BALL::ResidueTorsions Class Reference
[Force Field Parameters]

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

Inheritance diagram for BALL::ResidueTorsions:

[legend]

List of all members.

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

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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.

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Constructor & Destructor Documentation

BALL::ResidueTorsions::ResidueTorsions

(

)

Default constructor.

virtual BALL::ResidueTorsions::~ResidueTorsions

(

)

[virtual]

Destructor.

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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	(	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 to the data.

Parameters:

	parameters	the parameters defining the inifile to be read from
	section_name	the name of the section to be read (without the squared brackets)

Returns:

bool - true if the section could be read, false otherwise

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.

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.

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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.