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;
}
void RotLibConvert_Dunbrack_BBInd::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 + "'!" ));
sb << torsionFile;
ASSERT( sb.size() >= 36 && sb.compare("Backbone-independent rotamer library",0,36,0,false),
ParseException,
"The input coordinate file does not appear to be in Dunbrack BB-independent format");
const char* initLine = "Res Rotamer n(r1) n(r1234) p(r1234) sig p(r234|r1) sig chi1 sig chi2 sig chi3 sig chi4 sig";
int initLineLength = strlen(initLine);
bool begun = false;
while( sb << torsionFile )
{
if( sb.size() >= initLineLength &&
sb.compare( initLine, 0, initLineLength, 0 ) )
{
begun = true;
break;
}
}
ASSERT(begun,ParseException,"Unexpected EOF whilst parsing the Dunbrack BB-independent format library");
sb << torsionFile; // Two blanking lines are present here
sb << torsionFile; // So eradicate them - mwa ha ha ha!
while( sb << torsionFile )
{
sb.Trim();
if( sb.size() == 0 ) continue;
readDefinition( sb, _RotLib );
}
// 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;
}
}
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;
}
}
