FAS_RING_ATOM;
51			const int apCStereo = FAS_CSTEREO_ATOM;
52			const int apACStereo = FAS_ACSTEREO_ATOM;
53			const int apDonor = FAS_DONOR_ATOM;
54			const int apAcceptor = FAS_ACCEPTOR_ATOM;
55	tim	77	const int apChiral = FAS_CHIRAL_ATOM;
56	tim	66	};
57
58			class TFASAtom
59			{
60			protected:
61			unsigned int _index;
62			unsigned int _atomicNum;
63			unsigned int _nameIndex;
64			unsigned int _typeIndex;
65			unsigned int _resid;
66			unsigned int _residIndex;
67			unsigned int _resnameIndex;
68			unsigned int _chainIndex;
69			unsigned int _segnameIndex;
70			int _atomProp;
71
72			//actually we can put these properties on an element table, but we may want to change them sometime, who
73			//knows, anyway it is a trade off between space and speed
74			float _mass;
75			float _charge;
76			float _covRadius;
77			float _bondRadius;
78			float _vdwRadius;
79			float _maxBonds;
80			float _pcharge;
81			unsigned int _hyb;
82			unsigned int _impval;
83
84			TFASResidue *_residue;
85			TFASMolecule *_mol;
86			TFASModel * _model;
87			vector<TFASBond *> _bondList;
88			bool _pseudo;
89
90			void SetAtomProp(int atomProp) { _atomProp \|= atomProp;}
91			void Clear();
92			public:
93			TFASAtom(int index);
94			~TFASAtom();
95
96			//methods to set atomic information
97			void SetIndex(unsigned int index) { _index = index;}
98			void SetAtomicNum(unsigned int atomicNum) { _atomicNum = atomicNum;}
99			void SetNameIndex(unsigned int nameIndex) { _nameIndex = nameIndex;}
100			void SetTypeIndex(unsigned int typeIndex) { _typeIndex = typeIndex;}
101			void SetResid(unsigned int resid) { _resid=resid;}
102			void SetResidIndex(unsigned int residIndex) { _residIndex = residIndex;}
103			void SetResnameIndex(unsigned int resnameIndex) { _resnameIndex = resnameIndex;}
104			void SetChainIndex(unsigned int chainIndex) { _chainIndex = chainIndex;}
105			void SetSegnameIndex(unsigned int segnameIndex) { _segnameIndex = segnameIndex;}
106			void SetResidue(TFASResidue *residue) { _residue = residue;}
107			void SetMolecule(TFASMolecule *mol) { _mol = mol;}
108			void SetModel(TFASModel *model) { _model = model;}
109			void SetPseudo(bool pseudo) { _pseudo = pseudo;}
110			void SetMass(float mass) { _mass = mass;}
111			void SetCharge(float charge) { _charge = charge;}
112			void SetPartialCharge(float pcharge) { _pcharge = pcharge;}
113			void SetCovalentRadius(float covRadius) { _covRadius = covRadius;}
114			void SetBondRadius(float bondRadius) { _bondRadius = bondRadius;}
115			void SetVdwRadius(float vdwRadius) { _vdwRadius = vdwRadius;}
116			void SetMaxBonds(float maxBonds) { _maxBonds=maxBonds;}
117			void SetHyb(unsigned int hyb) { _hyb = hyb;}
118			void SetImplicitValence (unsigned int impval) { _impval = impval;}
119
120			//methods to get atomic information
121			unsigned int GetIndex() { return _index;}
122			unsigned int GetAtomicNum() { return _atomicNum;}
123			unsigned int GetNameIndex() { return _nameIndex;}
124			unsigned int GetTypeIndex() { return _typeIndex;}
125			unsigned int GetResid() { return _resid;}
126			unsigned int GetResidIndex() { return _residIndex;}
127			unsigned int GetResnameIndex() { return _resnameIndex;}
128			unsigned int GetChainIndex() { return _chainIndex;}
129			unsigned int GetSegnameIndex() { return _segnameIndex;}
130
131			TFASResidue *GetResidue() { return _residue;}
132			TFASMolecule *GetMolecule() { return _mol;}
133			TFASModel *GetModel() { return _model;}
134			bool IsPseudo() { return _pseudo;}
135
136			float GetMass() { return _mass;}
137			float GetCharge() { return _charge;}
138			float GetPartialCharge() { return _pcharge;}
139			float GetCovalentRadius() { return _covRadius;}
140			float GetBondRadius() { return _bondRadius;}
141			float GetVdwRadius() { return _vdwRadius;}
142			float GetMaxBonds() { return _maxBonds;}
143			unsigned int GetHyb() { return _hyb;}
144			unsigned int GetImplicitValence() { return _impval;}
145			unsigned int GetHvyValence();
146			unsigned int GetValence() {return (unsigned int)_bondList.size();}
147
148			//meothds to manipulate bond
149			void AddBond(TFASBond * bond);
150			void DeleteBond(TFASBond *bond);
151			TFASBond BeginBond(vector<TFASBond >::iterator &i);
152			TFASBond NextBond(vector<TFASBond >::iterator &i);
153			TFASBond GetBond(TFASAtom nbrAtom);
154			//methods to traverse neighbor atoms
155			TFASAtom BeginNbrAtom(vector<TFASBond >::iterator &i);
156			TFASAtom NextNbrAtom(vector<TFASBond >::iterator &i);
157
158			//
159
160			int GetAtomProp() { return _atomProp;}
161			bool HasAtomProp(int atomProp) { return _atomProp & atomProp;}
162			void SetAromatic() { SetAtomProp(TAtomProp::apAromatic);}
163			void UnSetAromatic() { _atomProp &= ~TAtomProp::apAromatic;}
164
165			void SetClockwiseStereo()
166			{
167			_atomProp &= ~TAtomProp::apACStereo;
168			SetAtomProp(TAtomProp::apCStereo\|TAtomProp::apChiral);
169			}
170
171			void SetAntiClockwiseStereo()
172			{
173			_atomProp &= ~TAtomProp::apCStereo;
174			SetAtomProp(TAtomProp::apACStereo\|TAtomProp::apChiral);
175			}
176
177			void UnSetStereo()
178			{
179			_atomProp &= ~TAtomProp::apCStereo;
180			_atomProp &= ~TAtomProp::apACStereo;
181			_atomProp &= ~TAtomProp::apChiral;
182			}
183
184			void SetNormal()
185			{
186			_atomProp &= ~TAtomProp::apProtein;
187			_atomProp &= ~TAtomProp::apNucleic;
188			}
189
190			void SetProtein()
191			{
192			_atomProp &= ~TAtomProp::apNormal;
193			_atomProp &= ~TAtomProp::apNucleic;
194
195			}
196
197			void SetNucleic()
198			{
199			_atomProp &= ~TAtomProp::apNormal;
200			_atomProp &= ~TAtomProp::apProtein;
201
202			}
203
204			bool HasResidue() { return(_residue != NULL);}
205			bool IsHydrogen() { return(_atomicNum == 1);}
206			bool IsCarbon() { return(_atomicNum == 6);}
207			bool IsNitrogen() { return(_atomicNum == 7);}
208			bool IsOxygen() { return(_atomicNum == 8);}
209			bool IsSulfur() { return(_atomicNum == 16);}
210			bool IsPhosphorus() { return(_atomicNum == 15);}
211			bool IsConnected(TFASAtom *atom);
212			bool IsOneThree(TFASAtom *atom);
213			bool IsOneFour(TFASAtom *atom);
214			bool IsCarboxylOxygen();
215			bool IsPhosphateOxygen();
216			bool IsSulfateOxygen();
217			bool IsNitroOxygen();
218			bool IsAmideNitrogen();
219			bool IsPolarHydrogen();
220			bool IsNonPolarHydrogen();
221			bool IsInRing();
222			bool IsInRingSize(int ringSize);
223			bool IsAromatic();
224			bool IsAromaticNOxide();
225			bool IsChiral();
226			bool IsAxial();
227			bool IsClockwise() { return HasAtomProp(TAtomProp::apCStereo);}
228			bool IsAntiClockwise() { return HasAtomProp(TAtomProp::apACStereo);}
229			bool HasChiralitySpecified() { return IsClockwise()\|IsAntiClockwise(); }
230			bool HasAlphaBetaUnsat(bool includePandS=true);
231			bool HasBondOfOrder(int order);
232			int CountBondsOfOrder(int order);
233			bool HasSingleBond() { return(HasBondOfOrder(1)); }
234			bool HasDoubleBond() { return(HasBondOfOrder(2)); }
235			bool HasAromaticBond() { return(HasBondOfOrder(4)); }
236			};
237			#endif