static void
ScanCodeBlock(void)
{
int startline = yyline;
/* keutzer
char c;
*/
int c;
if(curCdBlock==NULL) {
curCdBlock = CodeGetBlock();
curCdBlock = CodeMarkLine(curCdBlock,yyline);
}
while((c=getc(fin))!=EOF) {
if (c=='}')
return;
else if (c=='$') ScanTreeReference();
else curCdBlock = CodeStoreChar(curCdBlock, c);
if (c=='\n') yyline++;
if (c=='"') ScanString(getput);
else if (c=='\'') ScanChar();
else if (c=='/') {
if ((c=getc(fin))=='*') {
curCdBlock = CodeStoreChar(curCdBlock, '*');
ScanComment(getput);
}
else ungetc(c, fin);
}
else if (c=='{') {
ScanCodeBlock();
curCdBlock = CodeStoreChar (curCdBlock, '}');
}
}
yyerror2("{ on line %d has no closing }", startline);
nerrors++;
}
static intstar4 SubScr( int info, char PGM *adv_ss_ptr, int size ) {
//==========================================================================
// Get a subscript list.
signed_32 ss[MAX_DIM];
act_dim_list dim_list;
intstar4 PGM *dim_ptr;
signed_32 PGM *ss_ptr;
intstar4 lo;
intstar4 offset;
int num_ss;
dim_list.dim_flags = 0;
_SetDimCount( dim_list.dim_flags, _GetNMLSubScrs( info ) );
dim_list.num_elts = 1;
dim_ptr = &dim_list.subs_1_lo;
num_ss = _GetNMLSubScrs( info );
ss_ptr = ss;
for(;;) {
if( !ScanSNum( ss_ptr ) ) return( FALSE );
++ss_ptr;
lo = *(intstar4 PGM *)adv_ss_ptr;
adv_ss_ptr += sizeof( intstar4 );
dim_list.num_elts *= *(uint PGM *)adv_ss_ptr;
*dim_ptr = lo;
++dim_ptr;
*dim_ptr = lo + *(uint PGM *)adv_ss_ptr - 1;
++dim_ptr;
adv_ss_ptr += sizeof( uint );
--num_ss;
if( num_ss == 0 ) break;
if( !ScanChar( ',' ) ) break;
}
if( !ScanChar( ')' ) ) return( FALSE );
if( !DoSubscript( &dim_list, ss, &offset ) ) return( FALSE );
NmlInAddr = (char HPGM *)NmlInAddr + offset * size;
return( TRUE );
}
inline char DecodeHalf(short s) const {
IMatrix r;
#ifdef DEBUG
cout << "Half word to decode: ";
Print(s, 8);
#endif
MatrixProduct(ScanChar(s), hm, r);
#ifdef DEBUG
cout << "Product Vector: ";
PrintArray(r[0]);
#endif
return FindChar(r[0]);
}
static bool SubStr( string *scb ) {
//=====================================
// Get a substring list.
intstar4 ss1;
intstar4 ss2;
ss1 = 1;
ss2 = scb->len;
if( !ScanChar( ':' ) ) {
if( !ScanSNum( &ss1 ) ) return( FALSE );
if( !ScanChar( ':' ) ) return( FALSE );
}
if( !ScanChar( ')' ) ) {
if( !ScanSNum( &ss2 ) ) return( FALSE );
if( !ScanChar( ')' ) ) return( FALSE );
}
if( !DoSubstring( ss1, ss2, scb->len ) ) return( FALSE );
scb->len = ss2 - ss1 + 1;
scb->strptr = scb->strptr + ss1 - 1;
return( TRUE );
}
// ****************************************************************************
// Constructor: Atom::Atom
//
// Arguments:
// line the line of text in a PDB file
//
// Programmer: Jeremy Meredith
// Creation: March 23, 2006
//
// Modifications:
// Brad Whitlock, Fri Jun 2 13:15:47 PST 2006
// Added Jeremy's fix for yet another style of ATOM line.
//
// Jeremy Meredith, Mon Aug 28 17:58:02 EDT 2006
// Changed the scanning to (a) match the PDB spec document more
// effectively, (b) be faster, and (c) handle some missing elements
// (short lines) better.
//
// Jeremy Meredith, Wed Oct 17 11:27:10 EDT 2007
// Added compound support.
//
// ****************************************************************************
eavlPDBImporter::Atom::Atom(const char *line, int cmpnd)
{
char record[7];
int len = strlen(line);
ScanString(line, len, 1, 6, record);
ScanInt (line, len, 7, 11, &serial);
ScanString(line, len, 13, 16, name);
ScanChar (line, len, 17, &altloc);
ScanString(line, len, 18, 20, resname);
ScanChar (line, len, 22, &chainid);
ScanInt (line, len, 23, 26, &resseq);
ScanChar (line, len, 27, &icode);
ScanFloat (line, len, 31, 38, &x);
ScanFloat (line, len, 39, 46, &y);
ScanFloat (line, len, 47, 54, &z);
ScanFloat (line, len, 55, 60, &occupancy);
ScanFloat (line, len, 61, 66, &tempfactor);
ScanString(line, len, 73, 76, segid);
ScanString(line, len, 77, 78, element);
ScanString(line, len, 79, 80, charge);
// Left-justify element names
if (element[0] == ' ')
{
element[0] = element[1];
element[1] = '\0';
}
if((atomicnumber = ElementNameToAtomicNumber(element)) < 0)
{
// We have a weird file that does not keep the element name in
// the place designated by the ATOM record. Files like this seem
// to use the space for a line number. Check columns 12,13
// for the atom number.
if(line[12] == ' ' || (line[12] >= '0' && line[12] <= '9'))
{
element[0] = line[13];
element[1] = '\0';
}
else if (line[13] >= '0' && line[13] <= '9')
{
element[0] = line[12];
element[1] = '\0';
}
else
{
element[0] = line[12];
element[1] = line[13];
}
atomicnumber = ElementNameToAtomicNumber(element);
if (atomicnumber < 0 &&
element[1] != '\0')
{
element[1] = '\0';
atomicnumber = ElementNameToAtomicNumber(element);
}
if (atomicnumber < 0)
{
char msg[2000];
snprintf(msg, 2000, "Unknown element name <%s> in line: %s",
element, line);
THROW(eavlException, msg);
}
}
// Shift spaces out of the resname.
if(resname[0] == ' ')
{
if(resname[1] == ' ')
{
resname[0] = resname[2];
resname[1] = '\0';
}
else
{
resname[0] = resname[1];
resname[1] = resname[2];
resname[2] = '\0';
}
}
// Look up the residue number from the name.
if((residuenumber = ResiduenameToNumber(resname)) < 0)
{
residuenumber = 0;
}
backbone = false;
if (strcmp(name, " N ")==0 ||
strcmp(name, " C ")==0 ||
strcmp(name, " CA ")==0)
{
backbone = true;
}
compound = cmpnd;
}
