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;
}
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);
}
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;
}
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;
}
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;
}
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;
}
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;
}