#include <BALL/NMR/empiricalHSShiftProcessor.h>

Inheritance diagram for BALL::EmpiricalHSShiftProcessor:

Classes
struct	Default
	Default values for options. More...

struct	Option
	Option names. More...

class	PropertiesForShift_

class	ShiftHyperSurface_

Public Member Functions
Constructors and Destructors.
	EmpiricalHSShiftProcessor ()

virtual	~EmpiricalHSShiftProcessor ()

Accessors.
virtual void	init ()

Processor specific functions.
virtual bool	start ()

virtual Processor::Result	operator() (Composite &composite)

virtual bool	finish ()

Public Member Functions inherited from BALL::ShiftModule
	ShiftModule ()

	ShiftModule (Parameters &parameters, const String &name="")

	ShiftModule (const ShiftModule &module)

virtual	~ShiftModule ()

virtual void	clear ()

const ShiftModule &	operator= (const ShiftModule &module)

void	setName (const String &name)

const String &	getName () const

void	setParameters (Parameters &parameters)

const Parameters *	getParameters () const

bool	isValid () const

Public Member Functions inherited from BALL::UnaryProcessor< Composite >
	UnaryProcessor ()

	UnaryProcessor (const UnaryProcessor &)

virtual	~UnaryProcessor ()

Static Public Attributes
static const int	VERBOSITY_LEVEL_CRITICAL

static const int	VERBOSITY_LEVEL_DEBUG

Enums and Constants.
static const char *	PROPERTY__EHS_SHIFT

Static Public Attributes inherited from BALL::ShiftModule
static const char *	PROPERTY__SHIFT

static const char *	PROPERTY__EXPERIMENTAL__SHIFT

Protected Attributes
std::vector< PropertiesForShift_ >	targets_

vector< String >	target_names_

vector< std::set< String > >	target_property_names_

vector< std::map< std::pair < String, String >, String > >	property_files_

std::map< String, vector < std::pair< String, String > > >	property_pairs_

std::map< String, std::map < std::pair< String, String > , EmpiricalHSShiftProcessor::ShiftHyperSurface_ > >	hypersurfaces_

bool	exclude_prolins_

std::map< String, float >	ssbond_correction_

Protected Attributes inherited from BALL::ShiftModule
String	module_name_

Parameters *	parameters_

bool	valid_

Private Member Functions
void	printParameters_ ()

void	printTargets_ ()

void	postprocessing_ ()

Private Attributes
int	verbosity_
	The verbosity of this class as taken from the options. More...

Public Attributes
Options	options
	options More...

void	setDefaultOptions ()

Additional Inherited Members
Public Types inherited from BALL::UnaryFunctor< Composite, Processor::Result >
typedef Processor::Result	result_type

typedef Composite	argument_type

typedef Composite &	argument_reference

typedef const Composite &	const_argument_reference

typedef Composite *	argument_pointer

typedef const Composite *	const_argument_pointer

Detailed Description

Shift assignment processor implementing the empirical hypersurface contribution.

Definition at line 40 of file empiricalHSShiftProcessor.h.

Constructor & Destructor Documentation

BALL::EmpiricalHSShiftProcessor::EmpiricalHSShiftProcessor ( )

Default constructor.

virtual BALL::EmpiricalHSShiftProcessor::~EmpiricalHSShiftProcessor ( )

virtual

Destructor.

Member Function Documentation

virtual bool BALL::EmpiricalHSShiftProcessor::finish ( )

virtual

Finish method. This method performs the chemical shift calculation for all previously collected target atoms (targets_ ) iteratively by evaluating all atom type relevant hypersurfaces (hypersurfaces_ ) iteratively using the precomputed atoms properties (targets_). For disulfid bonds, a special term as specified in section { SSBondCorrection} of the { ShiftX.ini} - file is added. According to the flag { exclude_prolins_} (default false) (pecification in the { ShiftX.ini} - file) prolins my by excluded from shift computations. If the processor found no target atoms or had no hypersurfaces, the processor returns immediately. The empirical hypersurface related chemical shift is stored for each target atom using the named property PROPERTY__EF_SHIFT and added to the named property ShiftModule::PROPERTY__SHIFT .

Returns: bool, false if invalid_

Reimplemented from BALL::ShiftModule.

virtual void BALL::EmpiricalHSShiftProcessor::init ( )

virtual

Initialization method. This method reads the parameter section SSBondCorrection, parses, and stores its content in the vector ssbond_correction_ . The parameter section SSBondCorrection defines atom types of residues, which have a disulfid bond, and the corresponding shift contribution. In addition, this method reads the parameter section EmpiricalShiftHyperSurfaces and parses its content. The parameter section EmpiricalShiftHyperSurfaces defines target atom types, associated hypersurface property pairs and the corresponding datafiles. All target atom types are stored in a vector target_names_ . All properties relevant for an atom type are stored in a set. The sets are stored per target atom in the vector target_property_names_ in the same order as in the vector target_names.

The property pairs for each atom type are stored as pairs in vectors. These vectors are themselves stored per atom type in a map property_pairs_ .

The file names of the hypersurface data files of an atom type are stored in a map, whose key is the pair of properties, to which the hypersurface data belong. The maps themselfes are stored per target atom type in the vector property_files_ the same order as the atom types in the vector target_names.

For each atom type's property combinations a hypersurface is created and stored in the map hypersurfaces_ key { atom type} of maps with key property pair. The hypersurfaces will be evaluated for each target atom in () finish () .

The flag { exclude_prolins}, denoting the consideration of prolins in the shift computations, is read from this section too.

See Also: finish ()

Reimplemented from BALL::ShiftModule.

virtual Processor::Result BALL::EmpiricalHSShiftProcessor::operator() ( Composite & composite )

virtual

operator (). This method collects all target atoms, whose atom type was specified in the section { EmpiricalShiftHyperSurfaces} of the { ShiftX.ini} - file and stored in target_names_ , and computes all target atoms properties, which were likewise specified for each target atom type in the { ShiftX.ini} - file and stored in target_property_names_ . The atoms and their properties are stored in the list targets_ .