std::vector<std::string> StringBuilder::tokenise( const std::string &_delimiters ) const
{
std::vector<std::string> parts;
size_t i;
size_t j = 0;
size_t x = 0;
StringBuilder sub;
while( SIZE_T_FAIL != (i = XthOf(x++,_delimiters) ) )
{
sub.setTo(*this,j,i-j);
j = i;
sub.Trim(_delimiters);
if( sub.size() > 0 )
{
parts.push_back(sub.toString());
}
}
if( j != m_pos )
{
sub.setTo(*this,j,m_pos-j);
sub.Trim(_delimiters);
if( sub.size() > 0 )
{
parts.push_back(sub.toString());
}
}
return parts;
}
bool ParseData::parse(StringBuilder& sb)
{
if( sb.size() < 107 )
return false;
phi = (short)sb.parseInt(5,4);
psi = (short)sb.parseInt(10,4);
ASSERT(
180 >= phi &&
-180 <= phi &&
180 >= psi &&
-180 <= psi,
ParseException, "Phi/Psi range error");
rotID.setTo(sb, 24, 7 );
rotID.removeAll(' ');
ASSERT(rotID.size() == 4, ParseException, "RotID is bad");
probability = (float)sb.parseDouble(33, 8);
float chi;
chis.clear();
chi = (float)sb.parseDouble( 42, 7 );
if( chi != 0.0 ) // As a coder, this line makes me vomit, but unfortunatly their library is written this way. Eugh!
chis.push_back(chi);
chi = (float)sb.parseDouble( 50, 7 );
if( chi != 0.0 ) // Why could they not have a gap, or at least use NULL or something ?!?
chis.push_back(chi);
chi = (float)sb.parseDouble( 58, 7 );
if( chi != 0.0 )
chis.push_back(chi);
chi = (float)sb.parseDouble( 66, 7 );
if( chi != 0.0 )
chis.push_back(chi);
return true;
}
void RotLibConvert_Dunbrack_BBDep::readLib( const std::string& _LibraryFilename, RotamerLibrary& _RotLib )
{
StringBuilder sb;
std::ifstream* p_torsionFile;
try
{
if( _RotLib.isFinalised() )
throw ProcedureException("readLib() is not allowed, the rotamer library has been finalised, no further import can occur");
// Mappings for things like HIS -> HIE HID HIP
_RotLib.addIonisationAliasWorkingDefaults();
// Make sure Alanine and Glycine are defined non-rotamer residues (the library itself ignores them)
_RotLib.addAsBlankRotamer("ALA");
_RotLib.addAsBlankRotamer("GLY");
p_torsionFile = new std::ifstream(_LibraryFilename.c_str(), std::ifstream::in);
std::ifstream& torsionFile = *p_torsionFile;
if( !torsionFile.is_open() )
throw(IOException( "Dunbrack BB-independent torsional definition file not found: '" + _LibraryFilename + "'!" ));
ParseData pd;
ContainerType data;
StringBuilder prevResName(3);
StringBuilder currResName(4);
StringBuilder cacheLine;
while( true )
{
if( cacheLine.size() > 0 )
{
sb.setTo(cacheLine);
cacheLine.clear();
}
else if( !(sb << torsionFile) )
{
break;
}
sb.Trim();
if( sb.size() == 0 )
continue; // blank line
currResName.setTo(sb,0,3);
if( prevResName.size() == 0 )
{
prevResName.setTo( currResName );
ASSERT( pd.parse( sb ), ParseException, "Malformed line");
data.push_back( pd );
}
else if( prevResName.compare( currResName, 0, 3, 0 ) )
{
// Woooo - we found one :-D
ASSERT( pd.parse( sb ), ParseException, "Malformed line");
data.push_back( pd );
}
else
{
if( data.size() > 0 )
{
processResData( prevResName.toString(), data, _RotLib, switchImportMode );
ASSERT( data.size() == 0, CodeException, "CodeFail");
}
prevResName.setTo( currResName );
cacheLine.setTo( sb ); // we havent actually processed the current line! Store it.
}
}
if( data.size() > 0 )
{
processResData( prevResName.toString(), data, _RotLib, switchImportMode );
ASSERT( data.size() == 0, CodeException, "CodeFail");
}
// Ensure file-handle cleanup
p_torsionFile->close();
delete p_torsionFile;
}
catch( ExceptionBase ex )
{
// Ensure file-handle cleanup
p_torsionFile->close();
delete p_torsionFile;
throw ex;
}
}
