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

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

Inheritance diagram for BALL::Templates:
BALL::ParameterSection

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
Assignment
Templatesoperator= (const Templates &templates)
void setMaximumUnassignedAtoms (Size nr)
Size getMaximumUnassignedAtoms () const
Size getNumberOfUnassignedAtoms () const
 Get the number of atoms, for which the assignment failed.
HashSet< const Atom * > & getUnassignedAtoms ()
 Get the atoms, for which the assignment failed.
- 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 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< floatcharges_
StringHashMap< Stringtype_names_
HashSet< const Atom * > unassigned_atoms_
Size max_number_unassigned_atoms_
- 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

Force Field Residue Template Class.

Definition at line 31 of file templates.h.

Constructor & Destructor Documentation

BALL::Templates::Templates ( )

Default constructor.

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

Copy constructor.

virtual BALL::Templates::~Templates ( )
virtual

Destructor.

Member Function Documentation

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

Assign charges and type names

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

Assign charges and type names

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

Assign type names

virtual void BALL::Templates::clear ( )
virtual

Clear method.

Reimplemented from BALL::ParameterSection.

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

Parameter extractionReads 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.

Reimplemented from BALL::ParameterSection.

float BALL::Templates::getCharge ( const String name) const

Returns the numeric type for a given string.

Size BALL::Templates::getMaximumUnassignedAtoms ( ) const

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

Size BALL::Templates::getNumberOfUnassignedAtoms ( ) const

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

String BALL::Templates::getTypeName ( const String name) const

Returns the name for a given index

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

Get the atoms, for which the assignment failed.

bool BALL::Templates::has ( const String name) const

Queries whether a given template atom is defined

Reimplemented from BALL::ParameterSection.

Templates& BALL::Templates::operator= ( const Templates templates)

Assignment operator. Copy the contents of templates into this residue template object.

Parameters
templatesthe residue template object to be copied
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

StringHashMap<float> BALL::Templates::charges_
protected

Definition at line 128 of file templates.h.

Size BALL::Templates::max_number_unassigned_atoms_
protected

Definition at line 138 of file templates.h.

StringHashMap<String> BALL::Templates::type_names_
protected

Definition at line 132 of file templates.h.

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

Definition at line 135 of file templates.h.