BioAtom.h

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/****************************************************************************
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
The BioBhasha : The Biologist's Programming Language 
Version 1.0 (19th December 2001)
Prasad, B.V.L.S.
Contact: burrashiva@yahoo.com
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
*****************************************************************************/
#ifndef BIOATOM_H
#define BIOATOM_H

#include <fstream>
#include <string>
#include <cmath>
#include <vector>
#include "BioUtilities.h"
#include "BioHelperClass.h"
#include "BioPoint.h"

using namespace std;

/*****************************************************************************
 *
 * COMMENTARY on Each Class/Concept: Hows and Whys:
 *
 * BioAtom:
 *              A qualified Point is an Atom. 
 *              At Atom "Is-A" Point, even though At Atom "Has-A" Point can 
 *              also be considered. A Point when is qualified with an AtomName,
 *              AtomNumber, Occupancy and Bfactor(Atomic Displacement Parameter)
 *              it gets transformed into an Atom. Using this philosophy, 
 *              the BioAtom inherits from BioPoint. BioPoint is NOT composed into 
 *              BioAtom. 
 *****************************************************************************/

class BioAtom : public BioPoint
{
        string at_Name;
        long at_Number;
        float oc_,bf_;
        string at_Record_;      // This field has been created to facilitate the 
                                //the user to change the RECORD according to his/
                                //her wish. At times even the Atom is water coordinates, 
                                //the RECORD should be ATOM. Some Programs identify 
                                //only ATOM RECORD not HETATM RECORD. For Example,
                                //ALIGN(Cohen), to align water coordinates also, the 
                                //RECORD should be ATOM.This has either "ATOM  " or 
                                //"HETATM". By default it is   "ATOM  ". This is the 
                                //reason why it is put at the last argument which 
                                //can defaulted. 
           friend bool operator >(const BioAtom& , const BioAtom&);
           friend bool operator <(const BioAtom& , const BioAtom&);
           friend bool operator ==(const BioAtom& , const BioAtom&);

public:
// Default Constructor...
        BioAtom();
/* The following constructor expects a file name which has ATOM/HETATM RECORD.
 * When this constructor is used, it takes only first/one line of ATOM/HETATM RECORD,
 * because BioAtom should hold information of only one atom coordinates.
 * This constructor may not be of much use.
 * *******************************************************************************/
        BioAtom(const string& );
        BioAtom(const BioAtom&);
        BioAtom& operator=(const BioAtom& );
/*
 * This Constructor is specially useful, when one wants to transform the information 
 * of BioPoint to BioAtom. Hence it expects the user to give AtomName, AtomNumber ,
 * Occupancy, Bfactor. But the Occupancy and Bfactor are defaulted to 1.0 and 15.0.
 * ********************************************************************************/

        BioAtom(const unsigned long atnum_, const string atname_, const BioPoint& , 
                        const float oc1=1.0 , const float bf1=15.0, 
                        const string atrec = "ATOM  "); 
/*
 * This constructor is useful for filling the BioAtom from a file which follows 
 * PDB format 2.2v, strictly. This is the constructor which is used very extensively
 * to write the PDB File Parser and Abstracting the Atom, Residue and Chain Information.
 * ********************************************************************************/
        BioAtom(const unsigned long atnumber,const string atname,
                const float x1, const float y1, const float z1,
                const float oc=1.0,const float bf=15.0,
                const string atrec = "ATOM  "); 
// Setting Options of all the information required for an Atom to become qualified. 
// Unless necessary, these options need not be used as they directly change the
// state of the Object. so, one should exercise these options with CARE!!!

        void setAtomName(string ) ;
        void setAtomNumber( unsigned long ) ;
        void setBfactor(float ) ;
        void setOccupancy(float ) ;

        void setAtom(const unsigned  long atnumber,const string atname,
                const float x1, const float y1, const float z1,
                const float oc=1.0,const float bf=15.0,
                const string atrec = "ATOM  "); 
        
// These options are for accessing the information, these have been very extensively
// used for conditional and logical expressions and testing.
        string getAtomName() const ;

        unsigned long getAtomNumber() const ;

        float getBfactor() const ;

        float getOccupancy() const ;

        string getAtomRecord () const;

// This Method gives the user to output the information of Atom in PDB format. 
// By default it prints on the console. One can divert it to output stream i.e 
// to any other device like another file..etc..
// An Atom doesnot have any information about Residue Number, ResidueName, Chain, 
// so PDB format would be expected  to have blanks at those respective places, 
// which would not be read by many softwares if the Residue information is not 
// given. To avoid such troubles, the user is given option of giving the ChainId, 
// ResidueNumber, Residue Name as Arguments. The Atom will be displayed in PDB format
// with ResidueName ....etc...as specified in the argument. Providing this option
// is very advantages. This will become obvious when BioResidue is discussed. 

        void showAtom( ostream& = cout,string="AAA" ,int  = 0, char='A');
        friend ostream& operator<<(ostream& os, const BioAtom& ip);

// Inherit the Comments from BioPoint. :-) :-).
// This is created for User's Convinience.They might feel comfortable with a 
// Qualified Point(BioAtom) than a Point (BioPoint).
        BioAtom getRotatedAtom(const float **a_ );
        BioAtom getRotatedAtom(const float a_, const char axis_);  
        BioAtom getTranslatedAtom(const float *a_);
        BioAtom getRotoTranslatedAtom(const float **a_,const float *b_ );
        BioAtom getRotoTranslatedAtom(const float a_ ,const char axis_ , 
                                                        const float *b_ );

};


float BioDistance( const BioAtom& , const BioAtom& );
float BioAngle( const BioAtom& , const BioAtom& , const BioAtom&);
float BioTorsion( const BioAtom&, const BioAtom& , const BioAtom& ,
        const BioAtom& );

vector <float> BioDirectionCosines( const BioAtom& , const BioAtom& );
vector <float> BioVectorCrossProduct( const BioAtom&, const BioAtom& , const BioAtom&);
vector <float> BioVectorCrossProduct( const BioAtom&, const BioAtom& );

BioAtom BioDifferenceVector(const BioAtom& , const BioAtom& );
float BioDotProduct(const BioAtom& , const BioAtom&);
float BioDotMagnitude(const BioAtom& , const BioAtom&);
BioAtom BioNormalize(const BioAtom& );
BioMatrix helix(BioAtom c1, BioAtom c2, BioAtom c3, BioAtom c4);
void helixAxisDirectionCosines(BioAtom c1, BioAtom c2, BioAtom c3, BioAtom c4,
                float& l, float& m , float& n);
#endif