BioPoint.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 BIOPOINT_H
#define BIOPOINT_H

#include <iostream>
#include <vector>
#include <fstream>
#include <cmath>
#include "BioUtilities.h"

using namespace std;
/****************************************************************************
 * 
 * COMMENTARY on Each Class/Concept/:  Hows and Whys : 
 *
 * BioPoint: 
 *              To describe a position of any matter in Space, 3 axes form a
 *              necessary condition. Hence to reach that Point/Matter from 
 *              an Origin of 3 axes named X,Y,Z, one should know the 
 *              contribution of each axis to reach that point. This 
 *              contribution is represented by each axis as x,y,z.
 *              In general a Cartsian System is followed i.e the 3 axes are 
 *              mutually perpendicular.
 *              In Crystallography, 3 axes are used to describe a unit cell
 *              which  is called fractional coordinate system, in  which the 
 *              axes may not be mutually perpendicular.
 *              
 *              A Point has a state to be maintained, which can be 
 *              altered, hence is Eligible to become an ADT.
 *              It can be said that: "A Point is the Fundamental Particle and 
 *              Foundation Stone of Structural BioInformatics."
 ***************************************************************************/

class BioPoint
{

protected: 

        float x_, y_, z_;

public:
/* Constructors:
 *      2 Constructors are Provided here. A Point is characterized by 
 *      simply x,y,z coordinates only. Hence the 2nd constructor is 
 *      provided to initialise the Object with x,y,z.
 ***********************************************************************/
        BioPoint();
        BioPoint(const BioPoint& );
        BioPoint& operator=(const BioPoint&);
        BioPoint(const float x1,const float y1, const float z1);

/* Accessing each Coordinate:*/


        float getX() const ;
        float getY() const ;
        float getZ() const ;

/* Setting the x,y,z coordinates when a Object is constructed through its
 * default constructor. 
 * It can also be used to set "DESIRED" x,y,z coordinate values at any 
 * point of programming irrespective of the initial coordinate set.
 * *********************************************************************/
        void setXYZ(float, float , float );
        void setX(float);
        void setY(float);
        void setZ(float);

/*Printing the x,y,z coordinates, ONTO THE CONSOLE by DEFAULT.
 * Provision is provided to write into a file, if the output stream is 
 * set to a file. Ex. ofstream output("xyz.coor"); showXYZ(output);
 * will put coordinates , x,y,z in file called xyz.coor.
 * *********************************************************************/
        void  showPoint(ostream& os = cout) const ;
        friend ostream& operator<<(ostream& os , const BioPoint& );

/* Very Useful Methods of BioPoint Class:
 * These are expected to be most frequently used for manipulation.
 * The requirements of a user are generally:
 * a) To rotate a point or translate a point
 * b) to rotate and translate,
 * as is needed in understanding the equivalent points in Crystallographic
 * symmetry.
 * **********************************************************************/

/* Expects a 3x3 Rotation Matrix as argument. 
 * This Rotation Matrix is used on the data and the Rotated Point is 
 * returned as Point. This returning as a Point has great importance from 
 * a programmer's point of view. 
 * a) It strictly abides to OOPs concept as it keeps the Data Safe.
 * ***********************************************************************/
        BioPoint getRotatedPoint(const float **a_ );
        BioPoint getRotatedPoint( const BioMatrix& a_);
/* A Point can also be rotated about an Axis with a certain angle.
 * This facility is provided for the user by OverLoading the getRotatedPoint()
 * function.
 * ************************************************************************/
        BioPoint getRotatedPoint(const float th, const char axis);

// Similar to Rotation Matrix , it expects a 3x1 Translation Matrix.
        BioPoint getTranslatedPoint(const float *a_);

//Both Translation and Rotation Matrices are given and the result is returned.
        BioPoint getRotoTranslatedPoint(const float **a_,const float *b_ );

// Rotation about an axis and a translation facility is given here. 
        BioPoint getRotoTranslatedPoint(const float th, const char ax,const float *b_ );

// Distance between the (this) Point and Desired Point provided as argument is given.
        float getDistance(const BioPoint& );

// Distance can also obtained between the (this)Point and an arbitrary x,y,z coordinates.
        float getDistance(const float, const float, const float );


/*
 *      To Be Added:  return the rotation and translation matrices in the form of BioMatrix.
 *      
 *
 * ***********************************************************/
};

float BioDistance( const BioPoint& , const BioPoint& );
float BioAngle( const BioPoint& , const BioPoint& , const BioPoint&);
float BioTorsion( const BioPoint&, const BioPoint& , const BioPoint& ,
                        const BioPoint&);
vector <float> BioDirectionCosines( const BioPoint& , const BioPoint&);
vector <float> BioVectorCrossProduct( const BioPoint&, const BioPoint& , const BioPoint& );

#endif