BALL  1.4.1
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Classes | Protected Attributes | List of all members
BALL::ResidueTorsions Class Reference

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

Inheritance diagram for BALL::ResidueTorsions:
BALL::ParameterSection

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 ()
const StringgetSectionName () const
const StringgetValue (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 StringgetValue (Position key_index, Position variable_index) const
const StringgetKey (Position key_index) const
const ParameterSectionoperator= (const ParameterSection &section)
virtual bool isValid () const
bool operator== (const ParameterSection &parameter_section) const

Protected Attributes

StringHashMap< vector< Data > > torsions_
HashSet< Stringall_torsions_
- Protected Attributes inherited from BALL::ParameterSection
String section_name_
String format_line_
StringHashMap< Indexsection_entries_
StringHashMap< Indexvariable_names_
std::vector< Stringentries_
std::vector< Stringkeys_
Size number_of_variables_
std::vector< floatversion_
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
namethe residue name (including modifiers like -S or -N);
ithe index. 0 $<$ i $<$ getNumberOfResidueTorsions
ResidueTorsionthe 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

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
parametersthe parameters defining the inifile to be read from
section_namethe 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.

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.