BioWater.h

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/****************************************************************************
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
The BioBhasha : A Programming Language for Biologist
Version 1.0 (19th December 2001)
Dr. Prasad, B.V.L.S.
Contact: prasadbvls@helixgenomics.com
Version 1.1 (23th January 2003)
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
*****************************************************************************/
#ifndef BIOWATER_H
#define BIOWATER_H

#include <string>
#include <fstream>
#include "BioResidue.h"
#include "BioPostScript.h"

/****************************************************************************
 *
 * COMMENTARY on Each Class/Concept: Hows and Whys :
 *
 * BioWater:
 *      It has long been known the Very crucial role played by the crystallographic
 *      waters ..like catalytic water, involved in the formation of Proton Wires
 *      in Serine Proteinases and my recent Papers on "Role of Crystallographic
 *      Waters in Aspartic Proteinase Family emphasizes the role of invariant
 *      waters at a greater length and insight. 
 *      Water can be considered as Residue with 2 Hydrogens Atoms and 1 Oxygen Atom. 
 *      The number of waters included in a PDB file is arbitrary or not fixed, hence
 *      again, vector<BioResidue> is most apt.
 *      Once feature of BioWater is that it is Conceptualized as a BioChain.. 
 *      This is because of the Importance of Water in and around Protein. 
 *      Water is also an integral Part of a Protein molecule. It is rightly said 
 *      the water molecules give respective proteins extra breathing space. They 
 *      increase the Overall Molecular Surface Area. 
 *      Hence, these waters are felt like behaving as a seperate chain. 
 *      A provision is also made to give/set a ChainId to all these Water molecules.
 *      The role of water played in Proteins is gaining importance.
 *      There would grow a lot of other mathematical tools which would be operated on 
 *      water data exclusively, hence conceptualizing Water as seperate ADT
 *      is very much relevant. The Data related to Water is set in BioWater.
 ****************************************************************************/  

// As far as possible the names of Methods have been used with very less variation
// as this will reduce the burden of a user to memorise more and also drives the 
// user to use his/her Intution more.. 
// The Methods are self explanatory. If not please do refer to BioResidue.h, 
// BioAtom.h, BioChain.h for detailed explanatory notes. 
class BioWater 
{
        vector<BioResidue>water;
        char chainId_;
     double startX_,startY_,size_;
     double SETAREACALLED;

        public:
// Default Constructor;
                BioWater();
                ~BioWater();
// This constructor expects a PDB filename. This checks for Water name to 
// terminate its populating work.The Water names which it checks are "HOH",
// "WAT", "H2O", "SOL", "TIP". This should be taken care off.  
                BioWater(const string&);

// this constructor is used to return an Object .. 
// ONe initially populates the BioResidue Vector Container,
// then it is passed on to BioWater. 
                BioWater(const char&  , const vector<BioResidue>& );

// shows the Water in PDB format. It can be put into a file also.
                void showWater(ostream& = cout);
// to get the NumberOf Waters 
                int getNumberOfWaters() const;
// Generally, users remember the Water Number, and if one wants 
// to get the index from the water container, then this Method is used. 
// This method is expected to be used most widely in any type of Computational 
// work. 
//   Difference between Index and Water Number:
//   vector<BioResidue>water;
//   water[Index].someMethod();
//   Water Number is the one given in the PDB file at the Residue Number 
//   position. 
                int getWaterIndex(const int& ) const;
        
// The water numbers provided in a PDB dont have a standard rule. They can have any
// starting number. To access or to run through all the water numbers for some 
// other use, one can give some Index, ofcourse < getNumberOfWaters(), and one 
// can get the number of Waters with that particular index. 
// Suggestion is "ALWAYS USE THE INDEX OF THE WATER THAN THE 
// NUMBER OF THE WATER MOLECULE.......................
                int getWaterNumber(const int& ) const;

// To give a better handling of Water Data , a chain can be given. 
// getChainId...is self explanatory. 
                void setChainId(const char& );
                char getChainId() const ;
                
// If the water coordinates have Hydrogen Atom information and is not needed 
// for the analysis, then one can get a copy of the data of Water with out 
// the Hydrogen Information. This is a very useful option.
                BioWater eraseHydrogen();

// In this Method, the waterIndex  is expected and *NOT* waterNumber as per the 
// conventions followed all through BioBhasha...............
// This returns the whole information about that particular water in 
// the form of a BioResidue. This also has high usability during analysis.
                BioResidue& getWater(const int& );
   void setDisplayArea(double startx=80,double starty=250,double size=450);
   void showWater(BioPostScript& ps,double width=1,double r=255, double g=0, double b=0);
};

#endif