model.cpp 7.92 KB
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#include <fstream>
#include <iostream>
#include <stdio.h>
#include <stdlib.h>
#include <cstring>

#include "model.h"

using namespace std;


int bioem_model::readModel()
{
    /**************************************************************************************/
    /***************Reading reference Models either PDB or x,y,z,r,d format****************/
    /**************************************************************************************/

    ofstream exampleReadCoor;
    exampleReadCoor.open ("COORDREAD");

    std::ifstream input(filemodel);
    if(readPDB)
    {
        ifstream input(filemodel);
        if (!input.good())
        {
            cout << "PDB Failed to open file" << endl ; // pdbfilename << " ("<<filename<<")\n";
            exit(0);
        }

        char line[512] = {' '};
        char tmpLine[512] = {' '};
        int numres=0;

        //  cout << " HERE    " << filemodel ;
        // for eachline in the file
        while (!input.eof())
        {
            input.getline(line,512);

            strncpy(tmpLine,line,strlen(line));
            char *token = strtok(tmpLine," ");

            if (strcmp(token,"ATOM")==0) // Optional,Mandatory if standard residues exist
            {
                /*
                1-6 			"ATOM  "
                7 - 11         Integer         serial        Atom serial number.
                13 - 16        Atom            name          Atom name.
                17             Character       altLoc        Alternate location indicator.
                18 - 20        Residue name    resName       Residue name.
                22             Character       chainID       Chain identifier.
                23 - 26        Integer         resSeq        Residue sequence number.
                27             AChar           iCode         Code for insertion of residues.
                31 - 38        Real(8.3)       x             Orthogonal coordinates for X in
                39 - 46        Real(8.3)       y             Orthogonal coordinates for Y in
                47 - 54        Real(8.3)       z             Orthogonal coordinates for Z in
                     */

                char name[5] = {"PPP"};
                char resName[3] = {' '};
                float x=0.0;
                float y=0.0;
                float z=0.0;
                char tmp[6] = {' '};


                // parse name
                strncpy(tmp,line+12,4);
                sscanf (tmp,"%s",name);

                // parse resName
                strncpy(tmp,line+17,3);
                sscanf (tmp,"%s",resName);

                // parse x, y, z
                char tmpVals[36]  = {' '};

                strncpy (tmpVals,line+30,8);
                sscanf (tmpVals,"%f",&x);

                strncpy (tmpVals,line+38,8);
                sscanf (tmpVals,"%f",&y);

                strncpy (tmpVals,line+46,8);
                sscanf (tmpVals,"%f",&z);

                if (strcmp(name,"CA") == 0)
                {
					if (numres >= BIOEM_MODEL_SIZE)
					{
						cout << "BIOEM_MODEL_SIZE too small\n";
						exit(1);
					}
                    //Getting residue Radius and electron density
                    radiusPointsModel[numres]=getAminoAcidRad(resName);
                    densityPointsModel[numres]=getAminoAcidDensity(resName);

                    //Getting the coordinates
                    PointsModel[numres].pos[0]=x;
                    PointsModel[numres].pos[1]=y;
                    PointsModel[numres].pos[2]=z;
                    exampleReadCoor << "RESIDUE " << numres << " " << PointsModel[numres].pos[0] << " " <<  PointsModel[numres].pos[1] << " " << PointsModel[numres].pos[2] << " " <<densityPointsModel[numres]  << "\n";
                    numres++;
                }
            }


        }
        nPointsModel=numres;
        cout << "Protein structure read from PDB\nTotal Number of Residues " << nPointsModel;
        cout << "\n+++++++++++++++++++++++++++++++++++++++++ \n";
    }
    else //Reading model from FILE FORMAT x,y,z,rad,density
    {
        char line[128];
        int numres=0;
        FILE *file = fopen ( filemodel , "r" );
        if ( file != NULL )
        {
            while ( fgets ( line, sizeof line, file ) != NULL )
            {
				if (numres >= BIOEM_MODEL_SIZE)
				{
					cout << "BIOEM_MODEL_SIZE too small\n";
					exit(1);
				}
                sscanf(line, "%f %f %f %f %f",&PointsModel[numres].pos[0],&PointsModel[numres].pos[1],&PointsModel[numres].pos[2],&radiusPointsModel[numres],&densityPointsModel[numres]);
                exampleReadCoor << "RESIDUE " << numres << " " << PointsModel[numres].pos[0] << " " <<  PointsModel[numres].pos[1] << " " << PointsModel[numres].pos[2] << " " <<densityPointsModel[numres]<< "\n";
                numres++;
            }
            nPointsModel=numres;
            cout << "Protein structure read from Standard File \nTotal Number of Residues " << nPointsModel ;
            cout << "\n+++++++++++++++++++++++++++++++++++++++++ \n";
        }
    }
    exampleReadCoor.close();

    //Moving to Model to its center of mass:
    myfloat3_t r_cm;

    for(int n=0; n < 3; n++)r_cm.pos[n] = 0.0;

    for(int n=0; n < nPointsModel; n++)
    {
        r_cm.pos[0] += PointsModel[n].pos[0];
        r_cm.pos[1] += PointsModel[n].pos[1];
        r_cm.pos[2] += PointsModel[n].pos[2];
    }
    r_cm.pos[0]=r_cm.pos[0]/float(nPointsModel);
    r_cm.pos[1]=r_cm.pos[1]/float(nPointsModel);
    r_cm.pos[2]=r_cm.pos[2]/float(nPointsModel);
    for(int n=0; n < nPointsModel; n++)
    {
        PointsModel[n].pos[0]-= r_cm.pos[0];
        PointsModel[n].pos[1]-= r_cm.pos[1];
        PointsModel[n].pos[2]-= r_cm.pos[2];

    }

    return(0);
}



myfloat_t bioem_model::getAminoAcidRad(char *name)
{
    /*************** Function that gets the radius for each amino acid ****************/
    myfloat_t iaa=0;

    if(std::strcmp(name,"CYS")==0)iaa=2.75;
    if(std::strcmp(name,"PHE")==0)iaa=3.2;
    if(std::strcmp(name,"LEU")==0)iaa=3.1;
    if(std::strcmp(name,"TRP")==0)iaa=3.4;
    if(std::strcmp(name,"VAL")==0)iaa=2.95;
    if(std::strcmp(name,"ILE")==0)iaa=3.1;
    if(std::strcmp(name,"MET")==0)iaa=3.1;
    if(std::strcmp(name,"HIS")==0)iaa=3.05;
    if(std::strcmp(name,"TYR")==0)iaa=3.25;
    if(std::strcmp(name,"ALA")==0)iaa=2.5;
    if(std::strcmp(name,"GLY")==0)iaa=2.25;
    if(std::strcmp(name,"PRO")==0)iaa=2.8;
    if(std::strcmp(name,"ASN")==0)iaa=2.85;
    if(std::strcmp(name,"THR")==0)iaa=2.8;
    if(std::strcmp(name,"SER")==0)iaa=2.6;
    if(std::strcmp(name,"ARG")==0)iaa=3.3;
    if(std::strcmp(name,"GLN")==0)iaa=3.0;
    if(std::strcmp(name,"ASP")==0)iaa=2.8;
    if(std::strcmp(name,"LYS")==0)iaa=3.2;
    if(std::strcmp(name,"GLU")==0)iaa=2.95;

    if(iaa == 0)
    {
        cout << "PROBLEM WITH AMINO ACID " << name << endl;
        exit(0);
    }
    return iaa;

}


myfloat_t bioem_model::getAminoAcidDensity(char *name)
{
    /*************** Function that gets the number of electrons for each amino acid ****************/
    myfloat_t iaa=0.0;

    if(std::strcmp(name,"CYS")==0)iaa=64.0;
    if(std::strcmp(name,"PHE")==0)iaa=88.0;
    if(std::strcmp(name,"LEU")==0)iaa=72.0;
    if(std::strcmp(name,"TRP")==0)iaa=108.0;
    if(std::strcmp(name,"VAL")==0)iaa=64.0;
    if(std::strcmp(name,"ILE")==0)iaa=72.0;
    if(std::strcmp(name,"MET")==0)iaa=80.0;
    if(std::strcmp(name,"HIS")==0)iaa=82.0;
    if(std::strcmp(name,"TYR")==0)iaa=96.0;
    if(std::strcmp(name,"ALA")==0)iaa=48.0;
    if(std::strcmp(name,"GLY")==0)iaa=40.0;
    if(std::strcmp(name,"PRO")==0)iaa=62.0;
    if(std::strcmp(name,"ASN")==0)iaa=66.0;
    if(std::strcmp(name,"THR")==0)iaa=64.0;
    if(std::strcmp(name,"SER")==0)iaa=56.0;
    if(std::strcmp(name,"ARG")==0)iaa=93.0;
    if(std::strcmp(name,"GLN")==0)iaa=78.0;
    if(std::strcmp(name,"ASP")==0)iaa=59.0;
    if(std::strcmp(name,"LYS")==0)iaa=79.0;
    if(std::strcmp(name,"GLU")==0)iaa=53.0;

    if(iaa == 0.0)
    {
        cout << "PROBLEM WITH AMINO ACID " << name << endl;
        exit(0);
    }
    return iaa;

}