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/********************************************************************** |
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* Copyright (C) 2002-2003 by Gezelter's Group
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*This program is free software; you can redistribute it and/or modify
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*it under the terms of the GNU General Public License as published by
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*the Free Software Foundation version 2 of the License.
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*
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*This program is distributed in the hope that it will be useful,
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*but WITHOUT ANY WARRANTY; without even the implied warranty of
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*MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
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*GNU General Public License for more details.
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*
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************************************************************************ |
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*Author: Teng Lin Email: tlin@nd.edu |
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*Date: 08/13/2002 Version: 1.0 |
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* |
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************************************************************************ |
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*Description: |
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* |
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***********************************************************************/ |
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#ifndef FASATOM_H |
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#define FASATOM_H |
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#include <iostream> |
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#include <vector> |
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#include "fasbond.h" |
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using namespace std; |
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|
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class TFASModel; |
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class TFASBond; |
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class TFASResidue; |
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class TFASMolecule; |
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|
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//ATOM Property Macros |
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#define FAS_NORMAL_ATOM (1<<1) |
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#define FAS_PROTEINBACK_ATOM (1<<2) |
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#define FAS_NUCLEIC_ATOM (1<<3) |
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#define FAS_AROMATIC_ATOM (1<<4) |
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#define FAS_RING_ATOM (1<<5) |
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#define FAS_CSTEREO_ATOM (1<<6) |
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#define FAS_ACSTEREO_ATOM (1<<7) |
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#define FAS_DONOR_ATOM (1<<8) |
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#define FAS_ACCEPTOR_ATOM (1<<9) |
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#define FAS_CHIRAL_ATOM (1<<10) |
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|
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namespace TAtomProp |
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{ |
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const int apNormal = FAS_NORMAL_ATOM; |
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const int apProtein = FAS_PROTEINBACK_ATOM; |
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const int apNucleic = FAS_NUCLEIC_ATOM; |
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const int apAromatic = FAS_AROMATIC_ATOM; |
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const int apRing = FAS_RING_ATOM; |
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const int apCStereo = FAS_CSTEREO_ATOM; |
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const int apACStereo = FAS_ACSTEREO_ATOM; |
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const int apDonor = FAS_DONOR_ATOM; |
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const int apAcceptor = FAS_ACCEPTOR_ATOM; |
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const int apChiral = FAS_CHIRAL_ATOM; |
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}; |
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|
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class TFASAtom |
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{ |
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protected: |
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unsigned int _index; |
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unsigned int _atomicNum; |
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unsigned int _nameIndex; |
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unsigned int _typeIndex; |
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unsigned int _resid; |
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unsigned int _residIndex; |
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unsigned int _resnameIndex; |
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unsigned int _chainIndex; |
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unsigned int _segnameIndex; |
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int _atomProp; |
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|
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//actually we can put these properties on an element table, but we may want to change them sometime, who |
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//knows, anyway it is a trade off between space and speed |
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float _mass; |
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float _charge; |
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float _covRadius; |
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float _bondRadius; |
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float _vdwRadius; |
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float _maxBonds; |
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float _pcharge; |
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unsigned int _hyb; |
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unsigned int _impval; |
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|
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TFASResidue *_residue; |
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TFASMolecule *_mol; |
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TFASModel * _model; |
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vector<TFASBond *> _bondList; |
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bool _pseudo; |
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|
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void SetAtomProp(int atomProp) { _atomProp |= atomProp;} |
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void Clear(); |
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public: |
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TFASAtom(int index); |
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~TFASAtom(); |
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|
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//methods to set atomic information |
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void SetIndex(unsigned int index) { _index = index;} |
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void SetAtomicNum(unsigned int atomicNum) { _atomicNum = atomicNum;} |
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void SetNameIndex(unsigned int nameIndex) { _nameIndex = nameIndex;} |
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void SetTypeIndex(unsigned int typeIndex) { _typeIndex = typeIndex;} |
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void SetResid(unsigned int resid) { _resid=resid;} |
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void SetResidIndex(unsigned int residIndex) { _residIndex = residIndex;} |
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void SetResnameIndex(unsigned int resnameIndex) { _resnameIndex = resnameIndex;} |
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void SetChainIndex(unsigned int chainIndex) { _chainIndex = chainIndex;} |
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void SetSegnameIndex(unsigned int segnameIndex) { _segnameIndex = segnameIndex;} |
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void SetResidue(TFASResidue *residue) { _residue = residue;} |
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void SetMolecule(TFASMolecule *mol) { _mol = mol;} |
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void SetModel(TFASModel *model) { _model = model;} |
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void SetPseudo(bool pseudo) { _pseudo = pseudo;} |
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void SetMass(float mass) { _mass = mass;} |
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void SetCharge(float charge) { _charge = charge;} |
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void SetPartialCharge(float pcharge) { _pcharge = pcharge;} |
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void SetCovalentRadius(float covRadius) { _covRadius = covRadius;} |
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void SetBondRadius(float bondRadius) { _bondRadius = bondRadius;} |
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void SetVdwRadius(float vdwRadius) { _vdwRadius = vdwRadius;} |
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void SetMaxBonds(float maxBonds) { _maxBonds=maxBonds;} |
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void SetHyb(unsigned int hyb) { _hyb = hyb;} |
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void SetImplicitValence (unsigned int impval) { _impval = impval;} |
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|
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//methods to get atomic information |
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unsigned int GetIndex() { return _index;} |
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unsigned int GetAtomicNum() { return _atomicNum;} |
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unsigned int GetNameIndex() { return _nameIndex;} |
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unsigned int GetTypeIndex() { return _typeIndex;} |
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unsigned int GetResid() { return _resid;} |
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unsigned int GetResidIndex() { return _residIndex;} |
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unsigned int GetResnameIndex() { return _resnameIndex;} |
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unsigned int GetChainIndex() { return _chainIndex;} |
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unsigned int GetSegnameIndex() { return _segnameIndex;} |
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TFASResidue *GetResidue() { return _residue;} |
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TFASMolecule *GetMolecule() { return _mol;} |
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TFASModel *GetModel() { return _model;} |
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bool IsPseudo() { return _pseudo;} |
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float GetMass() { return _mass;} |
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float GetCharge() { return _charge;} |
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float GetPartialCharge() { return _pcharge;} |
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float GetCovalentRadius() { return _covRadius;} |
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float GetBondRadius() { return _bondRadius;} |
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float GetVdwRadius() { return _vdwRadius;} |
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float GetMaxBonds() { return _maxBonds;} |
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unsigned int GetHyb() { return _hyb;} |
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unsigned int GetImplicitValence() { return _impval;} |
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unsigned int GetHvyValence(); |
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unsigned int GetValence() {return (unsigned int)_bondList.size();} |
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//meothds to manipulate bond |
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void AddBond(TFASBond * bond); |
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void DeleteBond(TFASBond *bond); |
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TFASBond *BeginBond(vector<TFASBond *>::iterator &i); |
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TFASBond *NextBond(vector<TFASBond *>::iterator &i); |
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TFASBond *GetBond(TFASAtom *nbrAtom); |
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//methods to traverse neighbor atoms |
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TFASAtom *BeginNbrAtom(vector<TFASBond *>::iterator &i); |
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TFASAtom *NextNbrAtom(vector<TFASBond *>::iterator &i); |
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// |
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|
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int GetAtomProp() { return _atomProp;} |
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bool HasAtomProp(int atomProp) { return _atomProp & atomProp;} |
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void SetAromatic() { SetAtomProp(TAtomProp::apAromatic);} |
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void UnSetAromatic() { _atomProp &= ~TAtomProp::apAromatic;} |
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void SetClockwiseStereo() |
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{ |
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_atomProp &= ~TAtomProp::apACStereo; |
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SetAtomProp(TAtomProp::apCStereo|TAtomProp::apChiral); |
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} |
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void SetAntiClockwiseStereo() |
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{ |
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_atomProp &= ~TAtomProp::apCStereo; |
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SetAtomProp(TAtomProp::apACStereo|TAtomProp::apChiral); |
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} |
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void UnSetStereo() |
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{ |
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_atomProp &= ~TAtomProp::apCStereo; |
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_atomProp &= ~TAtomProp::apACStereo; |
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_atomProp &= ~TAtomProp::apChiral; |
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} |
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void SetNormal() |
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{ |
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_atomProp &= ~TAtomProp::apProtein; |
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_atomProp &= ~TAtomProp::apNucleic; |
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} |
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void SetProtein() |
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{ |
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_atomProp &= ~TAtomProp::apNormal; |
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_atomProp &= ~TAtomProp::apNucleic; |
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} |
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void SetNucleic() |
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{ |
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_atomProp &= ~TAtomProp::apNormal; |
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_atomProp &= ~TAtomProp::apProtein; |
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} |
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bool HasResidue() { return(_residue != NULL);} |
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bool IsHydrogen() { return(_atomicNum == 1);} |
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bool IsCarbon() { return(_atomicNum == 6);} |
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bool IsNitrogen() { return(_atomicNum == 7);} |
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bool IsOxygen() { return(_atomicNum == 8);} |
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bool IsSulfur() { return(_atomicNum == 16);} |
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bool IsPhosphorus() { return(_atomicNum == 15);} |
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bool IsConnected(TFASAtom *atom); |
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bool IsOneThree(TFASAtom *atom); |
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bool IsOneFour(TFASAtom *atom); |
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bool IsCarboxylOxygen(); |
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bool IsPhosphateOxygen(); |
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bool IsSulfateOxygen(); |
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bool IsNitroOxygen(); |
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bool IsAmideNitrogen(); |
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bool IsPolarHydrogen(); |
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bool IsNonPolarHydrogen(); |
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bool IsInRing(); |
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bool IsInRingSize(int ringSize); |
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bool IsAromatic(); |
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bool IsAromaticNOxide(); |
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bool IsChiral(); |
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bool IsAxial(); |
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bool IsClockwise() { return HasAtomProp(TAtomProp::apCStereo);} |
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bool IsAntiClockwise() { return HasAtomProp(TAtomProp::apACStereo);} |
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bool HasChiralitySpecified() { return IsClockwise()|IsAntiClockwise(); } |
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bool HasAlphaBetaUnsat(bool includePandS=true); |
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bool HasBondOfOrder(int order); |
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int CountBondsOfOrder(int order); |
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bool HasSingleBond() { return(HasBondOfOrder(1)); } |
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bool HasDoubleBond() { return(HasBondOfOrder(2)); } |
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bool HasAromaticBond() { return(HasBondOfOrder(4)); } |
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}; |
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#endif |
