Computation of hydrogen bonds from topology information. More...

#include <BALL/STRUCTURE/HBondProcessor.h>

Inheritance diagram for BALL::HBondProcessor:

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

class	HBond

struct	Option
	Option names. More...

struct	PredictionMethod
	Default values for options. More...

struct	ResidueData

Public Member Functions
Processor-related methods
virtual void	init ()

virtual bool	start ()

virtual Processor::Result	operator() (Composite &composite)
	in case of Kabsch Sander: determines per residue the N, O, C , More...

virtual bool	finish ()
	Finish computes all hbonds of the composite according. More...

Access methods
const std::vector< HBond > &	getHBonds () const

std::vector< HBond >	getHBonds ()

BALL_DEPRECATED const std::vector< std::vector < Position > > &	getBackboneHBondPairs () const

const std::vector< std::vector < Position > > &	getBackboneHBondPattern () const
	computes the HBond pattern as needed, e.g. by the SecondaryStructureProcessor More...

const std::vector< ResidueData > &	getResidueData () const

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

	UnaryProcessor (const UnaryProcessor &)

virtual	~UnaryProcessor ()

Protected Member Functions
void	preComputeBonds_ (ResidueIterator &data)

bool	finishKabschSander_ ()

bool	finishWishartEtAl_ ()

Protected Attributes
Kabsch Sander related objects
Vector3	upper_

Vector3	lower_

std::vector< ResidueData >	residue_data_

std::vector< std::vector < Position > >	backbone_h_bond_pairs_

Wishart et al related objects
std::vector< Atom * >	donors_

std::vector< Atom * >	acceptors_

std::map< Residue *, Position >	residue_ptr_to_position_

objects for both prediciton methods
std::vector< HBond >	h_bonds_
	store HBond More...

Constant Definitions
static float	MAX_LENGTH

static float	BOND_LENGTH_N_H

static float	BOND_LENGTH_C_O

static float	AMIDE_PROTON_OXYGEN_SEPARATION_DISTANCE

static float	ALPHA_PROTON_OXYGEN_SEPARATION_DISTANCE

	BALL_CREATE (HBondProcessor)

	HBondProcessor ()
	Default constructor. More...

	HBondProcessor (Options &new_options)
	Detailed constructor. More...

virtual	~HBondProcessor ()

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

Computation of hydrogen bonds from topology information.

Hydrogen Bond ProcessorThis processor computes hydrogen bonds and introduces for all hydrogen bonds found a BALL::Bond of type BALL::Bond::TYPE__HYDROGEN, if the property ADD_BONDS is set. In all cases, the detected HBonds can be returned by calling getHBonds().

Please note that the properties of the bond are not recomputed automatically if the System changes! Thus, bonds and their properties (angle, length) might become obsolete!

Example code:

Protein* protein = ..; 
HBondProcessor hbp;
hbp.options.set(HBondProcessor::Option::PREDICTION_METHOD, 
                HBondProcessor::PredictionMethod::KABSCH_SANDER);
protein->apply(hbp);  
std::vector<std::vector<Position> > h_bond_indices = hbp.getBackboneHBondPattern();
std::vector<HBondProcessor::HBond>  h_bonds        = hbp.getHBonds(); 
for (Size i=0; i<h_bonds.size(); ++i)
{
   cout << h_bonds[i].getDonor()->getFullName()    << " bond to " 
        << h_bonds[i].getAcceptor()->getFullName() << ":" 
   cout << h_bonds[i].getLength() << endl;
}

The artifical indices of method getBackboneHBondPattern() are created by iterating with the ResidueIterator and assigning ascending numbers starting with zero. NOTE: After finishing the processor, the ResidueIterator may change the arrangement of the sequence thus the return value gets disrupted!!

The HBondProcessor offers two prediction methods: BALL::HBondProcessor::PredictionMethod::KABSCH_SANDER and BALL::HBondProcessor::PredictionMethod::WISHART_ET_AL Default prediction method is BALL::HBondProcessor::PredictionMethod::KABSCH_SANDER.

The BALL::HBondProcessor::PredictionMethod::KABSCH_SANDER computes all backbone hydrogen bonds occuring between amino acids in the composite it is applied to. Here, a hydrogen bond is created between donor and acceptor, e.g., between N and O.

The computation of the bonds follows the criterion given in "Kabsch W & Sander C (1983). Dictionary of protein secondary structure: pattern recognition of hydrogen-bonded and geometrical features. Biopolymers, 22, 2577-2637".

Please note that in the Kabsch Sander approach water is excluded from the computations.

The BALL::HBondProcessor::PredictionMethod::WISHART_ET_AL computes all hydrogen bonds occuring between amid and alpha hydrogens (H/HA) and carbonyl oxygens on the backbone (O) or sidechain oxygens (OD, OE, OG, OH) in the composite it is applied to. Here, a hydrogen bond is created between the hydrogen atom of the donor and the acceptor, e.g., between HA and O.

The computation of the bonds follows the criterion given in " Neal, S., Nip, A. M., Zhang, H., and Wishart, D. S. (2003). Rapid and accurate calculation of protein 1H, 13C and 15N chemical shifts. J Biomol NMR, 26(3):215-240.".

Definition at line 98 of file HBondProcessor.h.

Constructor & Destructor Documentation

BALL::HBondProcessor::HBondProcessor ( )

Default constructor.

Constructors and Descructor

BALL::HBondProcessor::HBondProcessor ( Options & new_options )

Detailed constructor.

virtual BALL::HBondProcessor::~HBondProcessor ( )

virtual

Member Function Documentation

BALL::HBondProcessor::BALL_CREATE ( HBondProcessor )

virtual bool BALL::HBondProcessor::finish ( )

virtual

Finish computes all hbonds of the composite according.

Reimplemented from BALL::UnaryProcessor< Composite >.

bool BALL::HBondProcessor::finishKabschSander_ ( )

protected

bool BALL::HBondProcessor::finishWishartEtAl_ ( )

protected

BALL_DEPRECATED const std::vector< std::vector<Position> >& BALL::HBondProcessor::getBackboneHBondPairs ( ) const

const std::vector< std::vector<Position> >& BALL::HBondProcessor::getBackboneHBondPattern ( ) const

computes the HBond pattern as needed, e.g. by the SecondaryStructureProcessor

const std::vector< HBond>& BALL::HBondProcessor::getHBonds ( ) const

inline

Definition at line 240 of file HBondProcessor.h.

std::vector< HBond> BALL::HBondProcessor::getHBonds ( )

inline

Definition at line 243 of file HBondProcessor.h.

const std::vector<ResidueData>& BALL::HBondProcessor::getResidueData ( ) const

virtual void BALL::HBondProcessor::init ( )

virtual

Initialization method.

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

virtual

in case of Kabsch Sander: determines per residue the N, O, C ,

in case of Wishart et Al: collects the donors (H, HA) and acceptors all kinds of O

Reimplemented from BALL::UnaryProcessor< Composite >.

void BALL::HBondProcessor::preComputeBonds_ ( ResidueIterator & data )

protected

void BALL::HBondProcessor::setDefaultOptions ( )

reset the options to default values

virtual bool BALL::HBondProcessor::start ( )

virtual

Processor start method.

Reimplemented from BALL::UnaryProcessor< Composite >.

Member Data Documentation

std::vector<Atom*> BALL::HBondProcessor::acceptors_

protected

Definition at line 302 of file HBondProcessor.h.

float BALL::HBondProcessor::ALPHA_PROTON_OXYGEN_SEPARATION_DISTANCE

static

Definition at line 179 of file HBondProcessor.h.

float BALL::HBondProcessor::AMIDE_PROTON_OXYGEN_SEPARATION_DISTANCE

static

Definition at line 178 of file HBondProcessor.h.

std::vector<std::vector<Position> > BALL::HBondProcessor::backbone_h_bond_pairs_

protected

Definition at line 287 of file HBondProcessor.h.

float BALL::HBondProcessor::BOND_LENGTH_C_O

static

Definition at line 175 of file HBondProcessor.h.

float BALL::HBondProcessor::BOND_LENGTH_N_H

static

Definition at line 174 of file HBondProcessor.h.

std::vector<Atom*> BALL::HBondProcessor::donors_

protected

Definition at line 298 of file HBondProcessor.h.

std::vector<HBond> BALL::HBondProcessor::h_bonds_

protected

store HBond

Definition at line 312 of file HBondProcessor.h.

Vector3 BALL::HBondProcessor::lower_

protected

Definition at line 281 of file HBondProcessor.h.

float BALL::HBondProcessor::MAX_LENGTH

static

Definition at line 173 of file HBondProcessor.h.

Options BALL::HBondProcessor::options

options

Definition at line 260 of file HBondProcessor.h.

std::vector<ResidueData> BALL::HBondProcessor::residue_data_

protected

Definition at line 284 of file HBondProcessor.h.

std::map< Residue*, Position> BALL::HBondProcessor::residue_ptr_to_position_

protected

Definition at line 304 of file HBondProcessor.h.

Vector3 BALL::HBondProcessor::upper_

protected

Definition at line 279 of file HBondProcessor.h.

Classes

Public Member Functions

Protected Member Functions

Protected Attributes

Constant Definitions

Public Attributes

Additional Inherited Members

Detailed Description

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation