Templates Class Reference
[Force Field Parameters]

Force Field Residue Template Class. More...

#include <templates.h>

Inheritance diagram for Templates:

List of all members.

Public Member Functions
Constructors and Destructors
	Templates ()
	Default constructor.
	Templates (const Templates &templates, bool deep=true)
	Copy constructor.
virtual	~Templates () throw ()
	Destructor.
virtual void	clear () throw ()
	Clear method.
virtual bool	extractSection (Parameters &parameters, const String &section_name)
	Reads a parameter section from an INI file.
float	getCharge (const String &name) const
	Returns the numeric type for a given string.
String	getTypeName (const String &name) const
	Returns the name for a given index.
bool	has (const String &name) const
	Queries whether a given template atom is defined.
void	assign (System &system, bool overwrite_existing_typenames=true, bool overwrite_non_zero_charges=true) const
	Assign charges and type names.
void	assignCharges (System &system, bool overwrite_non_zero_charges=true) const
	Assign charges and type names.
void	assignTypeNames (System &system, bool overwrite_existing_typenames=true) const
	Assign type names.
Assignment
Templates &	operator= (const Templates &templates)
	Assignment operator.
void	setMaximumUnassignedAtoms (Size nr)
	Set the number of atoms, for which the assignment can fail, until the assign() methods aborts and return false.
Size	getMaximumUnassignedAtoms () const
	Get the number of atoms, for which the assignment can fail, until the assign() methods aborts and return false.
Size	getNumberOfUnassignedAtoms () const
	Get the number of atoms, for which the assignment failed.
HashSet< const Atom * > &	getUnassignedAtoms ()
	Get the atoms, for which the assignment failed.
Protected Attributes
StringHashMap< float >	charges_
StringHashMap< String >	type_names_
HashSet< const Atom * >	unassigned_atoms_
Size	max_number_unassigned_atoms_

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Detailed Description

Force Field Residue Template Class.

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Constructor & Destructor Documentation

Templates::Templates (   )

Default constructor.

Templates::Templates (  const Templates &  templates, bool  deep = true )

Copy constructor.

virtual Templates::~Templates (   )  throw () [virtual]

Destructor.

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Member Function Documentation

virtual void Templates::clear (   )  throw () [virtual]

Clear method. Reimplemented from ParameterSection.

virtual bool Templates::extractSection (  Parameters &  parameters, const String &  section_name )  [virtual]

Reads a parameter section from an INI file. This method reads the section given in section_name from ini_file, interprets (if given) a format line, reads the data from this section according to the format, and builds some datastructures for fast and easy acces this data. The section is typically entitled ChargesAndTypeNames. Reimplemented from ParameterSection.

float Templates::getCharge (  const String &  name  )  const

Returns the numeric type for a given string.

Size Templates::getMaximumUnassignedAtoms (   )  const

Get the number of atoms, for which the assignment can fail, until the assign() methods aborts and return false.

Templates& Templates::operator= (  const Templates &  templates  )

Assignment operator. Copy the contents of templates into this residue template object. Parameters: templates  the residue template object to be copied

void Templates::setMaximumUnassignedAtoms (  Size  nr  )

Set the number of atoms, for which the assignment can fail, until the assign() methods aborts and return false. By default, there is no limit set.