BALL::EFShiftProcessor Class Reference
[Shift modules]

Shift assignment processor implementing the electric field effect. More...

#include <EFShiftProcessor.h>

Inheritance diagram for BALL::EFShiftProcessor:

[legend]


Public Member Functions
Constructors and Destructors.
	EFShiftProcessor ()
	Default constructor.
	EFShiftProcessor (const EFShiftProcessor &processor)
	Copy constructor.
virtual	~EFShiftProcessor ()
	Destructor.
Accessors.
virtual void	init ()
	Initialization method.
Processor specific functions.
virtual bool	start ()
	Processor start method.
virtual Processor::Result	operator() (Composite &composite)
	operator ().
virtual bool	finish ()
	Finish method.
Static Public Attributes
Enums and Constants
static const char *	PROPERTY__EF_SHIFT
	A symbolic name for the electric field contribution to the chemical shift.
Protected Attributes
std::list< Bond * >	bond_list_
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_
float	cut_off2_

Detailed Description

Shift assignment processor implementing the electric field effect.

Member Function Documentation

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

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]

Initialization method.

This method reads the parameter section ElectricFieldEffect and parses its contents. This section contains the definition of two expressions that define a bond (the first expression matches the atom whose shift is to be calculated, the second describes its bond partner). For each of these bonds, two parameters are given, $$ and $$.

Then, this method extracts the contents of the Charges section and thus constructs a hash map containing residue and atom names the corresponding charges. This processor is applied to all atoms in () operator () , so expect the atom charges to change!

See also:: operator ()

Reimplemented from BALL::ShiftModule.

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

operator ().

This method sets the charge for all atoms it encounters (using assign_charge_processor_ ). Charged atoms are stored in the atom list effector_list_ . All bonds are stored in bond_list_ .