bool XyzFileFormat::readMappedFile(const boost::iostreams::mapped_file_source &input, chemkit::MoleculeFile *file)
{
const char *data = input.data();
size_t position = 0;
// atom count line
unsigned int atomCount = 0;
int count = sscanf(&data[position], "%u", &atomCount);
if(count != 1){
setErrorString("Failed to read atom count line");
return false;
}
while(data[position++] != '\n');
// comment line
while(data[position++] != '\n');
// create molecule
boost::shared_ptr<chemkit::Molecule> molecule = boost::make_shared<chemkit::Molecule>();
// read atoms and coordinates
for(unsigned int i = 0; i < atomCount; i++){
char symbol[4];
double x, y, z;
count = sscanf(&data[position], "%3s %lf %lf %lf", symbol, &x, &y, &z);
if(count != 4){
setErrorString("Failed to read atom line");
continue;
}
while(data[position++] != '\n');
chemkit::Atom *atom = 0;
if(strlen(symbol) == 0){
continue;
}
else if(isdigit(symbol[0])){
chemkit::Element::AtomicNumberType atomicNumber =
boost::lexical_cast<chemkit::Element::AtomicNumberType>(symbol);
atom = molecule->addAtom(atomicNumber);
}
else{
atom = molecule->addAtom(symbol);
}
// set atom position
if(atom){
atom->setPosition(x, y, z);
}
}
// add molecule to file
file->addMolecule(molecule);
return true;
}
void StringLookups::Load(boost::iostreams::mapped_file_source &file_map, typeTypes Type)
{
UINT8 *buffer, *dataBegin;
buffer = const_cast<UINT8 *>(reinterpret_cast<const UINT8 *>(file_map.data()));
UINT32 stringCount = *reinterpret_cast<UINT32 *>(buffer);
buffer += 8; // 4 for stringCount, 4 for dataSize (skipped)
dataBegin = buffer + (stringCount * 8) + (Type == 0 ? 0 : 4);
for(UINT32 i = 0; i < stringCount; ++i)
{
UINT32 id = *reinterpret_cast<UINT32 *>(buffer);
UINT32 offset = *reinterpret_cast<UINT32 *>(buffer);
STRING value = reinterpret_cast<STRING>(dataBegin + offset);
Strings[id] = value;
}
}
void StringLookups::Open(STRING FileName, boost::iostreams::mapped_file_source &file_map)
{
try
{
file_map.open(FileName);
}
catch(std::ios::failure const &ex)
{
printer("StringLookups: Error - Unable to open \"%s\" as read only via memory mapping. The file is probably open in another application.\n", FileName);
throw ex;
}
catch(std::exception &ex)
{
printer("StringLookups: Error - Unable to open \"%s\" as read only via memory mapping.\n", FileName);
throw ex;
}
catch(...)
{
printer("StringLookups: Error - Unable to open \"%s\" as read only via memory mapping. An unhandled exception occurred.\n", FileName);
throw;
}
}
size_t map(T& val, boost::iostreams::mapped_file_source const& m, uint64_t flags = 0, const char* friendly_name = "<TOP>")
{
return map(val, m.data(), flags, friendly_name);
}
