Ejemplo n.º 1
0
bool getTotalCharge( char *pqrFile, double *tCharge )
{
   FILE *fp;

   fp = fopen( pqrFile, (char *)"rt" );

   if ( fp == NULL )
     {
        printError( (char *)"Failed to open PQR file (%s)!", pqrFile );
        return false;
     }
     
   *tCharge = 0;  
   char line[ 101 ];

   while ( fgets( line, 100, fp ) != NULL )
     {
        int i = 0, j;
        char tmp[ 101 ];

        i = getAlphaString( line, i, tmp );   // get 'ATOM'/'HETATM', and ignore

        if ( tmp[ 0 ] != 'A' ) continue;

        //i = getInt( line, i, &j );            // get atom number, and ignore
        //i = getString( line, i, tmp );        // get atom name, and ignore

	// don't use these either?
        getString1( line, tmp, 17, 3 );   // get residue name
	getInt1( line, &j, 22, 4 );            // get residue number
          
        double v;  
          
        //i = getDouble( line, i, &v );         // get X coordinate
        //i = getDouble( line, i, &v );         // get Y coordinate
        //i = getDouble( line, i, &v );         // get Z coordinate
    
        getDouble1( line, &v, 54, 9 );         // get charge
        
        *tCharge += v;

        //i = getDouble( line, i, &v );         // get radius
     }
     
   fclose( fp );

   return true;
}
Ejemplo n.º 2
0
void LevelOneDec::setVectorsToTables()
{
    for (size_t i = 0; i < row; ++i)
    {
        muVector.push_back(getMu(i));
        alphaVector.push_back(getAlphaString(i));
    }

    createVector2DSensReadingsLow(0.003);
    createVector2DSensReadingsHigh(0.003);

    for (size_t i = 0; i < row; ++i)
    {
        muLowerLimitVector.push_back(getMuLowerLimit(i));
        muUpperLimitVector.push_back(getMuHighLimit(i));
    }

#ifdef _DEBUG
    qDebug() << "Size of mu Low:" << muLowerLimitVector.size();
    qDebug() << "Size of mu High:" << muUpperLimitVector.size();
#endif

    avrg_mu = getAvrgMu();
    avrg_alpha = getAvrgAlpha();

    for (size_t i = 0; i <= row; ++i)
    {
        getMuForecast(i, 0.1);
        getAlphaForecast(i, 0.1);
    }

    tableLevelOneModel->setCurrencyVectors(vectorDateToLevelOne,
                                           muVector,
                                           muVectorForecast,
                                           alphaVector,
                                           alphaVectorForecast);

    tableStabilityLevelOneModel->setCurrencyVectors(vectorDateToLevelOne,
                                                    muLowerLimitVector,
                                                    muVector,
                                                    muUpperLimitVector);

    viewTableLevelOneModel->selectRow(row);
}
Ejemplo n.º 3
0
bool readGlycines( char *pqrFile, int *nAtm, double **atm )
{

   int nRes = 0, nChn = 0;
   RESIDUE *res = NULL;
   int *chn = NULL;
   
   if ( !readResidues( pqrFile, &nRes, &res, &nChn, &chn ) ) 
     {
       freeMem( res );
       freeMem( chn);
       return false;
     }  

   FILE *fp;

   fp = fopen( pqrFile, (char *)"rt" );

   if ( fp == NULL )
     {
        printError( (char *)"Failed to open PQR file (%s)!", pqrFile );
        return false;
     }

   int numAtoms = 0;

   char line[ 101 ];
   int k = -1, l = -1;

   while ( fgets( line, 100, fp ) != NULL )
     {
        int i = 0, j;
        char tmp[ 100 ];

        i = getAlphaString( line, i, tmp );   // get 'ATOM'/'HETATM', and ignore

        if ( tmp[ 0 ] != 'A' ) continue;

        numAtoms++;
     }

   fclose( fp );

   *nAtm = numAtoms;
   ( *atm ) = ( double * ) malloc( 5 * ( *nAtm ) * sizeof( double ) );

   if ( *atm == NULL )
     {
        printError( (char *)"Failed to allocate memory!" );
        return false;
     }

   fp = fopen( pqrFile, (char *)"rt" );

   if ( fp == NULL )
     {
         printError( (char *)"Failed to open PQR file (%s)!", pqrFile );
         return false;
     }

   int n = 0;
   k = -1; l = -1;   

   while ( fgets( line, 100, fp ) != NULL )
     {
        int i = 0, j;
        char tmp[ 100 ];

        i = getAlphaString( line, i, tmp );   // get 'ATOM'/'HETATM', and ignore

        if ( tmp[ 0 ] != 'A' ) continue;

        //i = getInt( line, i, &j );            // get atom number, and ignore
        //i = getString( line, i, tmp );        // get atom name, and ignore

        getString1( line, tmp, 17, 3 );   // get residue name

        getInt1( line, &j, 22, 4 );            // get residue number
        
        if ( j != l )
          {
            k++;
            l = j;
          }        
        
        if ( isGXY( nRes, res, k ) || isYXG( nRes, res, k ) 
          || ( ( k >= 1 ) && ( isGXY( nRes, res, k - 1 ) || isYXG( nRes, res, k - 1 ) ) ) 
          || ( ( k >= 2 ) && ( isGXY( nRes, res, k - 2 ) || isYXG( nRes, res, k - 2 ) ) ) )
          {
              double v;  
                
              getDouble1( line, &v, 30, 8 );         // get X coordinate
              ( *atm )[ 5 * n + 0 ] = v;    
        
              getDouble1( line, &v, 38, 8);         // get Y coordinate
              ( *atm )[ 5 * n + 1 ] = v;    
        
              getDouble1( line, &v, 46, 8 );         // get Z coordinate
              ( *atm )[ 5 * n + 2 ] = v;    
          
              getDouble1( line, &v, 54, 9 );         // get charge
              ( *atm )[ 5 * n + 3 ] = v;    
        
              getDouble1( line, &v, 63, 7 );         // get radius
              ( *atm )[ 5 * n + 4 ] = v;   
              
              n++;            
          }          
     }
     
   *nAtm = n;  
     
   fclose( fp );

   freeMem( res );
   freeMem( chn);

   return true;
}
Ejemplo n.º 4
0
bool readAtomsWithResidueInfo( char *pqrFile, int *nAtm, double **atm )
{
   FILE *fp;

   fp = fopen( pqrFile, (char *)"rt" );

   if ( fp == NULL )
     {
        printError( (char *)"Failed to open PQR file (%s)!", pqrFile );
        return false;
     }

   int numRes = 0;

   char line[ 101 ];
   int l = -1, r = -1;

   while ( fgets( line, 100, fp ) != NULL )
     {
        int i = 0, j;
        char tmp[ 100 ];

        i = getAlphaString( line, i, tmp );   // get 'ATOM'/'HETATM', and ignore

        if ( tmp[ 0 ] != 'A' ) continue;

        //i = getInt( line, i, &j );            // get atom number, and ignore
        //i = getString( line, i, tmp );        // get atom name, and ignore

        getString1( line, tmp, 17, 3 );   // get residue name
        
        int resID = getResidueID( tmp );

        getInt1( line, &j, 22, 4 );            // get residue number

        if ( ( j != l ) || ( resID != r ) ) numRes++;

        l = j;
        r = resID;
     }

   fclose( fp );
   
   printf( (char *)"\nnumRes = %d\n", numRes );
   fflush( stdout );

   *nAtm = numRes;
   ( *atm ) = ( double * ) malloc( 5 * ( *nAtm ) * sizeof( double ) );

   if ( *atm == NULL )
     {
        printError( (char *)"Failed to allocate memory!" );
        return false;
     }

   fp = fopen( pqrFile, (char *)"rt" );

   if ( fp == NULL )
     {
         printError( (char *)"Failed to open PQR file (%s)!", pqrFile );
         return false;
     }

   int n = 0;
   
   l = -1; r = -1;
   
   bool done = false;

   while ( fgets( line, 100, fp ) != NULL )
     {
        int i = 0, j;
        char tmp[ 100 ], atn[ 100 ];

        i = getAlphaString( line, i, tmp );   // get 'ATOM'/'HETATM', and ignore

        if ( tmp[ 0 ] != 'A' ) continue;

        //i = getInt( line, i, &j );            // get atom number, and ignore

        getString1( line, atn, 12, 4 );        // get atom name

        getString1( line, tmp, 17, 3 );   // get residue name
        
        int resID = getResidueID( tmp );
       
        getInt1( line, &j, 22, 4 );            // get residue number       
	
        if ( ( j != l ) || ( resID != r ) ) done = false;

        l = j;
        r = resID;        
                
	// arand: changed "CA" to " CA " and "CB" to " CB " to match the new method of reading data...
        if ( !done && ( resID != NONE ) && ( ( ( resID == GLY ) && !strcmp( atn, (char *)" CA " ) ) || ( ( resID != GLY ) && !strcmp( atn, (char *)" CB " ) ) ) )
          {              
            double v;  
              
            getDouble1( line, &v, 30, 8 );         // get X coordinate
            ( *atm )[ 5 * n + 0 ] = v;    
    
	    getDouble1( line, &v, 38, 8 );         // get Y coordinate
            ( *atm )[ 5 * n + 1 ] = v;    
    
            getDouble1( line, &v, 46, 8 );         // get Z coordinate
            ( *atm )[ 5 * n + 2 ] = v;    
        
            ( *atm )[ 5 * n + 3 ] = resID - 1;    
            
            ( *atm )[ 5 * n + 4 ] = j;   
            
            n++;
            
            done = true;
          }  
     }
   
   *nAtm = n;
     
   fclose( fp );

   return true;
}
Ejemplo n.º 5
0
bool readAtomsOnly( char *pqrFile, int *nAtm, double **atm )
{
   FILE *fp;

   fp = fopen( pqrFile, (char *)"rt" );

   if ( fp == NULL )
     {
        printError( (char *)"Failed to open PQR file (%s)!", pqrFile );
        return false;
     }

   int numAtoms = 0;

   char line[ 101 ];
   
   while ( fgets( line, 100, fp ) != NULL )
     {
        int i = 0, j;
        char tmp[ 100 ];

        i = getAlphaString( line, i, tmp );   // get 'ATOM'/'HETATM', and ignore

        if ( tmp[ 0 ] != 'A' ) continue;

        numAtoms++;
     }

   fclose( fp );

   *nAtm = numAtoms;
   ( *atm ) = ( double * ) malloc( 5 * ( *nAtm ) * sizeof( double ) );

   if ( *atm == NULL )
     {
        printError( (char *)"Failed to allocate memory!" );
        return false;
     }

   fp = fopen( pqrFile, (char *)"rt" );

   if ( fp == NULL )
     {
         printError( (char *)"Failed to open PQR file (%s)!", pqrFile );
         return false;
     }

   int n = 0;

   while ( fgets( line, 100, fp ) != NULL )
     {
        int i = 0, j;
        char tmp[ 100 ];

        i = getAlphaString( line, i, tmp );   // get 'ATOM'/'HETATM', and ignore

        if ( tmp[ 0 ] != 'A' ) continue;

        //i = getInt( line, i, &j );            // get atom number, and ignore
        //i = getString( line, i, tmp );        // get atom name, and ignore

        getString1( line, tmp, 17, 3 );   // get residue name

        getInt1( line, &j, 22, 4 );            // get residue number
          
        double v;  
          
        getDouble1( line, &v, 30, 8);         // get X coordinate
        ( *atm )[ 5 * n + 0 ] = v;    

        getDouble1( line, &v, 38, 8 );         // get Y coordinate
        ( *atm )[ 5 * n + 1 ] = v;    

        getDouble1( line, &v, 46, 8 );         // get Z coordinate
        ( *atm )[ 5 * n + 2 ] = v;    
    
        getDouble1( line, &v, 54, 9 );         // get charge
        ( *atm )[ 5 * n + 3 ] = v;    

        getDouble1( line, &v, 63, 7 );         // get radius
        ( *atm )[ 5 * n + 4 ] = v;   
        
        n++;  
     }
     
   fclose( fp );

   return true;
}
Ejemplo n.º 6
0
bool readAtomsAndResidues( char *pqrFile, int *nAtm, double **atm, int *nRes, RESIDUE **res, int *nChn, int **chn )
{
   FILE *fp;

   fp = fopen( pqrFile, (char *)"rt" );

   if ( fp == NULL )
     {
        printError( (char *)"Failed to open PQR file (%s)!", pqrFile );
        return false;
     }

   int numAtoms = 0, numRes = 0, numChains = 1;

   char line[ 101 ];
   int l = -1;

   while ( fgets( line, 100, fp ) != NULL )
     {
        int i = 0, j;
        char tmp[ 100 ];
        char tmp1[ 100 ];

        i = getAlphaString( line, i, tmp );   // get 'ATOM'/'HETATM', and ignore

        if ( tmp[ 0 ] != 'A' ) continue;

        //i = getInt( line, i, &j );            // get atom number, and ignore
        //i = getString( line, i, tmp );        // get atom name, and ignore
        //i = getAlphaString( line, i, tmp );   // get residue name, and ignore
        //i = getAlphaString( line, i, tmp1 );   // get residue name, and ignore

        getInt1( line, &j, 22, 4 );            // get residue number

        numAtoms++;

        if ( j != l ) numRes++;
        
        if ( j < l ) numChains++;

        l = j;
     }

   fclose( fp );

   *nAtm = numAtoms;
   *nRes = numRes;
   *nChn = numChains;
   ( *atm ) = ( double * ) malloc( 7 * ( *nAtm ) * sizeof( double ) );
   ( *res ) = ( RESIDUE * ) malloc( ( *nRes ) * sizeof( RESIDUE ) );
   ( *chn ) = ( int * ) malloc( ( *nChn + 1 ) * sizeof( int ) );   

   if ( ( *atm == NULL ) || ( *res == NULL ) || ( *chn == NULL ) )
     {
        printError( (char *)"Failed to allocate memory!" );
        return false;
     }

   fp = fopen( pqrFile, (char *)"rt" );

   if ( fp == NULL )
     {
         printError( (char *)"Failed to open PQR file (%s)!", pqrFile );
         return false;
     }

   int k = 0, n = 0, c = 1;
   l = -1;
   
   ( *chn )[ 0 ] = 0;

   while ( fgets( line, 100, fp ) != NULL )
     {
        int i = 0, j;
        char tmp[ 100 ];
        char tmp1[ 100 ];

        i = getAlphaString( line, i, tmp );   // get 'ATOM'/'HETATM', and ignore

        if ( tmp[ 0 ] != 'A' ) continue;

        //i = getInt( line, i, &j );            // get atom number, and ignore
        //i = getString( line, i, tmp );        // get atom name, and ignore

        getString1( line, tmp, 17, 3 );   // get residue name

        getInt1( line, &j, 22, 4 );            // get residue number

        if ( j != l )
          {
            if ( j < l ) ( *chn )[ c++ ] = k;

            ( *res )[ k ].resNum = j;
            ( *res )[ k ].chainID = c;
            ( *res )[ k ].resID = getResidueID( tmp );

            k++;
            
            l = j;
          }
          
        double v;  
          
        getDouble1( line, &v, 30, 8 );         // get X coordinate
        ( *atm )[ 7 * n + 0 ] = v;    

        getDouble1( line, &v, 38, 8 );         // get Y coordinate
        ( *atm )[ 7 * n + 1 ] = v;    

        getDouble1( line, &v, 46, 8 );         // get Z coordinate
        ( *atm )[ 7 * n + 2 ] = v;    
    
        getDouble1( line, &v, 54, 9 );         // get charge
        ( *atm )[ 7 * n + 3 ] = v;    

        getDouble1( line, &v, 63, 7 );         // get radius
        ( *atm )[ 7 * n + 4 ] = v;   

        ( *atm )[ 7 * n + 5 ] = j;            // residue number  
        
        ( *atm )[ 7 * n + 6 ] = c;            // chain number  
                          
        n++;  
     }
     
   ( *chn )[ c ] = k;  

   fclose( fp );

   return true;
}
Ejemplo n.º 7
0
bool readResidues( char *pqrFile, int *nRes, RESIDUE **res, int *nChn, int **chn )
{
   FILE *fp;

   fp = fopen( pqrFile, (char *)"rt" );

   if ( fp == NULL )
     {
        printError( (char *)"Failed to open PQR file (%s)!", pqrFile );
        return false;
     }

   int numRes = 0, numChains = 1;

   char line[ 101 ];
   int l = -1;

   while ( fgets( line, 100, fp ) != NULL )
     {
        int i = 0, j;
        char tmp[ 100 ];
        char tmp1[ 100 ];

        getString1( line, tmp, 0, 6 );   // get 'ATOM'/'HETATM', and ignore

        if ( tmp[ 0 ] != 'A' ) continue;

        //i = getInt( line, i, &j );            // get atom number, and ignore
        //i = getString( line, i, tmp );        // get atom name, and ignore

        getString1( line, tmp, 17, 3 );   // get residue name, and ignore	

        getInt1( line, &j, 22, 4 );            // get residue number

        if ( j != l ) numRes++;
        
        if ( j < l ) numChains++;

        l = j;
     }

   fclose( fp );

   *nRes = numRes;
   *nChn = numChains;
   ( *res ) = ( RESIDUE * ) malloc( ( *nRes ) * sizeof( RESIDUE ) );
   ( *chn ) = ( int * ) malloc( ( *nChn + 1 ) * sizeof( int ) );   

   if ( ( *res == NULL ) || ( *chn == NULL ) )
     {
        printError( (char *)"Failed to allocate memory!" );
        return false;
     }

   fp = fopen( pqrFile, (char *)"rt" );

   if ( fp == NULL )
     {
         printError( (char *)"Failed to open PQR file (%s)!", pqrFile );
         return false;
     }

   int k = 0, c = 1;
   l = -1;
   
   ( *chn )[ 0 ] = 0;

   while ( fgets( line, 100, fp ) != NULL )
     {
        int i = 0, j;
        char tmp[ 100 ];
        char tmp1[ 100 ];

        i = getAlphaString( line, i, tmp );   // get 'ATOM'/'HETATM', and ignore

        if ( tmp[ 0 ] != 'A' ) continue;

	// old
        //i = getInt( line, i, &j );            // get atom number, and ignore
        //i = getString( line, i, tmp );        // get atom name, and ignore

        getString1( line, tmp, 17, 3 );   // get residue name

        getInt1( line, &j, 22, 4 );            // get residue number

        if ( j != l )
          {
            if ( j < l ) ( *chn )[ c++ ] = k;

            ( *res )[ k ].resNum = j;
            ( *res )[ k ].chainID = c;
            ( *res )[ k ].resID = getResidueID( tmp );

            k++;
            
            l = j;
          }
     }
     
   ( *chn )[ c ] = k;  

   fclose( fp );

   return true;
}