BALL::ResidueTorsions Class Reference

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

Inheritance diagram for BALL::ResidueTorsions:

Classes
struct	Data

Public Member Functions
Constructors and Destructors
	ResidueTorsions ()
virtual	~ResidueTorsions ()
virtual void	clear ()
Accessors
virtual bool	extractSection (ForceFieldParameters &parameters, const String &section_name)
virtual bool	extractSection (Parameters &parameters, const String &section_name)
Size	getNumberOfResidueTorsions (const String &residue_name) const
bool	assignTorsion (const String &name, Position i, Data &torsion) const
bool	hasTorsion (const String &residue, const String &atom_A, const String &atom_B, const String &atom_C, const String &atom_D) 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

Protected Attributes
StringHashMap< vector< Data > >	torsions_
HashSet< String >	all_torsions_
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_

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

Detailed Description

Parameter class containing all proper torsions occuring in a residue. Several force fields (e.g. CHARMM) do not necessarily consider or parametrize all occurring torsions but explicitly list the torsions for each residue. This parameter section is used to represent this list. The class AMBER and CHARMM torsions components check for the presence of the parameter section [ResidueTorsions] and then decide whether they have to generate the torsions by itself (creating all torsions and complaining about missing parameters) or whether they have to read them from this section.

Definition at line 32 of file residueTorsions.h.

Constructor & Destructor Documentation

BALL::ResidueTorsions::ResidueTorsions

(

)

Default constructor.

virtual BALL::ResidueTorsions::~ResidueTorsions ( )

virtual

Destructor.

Member Function Documentation

bool BALL::ResidueTorsions::assignTorsion	(	const String &	name,
		Position	i,
		Data &	torsion
	)		const

Assign the i th torsion for a residue.

Parameters

name	the residue name (including modifiers like -S or -N);
i	the index. 0 $<$ i $<$ getNumberOfResidueTorsions
ResidueTorsion	the torsion to be assigned to

Returns

bool - true if the torsion was found, false otherwise

virtual void BALL::ResidueTorsions::clear ( )

virtual

Clear method.

Reimplemented from BALL::ParameterSection.

virtual bool BALL::ResidueTorsions::extractSection ( ForceFieldParameters &  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.

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

virtual

Size BALL::ResidueTorsions::getNumberOfResidueTorsions

(

const String &

residue_name

)

const

Return the number of torsions for this residue.

bool BALL::ResidueTorsions::hasTorsion	(	const String &	residue,
		const String &	atom_A,
		const String &	atom_B,
		const String &	atom_C,
		const String &	atom_D
	)		const

Return true if the torsion has to be considered for the residue.

Member Data Documentation

HashSet<String> BALL::ResidueTorsions::all_torsions_

protected

Definition at line 137 of file residueTorsions.h.

StringHashMap<vector<Data> > BALL::ResidueTorsions::torsions_

protected

Definition at line 131 of file residueTorsions.h.