//---------------------------------------------------------------------------
// readSection: position to BOF for a new section,
// do continuous reads until len < 0
//---------------------------------------------------------------------------
Int32 UdrCfgParser::readSection( const char *section, char *buf, Int32 bufLen
, NAString &errorText )
{
Int32 len = -1;
static NABoolean newSection = TRUE;
if (cfgFile)
{
if (!newSection)
len = readPair(cfgFile, buf, bufLen, errorText);
else
{
fseek(cfgFile, 0, SEEK_SET);
if( gotoSection( cfgFile, section, errorText ) )
len = readPair(cfgFile, buf, bufLen, errorText);
newSection = FALSE;
}
}
if (len < 0)
newSection = TRUE;
return len;
}
// Load translation from file
void Localization::loadFromFile(std::ifstream &f)
{
if (f.fail())
{
dprintf("Failed to open translation, skip.\n");
return;
}
dprintf("Read translation ...\n");
string strKey, strValue;
while (readPair(f, strKey, strValue))
{
set(strKey, strValue);
}
dprintf("Translation loaded to memory.\n");
}
void loadTOP(char* filename){
int i;
printf("Reading topology.\n");
FILE* topFile = fopen(filename, "r");
char buffer[buf_size];
if (topFile != NULL ){
while(fgets(buffer, buf_size, topFile) != NULL){
if(strncmp(buffer, "[ atoms ]", 9) == 0){
printf("Counting atoms...\n");
sop.aminoCount = countRows(topFile);
printf("%d found.\n", sop.aminoCount);
}
if(strncmp(buffer, "[ bonds ]", 9) == 0){
printf("Counting covalent bonds...\n");
sop.bondCount = countRows(topFile);
printf("%d found.\n", sop.bondCount);
}
if(strncmp(buffer, "[ native ]", 10) == 0){
printf("Counting native contacts...\n");
sop.nativeCount = countRows(topFile);
printf("%d found.\n", sop.nativeCount);
}
if(strncmp(buffer, "[ pairs ]", 9) == 0){
printf("Counting pairs...\n");
sop.pairCount = countRows(topFile);
printf("%d found.\n", sop.pairCount);
}
}
} else {
printf("ERROR: cant find topology file '%s'.\n", filename);
exit(0);
}
sop.aminos = (Atom*)calloc(sop.aminoCount, sizeof(Atom));
sop.bonds = (CovalentBond*)calloc(sop.bondCount, sizeof(CovalentBond));
sop.natives = (NativeContact*)calloc(sop.nativeCount, sizeof(NativeContact));
sop.pairs = (PossiblePair*)calloc(sop.pairCount, sizeof(PossiblePair));
rewind(topFile);
while(fgets(buffer, buf_size, topFile) != NULL){
if(strncmp(buffer, "[ atoms ]", 9) == 0){
fgets(buffer, buf_size, topFile);
for(i = 0; i < sop.aminoCount; i++){
readAtom(&sop.aminos[i], topFile);
}
}
if(strncmp(buffer, "[ bonds ]", 9) == 0){
fgets(buffer, buf_size, topFile);
for(i = 0; i < sop.bondCount; i++){
TOPPair pair = readPair(topFile);
sop.bonds[i].i = pair.i;
sop.bonds[i].j = pair.j;
sop.bonds[i].r0 = pair.c0;
}
}
if(strncmp(buffer, "[ native ]", 10) == 0){
fgets(buffer, buf_size, topFile);
for(i = 0; i < sop.nativeCount; i++){
TOPPair pair = readPair(topFile);
sop.natives[i].i = pair.i;
sop.natives[i].j = pair.j;
sop.natives[i].r0 = pair.c0;
sop.natives[i].eh = pair.c1;
}
}
if(strncmp(buffer, "[ pairs ]", 9) == 0){
fgets(buffer, buf_size, topFile);
for(i = 0; i < sop.pairCount; i++){
TOPPair pair = readPair(topFile);
sop.pairs[i].i = pair.i;
sop.pairs[i].j = pair.j;
}
}
}
fclose(topFile);
printf("Done reading topology.\n");
}
