BALL::HBondProcessor Class Reference
[Miscellaneous]

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 ,
virtual bool	finish ()
	Finish computes all hbonds of the composite according.
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
const std::vector< ResidueData > &	getResidueData () const
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
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.
	HBondProcessor (Options &new_options)
	Detailed constructor.
virtual	~HBondProcessor ()
Public Attributes

Options	options
	options
void	setDefaultOptions ()

Detailed Description

Computation of hydrogen bonds from topology information.

Hydrogen Bond Processor This 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.