EFShiftProcessor Class Reference
[Shift modules]

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

#include <EFShiftProcessor.h>

Inheritance diagram for EFShiftProcessor:

List of all members.

Public Member Functions
Constructors and Destructors.
	EFShiftProcessor () throw ()
	Default constructor.
	EFShiftProcessor (const EFShiftProcessor &processor) throw ()
	Copy constructor.
virtual	~EFShiftProcessor () throw ()
	Destructor.
Accessors.
virtual void	init () throw ()
	Initialization method.
Processor specific functions.
virtual bool	start () throw ()
	Processor start method.
virtual Processor::Result	operator() (Composite &composite) throw ()
	operator ().
virtual bool	finish () throw ()
	Finish method.
Static Public Attributes
Enums and Constants
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.

---

Constructor & Destructor Documentation

EFShiftProcessor::EFShiftProcessor (   )  throw ()

Default constructor.

EFShiftProcessor::EFShiftProcessor (  const EFShiftProcessor &  processor  )  throw ()

Copy constructor.

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

Destructor.

---

Member Function Documentation

virtual bool EFShiftProcessor::finish (   )  throw () [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 ShiftModule.

virtual void EFShiftProcessor::init (   )  throw () [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 ShiftModule.

virtual Processor::Result EFShiftProcessor::operator() (  Composite &  composite  )  throw () [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_ . Returns: Processor::CONTINUE Parameters: composite  an arbitrary composite. All non-atom objects are ignored. Reimplemented from UnaryProcessor< Composite >.

virtual bool EFShiftProcessor::start (   )  throw () [virtual]

Processor start method. This method clears the bond and effector list. It fails if no parameters were assigned. Returns: bool, false if parameters_ == 0 Reimplemented from ShiftModule.

---

Member Data Documentation

const char* EFShiftProcessor::PROPERTY__EF_SHIFT [static]

A symbolic name for the electric field contribution to the chemical shift. See also: ShiftModule::PROPERTY__SHIFT