#include <BALL/NMR/anisotropyShiftProcessor.h>

Inheritance diagram for BALL::AnisotropyShiftProcessor:

Public Member Functions
Constructors and Destructors
	AnisotropyShiftProcessor ()

	AnisotropyShiftProcessor (const AnisotropyShiftProcessor &processor)

virtual	~AnisotropyShiftProcessor ()

Processor specific functions.
virtual bool	finish ()

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

Accessors
virtual void	init ()

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

virtual bool	start ()

bool	isValid () const

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

	UnaryProcessor (const UnaryProcessor &)

virtual	~UnaryProcessor ()

Static Public Attributes
Enums and Constants
static const char *	PROPERTY__ANISOTROPY_SHIFT

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

static const char *	PROPERTY__EXPERIMENTAL__SHIFT

Protected Attributes
std::list< const Atom * >	proton_list_

std::list< const Bond * >	eff_list_

std::list< const Bond * >	eff_list_2_

bool	ignore_other_chain_

Protected Attributes inherited from BALL::ShiftModule
String	module_name_

Parameters *	parameters_

bool	valid_

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 Anisotropy.

Definition at line 29 of file anisotropyShiftProcessor.h.

Constructor & Destructor Documentation

BALL::AnisotropyShiftProcessor::AnisotropyShiftProcessor ( )

Default constructor.

BALL::AnisotropyShiftProcessor::AnisotropyShiftProcessor ( const AnisotropyShiftProcessor & processor )

Copy constructor

virtual BALL::AnisotropyShiftProcessor::~AnisotropyShiftProcessor ( )

virtual

Destructor

Member Function Documentation

virtual bool BALL::AnisotropyShiftProcessor::finish ( )

virtual

  Finish method.
  Here chemical shift calculation is done.
  An iteration over every Hydrogen in <tt>proton_list_</tt> is started.
  For each of these Hydrogens an iteration is started over every effector bounds
  in <tt>eff_list_</tt>.
  <tt>c_atom</tt> is assigned the first atom of effector bond and <tt>o_atom</tt> is the second.
  If the actual proton is in another residue then <tt>c_atom</tt> calculation is started.
  The next bounded carbonate atom of <tt>c_atom</tt> is stored in <tt>x_atom</tt>.
  Now we have three atoms with their positions stored in 
  <tt>c_pos</tt> , <tt>o_pos</tt> and <tt>x_pos</tt>.\par
  We then build a cartesian coordinate system with these vectors.\par
  <tt>vz</tt> = <tt>o_pos</tt> - <tt>c_pos</tt> and vz is normalized.
  <tt>vy</tt> is the vectorproduct of vz and the difference vector of <tt>x_pos</tt> and <tt>c_pos</tt>
  and is normalized.
  <tt>vx</tt> is the vectorproduct of vz and vy and is normalized.
  Then the center <tt>cen</tt> of the effector bound is set to\par

  <tt>c_pos</tt> + 1.1 * <tt>vz</tt>.\par

: Next three vectors are calculated : v1 is the difference vector of the actual hydrogen and cen. v2 is the vectorproduct of v1 and vy. v3 is the vectorproduct of v2 and vx. abstand is assigned the length of vector v1. Then stheta is assigned the sinus of the angle between v1 and vy. The sinus of the angle between v2 and vx is assigned to sgamma. Now preparations have finished and we can start the real shift calculation.

: calc1 = dX1 * ( ( 3.0 * stheta * stheta ) - 2.0 ).

: calc2 = dX2 * ( 1.0 - ( 3.0 * stheta * stheta * sgamma * sgamma ) )

: ts = ( calc1 + calc2 ) / ( 3.0 * distance * distance * distance )

: ts is added to gs.

: dX1 and dX2 are some constant floats. If the actual Hydrogens name is "H" the constant floats dXN1 and dXN2 are used instead.

: If eff_list_ has finished C=O anisotropy for actual Hydrogen is done and iteration over all C=N anisotropy effector bounds of eff_list_2_ is started.

: This calculation is very similar with just some differences : We got three position vectors called: c_pos o_pos position of n_pos position of the Nitrogen bonded to Carbonate.

: The cartesion coordinate system is built on vz = n_pos - c_pos

: vy is the vectorproduct of vz and the difference vector of o_pos and c_pos

: vx is the vectorproduct of vz and vy.

: The center of the effector bond is set to:

: cen = c_pos + ( vz * ( 0.85 * length of vz ) )

: The final calculation is just the same as above, except the use of different constants. Use ndX1 and ndX2 instead of dX1 and dX2 and ndXN1 and ndXN2 intead of dXN1 and dXN2. Finally C=N anisotropy has finished and gs is added to the actual hydrogens shift. Then iteration goes on with the next hydrogen.

Reimplemented from BALL::ShiftModule.

virtual void BALL::AnisotropyShiftProcessor::init ( )

virtual

Module initialization

Reimplemented from BALL::ShiftModule.

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

virtual

Application method. Atoms are stored in three different lists , named

: proton_list_ that contains all Hydrogens,

: eff_list_ that contains all effectors of C=O anisotropy and

: eff_list_2_ that contains all effectors of C=N anisotropy. Effectors of C=O anisotropy are all bounds between atoms named "C" and "O", as well as bounds between atoms named "CG" and "OD1" in residues called "ASP" or "ASN, and finally bounds between atoms named "CD" and "OE1" in residues called "GLU" and "GLN". Effectors of C=N anisotropy are all bounds between atoms named "C" and "N".

Reimplemented from BALL::UnaryProcessor< Composite >.