ResidueTorsions Class Reference
[Force Field Parameters]

Parameter class containing all proper torsions occuring in a residue. More...

#include <residueTorsions.h>

Inheritance diagram for ResidueTorsions:

List of all members.

Public Member Functions
Constructors and Destructors
	ResidueTorsions ()
	Default constructor.
virtual	~ResidueTorsions () throw ()
	Destructor.
virtual void	clear () throw ()
	Clear method.
Accessors
virtual bool	extractSection (ForceFieldParameters &parameters, const String &section_name)
	Reads a parameter section from an INI file.
virtual bool	extractSection (Parameters &parameters, const String &section_name)
	Reads a parameter section from an INI file.
Size	getNumberOfResidueTorsions (const String &residue_name) const
	Return the number of torsions for this residue.
bool	assignTorsion (const String &name, Position i, Data &torsion) const
	Assign the i th torsion for a residue.
bool	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.
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.

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Constructor & Destructor Documentation

ResidueTorsions::ResidueTorsions (   )

Default constructor.

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

Destructor.

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Member Function Documentation

bool 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 ResidueTorsions::clear (   )  throw () [virtual]

Clear method. Reimplemented from ParameterSection.

virtual bool 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 ParameterSection.

virtual bool 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 ResidueTorsions::getNumberOfResidueTorsions (  const String &  residue_name  )  const

Return the number of torsions for this residue.

bool 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.