static int scanSCREEN(IOStr *io,const char *what,int sn){
int rv;
int nl;
int di;
rv = getInt4(io,"WINDOW/root");
rv = getInt4(io,"COLORMAP/default-colormap");
rv = getInt4(io,"CARD32/white-pixel");
rv = getInt4(io,"CARD32/black-pixel");
rv = getInt4(io,"SETofEVENT/corrent-input-masks");
rv = getInt2(io,"CARD16/width-in-pixels");
rv = getInt2(io,"CARD16/height-in-pixels");
rv = getInt2(io,"CARD16/width-in-millimeters");
rv = getInt2(io,"CARD16/height-in-millimeters");
rv = getInt2(io,"CARD16/min-installed-maps");
rv = getInt2(io,"CARD16/max-installed-maps");
rv = getInt4(io,"VISUALID/root-visual");
rv = getInt1(io,"VISUALID/backing-stores");
rv = getInt1(io,"VISUALID/save-unders");
rv = getInt1(io,"VISUALID/root-depth");
nl = getInt1(io,"VISUALID/number-of-DEPTHs-in-allowed-depth");
for( di = 0; di < nl; di++ ){
if( remLeng(io) <= 0 ){
return EOF;
}
rv = scanDEPTH(io,"LISTofDEPTH/allowed-depath");
}
return 0;
}
static int relayFillPoly(XFlash *Xf,FILE *fc,FILE *ts,int len){
IOStr iob,*io = &iob;
IStr(buf,32*1024);
int rcc;
int wcc;
int rv;
int nl;
int d,g,s,m,x,y;
IStr(poly,1024);
refQStr(pp,poly);
rcc = fread(buf,1,(len-1)*4,fc);
IOinit(io,Xf," cs FP",buf,rcc);
fprintf(stderr," ----\n");
d = rv = getInt4(io,"DRAWABLE/drawable");
g = rv = getInt4(io,"GCONTEXT/gc");
s = rv = getInt1(io,"shape");
m = rv = getInt1(io,"coordinate-mode");
rv = getInt2(io,"unused");
while( 4 <= remLeng(io) ){
x = rv = getInt2(io,"INT16/x");
y = rv = getInt2(io,"INT16/y");
if( poly < pp ){
setVStrPtrInc(pp,',');
}
sprintf(pp,"%d/%d",x,y);
pp += strlen(pp);
}
toFlash(Xf,"FillPoly gc=%d poly={%s}",g,poly);
wcc = fwrite(buf,1,rcc,ts);
return 0;
}
static int scanFORMAT(IOStr *io,const char *what){
int rv;
rv = getInt1(io,"CARD8/depth");
rv = getInt1(io,"CARD8/bits-per-pixel");
rv = getInt1(io,"CARD8/scanline-pad");
rv = getInt1(io,"Pad");
rv = getInt4(io,"Pad");
return 0;
}
/* X11R6.7DRAFT p.122 */
static int scanVISUALTYPE(IOStr *io,const char *what){
int rv;
rv = getInt4(io,"VISUALID/visual-id");
rv = getInt1(io,"class");
rv = getInt1(io,"CARD8/bits-per-rgb-value");
rv = getInt2(io,"CARD16/colormap-entries");
rv = getInt4(io,"CARD32/red-mask");
rv = getInt4(io,"CARD32/green-mask");
rv = getInt4(io,"CARD32/blue-mask");
rv = getPadN(io,"unused",4);
return 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;
}
bool countResidues( char *pqrFile, int res, int *count, int *total )
{
FILE *fp;
fp = fopen( pqrFile, "rt" );
if ( fp == NULL )
{
printError( (char *)"Failed to open PQR file (%s)!", pqrFile );
return false;
}
*count = *total = 0;
char line[ 101 ];
int l = -1;
while ( fgets( line, 100, fp ) != NULL )
{
int i = 0, j;
char tmp[ 100 ];
getString1( line, tmp, 0, 6 ); // get 'ATOM'/'HETATM', and ignore
if ( tmp[ 0 ] != 'A' ) continue;
//getInt1( line, &j,6, 5 ); // get atom number, and ignore
//getString1( line, tmp ,12, 4); // 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 ( getResidueID( tmp ) == res ) ( *count )++;
( *total )++;
}
l = j;
}
fclose( fp );
return true;
}
static int scanDEPTH(IOStr *io,const char *what){
int di;
int rv;
int nl;
int iv;
rv = getInt1(io,"CARD8/depth");
rv = getPadN(io,"unused",1);
nl = getInt2(io,"number-of-VISUALTYPES-in-visuls");
rv = getPadN(io,"unused",4);
for( iv = 0; iv < nl; iv++ ){
if( remLeng(io) <= 0 ){
return EOF;
}
scanVISUALTYPE(io,"Visual");
}
return 0;
}
static int relayInitialResp(IOStr *io,int op){
int rv;
int vl;
int sl;
int nl;
int fi;
rv = getInt1(io,"Sucess");
rv = getPadN(io,"unused",1);
rv = getInt2(io,"major_version");
rv = getInt2(io,"minor_version");
rv = getInt2(io,"length/4");
rv = getInt4(io,"release-number");
rv = getInt4(io,"resource-id-base");
rv = getInt4(io,"resource-id-mask");
rv = getInt4(io,"motion-bufffer-size");
vl = getInt2(io,"length-of-vendor");
rv = getInt2(io,"maximum-request-length");
sl = getInt1(io,"number-of-SCREENs-in-roots");
nl = getInt1(io,"number-for-FORMATs-in-pixmap-formats");
rv = getInt1(io,"image-byte-order");
rv = getInt1(io,"bitmap-format-bit-order");
rv = getInt1(io,"bitmap-format-scanline-unit");
rv = getInt1(io,"bitmap-format-scanline-pad");
rv = getInt1(io,"min-keycode");
rv = getInt1(io,"max-keycode");
rv = getPadN(io,"unused",4);
rv = getSTRING8(io,"Vendor",vl);
rv = skipPad(io,"unused-Padding",4);
for( fi = 0; fi < nl; fi++ ){
rv = scanFORMAT(io,"Format");
}
rv = scanSCREEN(io,"Screen",sl);
rv = skipPad(io,"Pad",8);
return 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;
}
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;
}
static int scanresp(IOStr *io,int op,int seq,OpQue *qop,const char *resp,int rcc){
int rv;
int nl;
if( op == OP_InitialResp ){
relayInitialResp(io,op);
}else
if( resp[0] == EV_KeyPress ){
fprintf(stderr," seq=%d\n",seq);
rv = getInt1(io,"evcode");
rv = getInt1(io,"KEYCODE");
toFlash(io->in_Xf,"KeyPress code=%d",rv);
rv = getInt2(io,"CARD16/Seq#");
/*
if( resp[0] == EV_KeyPress ){
rv = getInt4(io,"TIMESTAMP/time");
rv = getInt4(io,"WINDOW/root");
rv = getInt4(io,"WINDOW/event");
rv = getInt4(io,"WINDOW/child");
rv = getInt2(io,"INT16/root-x");
rv = getInt2(io,"INT16/root-y");
rv = getInt2(io,"INT16/event-x");
rv = getInt2(io,"INT16/event-y");
rv = getInt2(io,"SETofKEYBUTMASK/state");
rv = getInt1(io,"BOOL/same-screen");
}
*/
}else{
fprintf(stderr," seq=%d\n",seq);
rv = getInt1(io,"Reply");
rv = getInt1(io,"opt");
rv = getInt2(io,"CARD16/Seq#");
if( op == OP_QueryExtension ){
rv = getInt4(io,"CARD32/length");
rv = getInt1(io,"BOOL/present");
rv = getInt1(io,"CARD8/major-opcode");
fprintf(stderr,"------------- #%d got opcode=%d, put it into Op Table\n",qop?qop->oq_seq:0,rv);
//addop(rv);
rv = getInt1(io,"CARD8/first-event");
rv = getInt1(io,"CARD8/first-error");
}else
if( op == OP_InternAtom ){
rv = getInt4(io,"CARD32/length");
rv = getInt4(io,"ATOM/atom");
}else
if( op == OP_GetProperty ){
rv = getInt4(io,"CARD32/length");
rv = getInt4(io,"ATOM/atom");
rv = getInt4(io,"CARD32/bytes-after");
rv = getInt4(io,"CARD32/length-of-value-in-format-units");
rv = getPadN(io,"unused",12);
}else
if( op == OP_QueryPointer ){
rv = getInt4(io,"CARD32/length");
rv = getInt4(io,"WINDOW/root");
rv = getInt4(io,"WINDOW/child");
rv = getInt2(io,"INT16/root-x");
rv = getInt2(io,"INT16/root-y");
rv = getInt2(io,"INT16/win-x");
rv = getInt2(io,"INT16/win-y");
rv = getInt2(io,"SETofKEYBUTMASK/mask");
}
}
return 0;
}
