BALL::EFShiftProcessor Class Reference
[Shift modules]

#include <BALL/NMR/EFShiftProcessor.h>

Inheritance diagram for BALL::EFShiftProcessor:

Public Member Functions
Constructors and Destructors.

	EFShiftProcessor ()
	EFShiftProcessor (const EFShiftProcessor &processor)
virtual	~EFShiftProcessor ()
Accessors.

virtual void	init ()
Processor specific functions.

virtual bool	start ()
virtual Processor::Result	operator() (Composite &composite)
virtual bool	finish ()
Static Public Attributes
Enums and Constants

static const char *	PROPERTY__EF_SHIFT
Protected Attributes
std::vector< std::pair< Atom , Atom > >	bond_list_
std::vector< Index >	expression_number_
std::list< Atom * >	effector_list_
std::vector< Expression >	first_atom_expressions_
std::vector< Expression >	second_atom_expressions_
std::vector< float >	epsilon1_
std::vector< float >	epsilon2_
StringHashMap< float >	charge_map_
bool	exclude_residue_field_
bool	exclude_adjacent_residue_field_
bool	carbonyl_influences_amide_field_
bool	exclude_solvent_field_
float	cut_off2_
float	charge_factor_
Private Member Functions
void	printParameters_ ()
void	printEffectors_ ()
void	printTargets_ ()
void	postprocessing_ ()

Detailed Description

Shift assignment processor implementing the electric field effect.

Definition at line 25 of file EFShiftProcessor.h.

Constructor & Destructor Documentation

BALL::EFShiftProcessor::EFShiftProcessor ( )

Default constructor.

BALL::EFShiftProcessor::EFShiftProcessor ( const EFShiftProcessor & processor )

Copy constructor.

virtual BALL::EFShiftProcessor::~EFShiftProcessor ( ) [virtual]

Destructor.

Member Function Documentation

virtual bool BALL::EFShiftProcessor::finish ( ) [virtual]

Processor finish method. This method performs the chemical shift calculation. It iterates over all bonds stored in bond_list_ . If the two bond atoms match a pair of expressions from first_atom_expressions_ and second_atom_expressions_ , the electric field vector is calculated at the bond position using Coulomb's law and the charges and positions of the atoms in the effector_list_ . The chemical shift induced by the electric field effect is calculated as ${EF} = * E_z + * E^2 $ where constants $$ and $$ are read from the parameter file (section ElectricFieldEffect). The chemical shift is stored in the {first} atom using the named property ShiftModule::PROPERTY__SHIFT and in the named property PROPERTY__EF_SHIFT .

Returns:: bool, false if parameters_ == 0

Reimplemented from BALL::ShiftModule.

virtual void BALL::EFShiftProcessor::init ( ) [virtual]

Parameter initalization. Use this method to implement the extraction and initialization of the module's parameters. init is called by ShiftModel as soon as the ShiftModule is constructed and parameters and name are assigned.

: All implementations in derived classes should set the valid_ flag to true if the initialization was successful and to false otherwise.

Reimplemented from BALL::ShiftModule.

virtual Processor::Result BALL::EFShiftProcessor::operator() ( Composite & composite ) [virtual]

Processor operator (). This method sets the charges for all atoms it encounters. The charges are given are given in parameter file (section Charges). Charged atoms are stored in the atom list effector_list_ . All tentative target bonds, specified in the parameter file (section ElectricFieldEffect), are stored in bond_list_ .