BALL::AssignRadiusProcessor Class Reference

#include <BALL/STRUCTURE/defaultProcessors.h>

Inheritance diagram for BALL::AssignRadiusProcessor:

Public Member Functions
	AssignRadiusProcessor ()
	Default constructor. More...
	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 ()
Public Member Functions inherited from BALL::UnaryProcessor< Atom >
	UnaryProcessor ()
	UnaryProcessor (const UnaryProcessor &)
virtual	~UnaryProcessor ()

Protected Member Functions
bool	buildTable_ () throw (Exception::FileNotFound)

Protected Attributes
String	filename_
StringHashMap< float >	table_
Size	number_of_errors_
Size	number_of_assignments_

Additional Inherited Members
Public Types inherited from BALL::UnaryFunctor< Atom, Processor::Result >
typedef Processor::Result	result_type
typedef Atom	argument_type
typedef Atom &	argument_reference
typedef const Atom &	const_argument_reference
typedef Atom *	argument_pointer
typedef const Atom *	const_argument_pointer

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.

Definition at line 62 of file defaultProcessors.h.

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

Definition at line 132 of file defaultProcessors.h.

Size BALL::AssignRadiusProcessor::number_of_assignments_

protected

Definition at line 135 of file defaultProcessors.h.

Size BALL::AssignRadiusProcessor::number_of_errors_

protected

Definition at line 134 of file defaultProcessors.h.

StringHashMap<float> BALL::AssignRadiusProcessor::table_

protected

Definition at line 133 of file defaultProcessors.h.