BALL::Templates Class Reference

#include <BALL/MOLMEC/PARAMETER/templates.h>

Inheritance diagram for BALL::Templates:

Public Member Functions
Constructors and Destructors
	Templates ()
	Templates (const Templates &templates, bool deep=true)
virtual	~Templates ()
virtual void	clear ()
virtual bool	extractSection (Parameters &parameters, const String &section_name)
float	getCharge (const String &name) const
String	getTypeName (const String &name) const
bool	has (const String &name) const
void	assign (System &system, bool overwrite_existing_typenames=true, bool overwrite_non_zero_charges=true) const
void	assignCharges (System &system, bool overwrite_non_zero_charges=true) const
void	assignTypeNames (System &system, bool overwrite_existing_typenames=true) const
Public Member Functions inherited from BALL::ParameterSection
	ParameterSection ()
	ParameterSection (const ParameterSection &parameter_section)
virtual	~ParameterSection ()
bool	extractSection (Parameters &parameters, const String &section_name)
const String &	getSectionName () const
const String &	getValue (const String &key, const String &variable) const
bool	has (const String &key, const String &variable) const
bool	has (const String &key) const
bool	hasVariable (const String &variable) const
Position	getColumnIndex (const String &variable) const
Size	getNumberOfVariables () const
Size	getNumberOfKeys () const
const String &	getValue (Position key_index, Position variable_index) const
const String &	getKey (Position key_index) const
const ParameterSection &	operator= (const ParameterSection &section)
virtual bool	isValid () const
bool	operator== (const ParameterSection &parameter_section) const

Assignment
StringHashMap< float >	charges_
StringHashMap< String >	type_names_
HashSet< const Atom * >	unassigned_atoms_
Size	max_number_unassigned_atoms_
Templates &	operator= (const Templates &templates)
void	setMaximumUnassignedAtoms (Size nr)
Size	getMaximumUnassignedAtoms () const
Size	getNumberOfUnassignedAtoms () const
	Get the number of atoms, for which the assignment failed. More...
HashSet< const Atom * > &	getUnassignedAtoms ()
	Get the atoms, for which the assignment failed. More...

Additional Inherited Members
Public Types inherited from BALL::ParameterSection
enum	{ MAX_FIELDS = 20 }
Public Attributes inherited from BALL::ParameterSection
Options	options
Static Public Attributes inherited from BALL::ParameterSection
static const String	UNDEFINED
Protected Attributes inherited from BALL::ParameterSection
String	section_name_
String	format_line_
StringHashMap< Index >	section_entries_
StringHashMap< Index >	variable_names_
std::vector< String >	entries_
std::vector< String >	keys_
Size	number_of_variables_
std::vector< float >	version_
bool	valid_

Detailed Description

Force Field Residue Template Class.

Definition at line 31 of file templates.h.

Constructor & Destructor Documentation

Templates() [1/2]

BALL::Templates::Templates

(

)

Default constructor.

Templates() [2/2]

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

Copy constructor.

~Templates()

virtual BALL::Templates::~Templates ( )

virtual

Destructor.

Member Function Documentation

assign()

void BALL::Templates::assign	(	System &	system,
		bool	overwrite_existing_typenames = true,
		bool	overwrite_non_zero_charges = true
	)		const

Assign charges and type names

assignCharges()

void BALL::Templates::assignCharges	(	System &	system,
		bool	overwrite_non_zero_charges = true
	)		const

Assign charges and type names

assignTypeNames()

void BALL::Templates::assignTypeNames	(	System &	system,
		bool	overwrite_existing_typenames = true
	)		const

Assign type names

clear()

virtual void BALL::Templates::clear ( )

virtual

Clear method.

Reimplemented from BALL::ParameterSection.

extractSection()

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

virtual

Parameter extraction 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.

getCharge()

float BALL::Templates::getCharge

(

const String &

name

)

const

Returns the numeric type for a given string.

getMaximumUnassignedAtoms()

Size BALL::Templates::getMaximumUnassignedAtoms

(

)

const

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

getNumberOfUnassignedAtoms()

Size BALL::Templates::getNumberOfUnassignedAtoms

(

)

const

Get the number of atoms, for which the assignment failed.

getTypeName()

String BALL::Templates::getTypeName

(

const String &

name

)

const

Returns the name for a given index

getUnassignedAtoms()

HashSet<const Atom*>& BALL::Templates::getUnassignedAtoms

(

)

Get the atoms, for which the assignment failed.

has()

bool BALL::Templates::has

(

const String &

name

)

const

Queries whether a given template atom is defined

operator=()

Templates& BALL::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

setMaximumUnassignedAtoms()

void BALL::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.

Member Data Documentation

charges_

StringHashMap<float> BALL::Templates::charges_

protected

Definition at line 128 of file templates.h.

max_number_unassigned_atoms_

Size BALL::Templates::max_number_unassigned_atoms_

protected

Definition at line 138 of file templates.h.

type_names_

StringHashMap<String> BALL::Templates::type_names_

protected

Definition at line 132 of file templates.h.

unassigned_atoms_

HashSet<const Atom*> BALL::Templates::unassigned_atoms_

protected

Definition at line 135 of file templates.h.