BALL::AssignRadiusProcessor Class Reference
[Miscellaneous]
#include <BALL/STRUCTURE/defaultProcessors.h>
Public Member Functions | |
| AssignRadiusProcessor () | |
Default constructor. | |
| AssignRadiusProcessor (const String &filename) throw (Exception::FileNotFound) | |
| virtual bool | start () |
| virtual bool | finish () |
| virtual Processor::Result | operator() (Atom &atom) |
| void | setFilename (const String &filename) throw (Exception::FileNotFound) |
| String & | getFilename () |
| Size | getNumberOfAssignments () |
| Size | getNumberOfErrors () |
Protected Member Functions | |
| bool | buildTable_ () throw (Exception::FileNotFound) |
Protected Attributes | |
| String | filename_ |
| StringHashMap< float > | table_ |
| Size | number_of_errors_ |
| Size | number_of_assignments_ |
Detailed Description
Assigns the radius to each atom. This processor reads a radius table from a file and assigns each atom a radius according to its name and the name of the fragment the atom is contained in.
Constructor & Destructor Documentation
| BALL::AssignRadiusProcessor::AssignRadiusProcessor | ( | ) |
Default constructor.
| BALL::AssignRadiusProcessor::AssignRadiusProcessor | ( | const String & | filename | ) | throw (Exception::FileNotFound) |
Detailled constructor. If the file can not be found in the actual path, FileNotFound is thrown.
Member Function Documentation
| bool BALL::AssignRadiusProcessor::buildTable_ | ( | ) | throw (Exception::FileNotFound) [protected] |
| virtual bool BALL::AssignRadiusProcessor::finish | ( | ) | [virtual] |
Finish method. Allways returns true and does nothing.
Reimplemented from BALL::UnaryProcessor< Atom >.
| String& BALL::AssignRadiusProcessor::getFilename | ( | ) |
Return the current filename
| Size BALL::AssignRadiusProcessor::getNumberOfAssignments | ( | ) |
Return the number of assigned atoms.
| Size BALL::AssignRadiusProcessor::getNumberOfErrors | ( | ) |
Return the number of unassignable atoms. Only the atoms from the container, which cannot be matched, count as errors. The unmatched atoms from the file dont care.
| virtual Processor::Result BALL::AssignRadiusProcessor::operator() | ( | Atom & | atom | ) | [virtual] |
Applicator method The full names of all atoms in the container are compared to the atomnames from the file. For all matching atoms, the radii from the file are set. If for an atom from the container no matching atom from the file can be found, a warning is displayed and the number of errors increases. If in the file, the is a nonmatching atom, nothing happens.
- The matching of the atoms from the file with the atom of the container works like this:
- 1.) The original atomnames are tested.
- 2.) The full name of the atoms are compared.
- 3.) Wild card matching:
"*:" + atom_name
- See also:
- Residue
Reimplemented from BALL::UnaryProcessor< Atom >.
Reimplemented in BALL::AssignChargeProcessor.
| void BALL::AssignRadiusProcessor::setFilename | ( | const String & | filename | ) | throw (Exception::FileNotFound) |
Set the filename to read the radii from. If the file can not be found in the actual path, FileNotFound is thrown.
| virtual bool BALL::AssignRadiusProcessor::start | ( | ) | [virtual] |
Start Method. The number of errors and the numbers of assignments are reset to 0. The radius data from the file is extracted.
- Returns:
- bool, allways true
Reimplemented from BALL::UnaryProcessor< Atom >.
Reimplemented in BALL::AssignChargeProcessor.
Member Data Documentation
String BALL::AssignRadiusProcessor::filename_ [protected] |
Size BALL::AssignRadiusProcessor::number_of_errors_ [protected] |
StringHashMap<float> BALL::AssignRadiusProcessor::table_ [protected] |