BALL::AddHydrogenProcessor Class Reference

#include <BALL/STRUCTURE/addHydrogenProcessor.h>

Inheritance diagram for BALL::AddHydrogenProcessor:

Public Member Functions
	AddHydrogenProcessor ()
	Default constructor. More...
virtual	~AddHydrogenProcessor ()
	Destructor. More...
virtual bool	start ()
virtual Processor::Result	operator() (Composite &composite)
Size	getConnectivity (const Atom &atom) const
void	setRings (const vector< vector< Atom * > > &rings)
Size	getNumberOfAddedHydrogens () const
Public Member Functions inherited from BALL::UnaryProcessor< Composite >
	UnaryProcessor ()
	UnaryProcessor (const UnaryProcessor &)
virtual	~UnaryProcessor ()
virtual bool	finish ()

Protected Member Functions
Processor::Result	placePeptideBondH_ (Residue *res)
Size	countBondOrders (const Atom &atom) const
void	addHydrogen_ (Atom &atom, Vector3 position)
bool	isRingAtom_ (const Atom &atom) const
vector< Atom * >	getPartners_ (Atom &atom) const
Vector3	getNormal_ (const Vector3 &v) const
bool	normalize_ (Vector3 &v) const
bool	hasMultipleBond_ (const Atom &atom) const
float	getBondLength_ (Position element) const

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

Saturate atoms with hydrogen atoms.

This processor only works for main group elements. The formal charge of the atoms are taken into account. The placement of the hydrogen atoms only depends on the direct neighbour atoms.

No additional optimization of the atom placement is performed. The optimal bond lengths are calculated by a modified Schomaker-Stevenson rule (adapted from the MMFF94 Force Field.). For hydrogen atoms located in a peptide bond the atom is placed taking the planarity of the bond into account. In this case bond length is taken from the rules used by DSSP (Kabsch-Sander) as implemented by the HydrogenBondProcessor.

Usage:

RingPerceptionProcessor rpp;
vector<vector<Atom*> > rings;
rpp.calculateSSSR(rings, system);
rings = rpp.getAllSmallRings();
AddHydrogenProcessor ap;
ap.setRings(rings);
system.apply(ap);

Keep in mind that the hydrogen positions obtained by using this method are usually not optimal. For better better Atom placment when adding hydrogens to Proteins and DNA you should use the ReconstructFragmentProcessor. Nevertheless in both cases it is recommended to optimize the obtained hydrogen atom positions using a force field (e.g. BALL::AmberFF, BALL::CharmmFF, BALL::MMFF94)

Definition at line 58 of file addHydrogenProcessor.h.

Constructor & Destructor Documentation

BALL::AddHydrogenProcessor::AddHydrogenProcessor

(

)

Default constructor.

virtual BALL::AddHydrogenProcessor::~AddHydrogenProcessor ( )

virtual

Destructor.

Member Function Documentation

void BALL::AddHydrogenProcessor::addHydrogen_ ( Atom &  atom, Vector3  position  )

protected

Adds a single hydrogen an atom.

Parameters

atom	The Atom to which a hydrogen should be added
position	The position of the newly added hydrogen

Size BALL::AddHydrogenProcessor::countBondOrders ( const Atom &  atom ) const

protected

Sums up the bond orders of all bonds the atom participates in.

Parameters

atom	The Atom for which the bond orders should be determined

Returns

The bond orders of the Atom.

float BALL::AddHydrogenProcessor::getBondLength_ ( Position  element ) const

protected

Get the ideal bond length for the given element with hydrogen atoms. This uses the Schomaker-Stevenson rule.

Parameters

element

The Element for which to compute the distance

Returns

The preferred distance of a hydrogen atom from the input Element

Size BALL::AddHydrogenProcessor::getConnectivity

(

const Atom &

atom

)

const

Computes the number of connections of a provided Atom the computation is solely based on the formal charge of the molecule as obtained from its group in the PTE. Hence only one connectivity is computed for every element.

Parameters

atom	The Atom for which the connectivity shoudl be computed

Returns

The number of connections the atom most likely will form. 0 if no connectivity could be computed.

Vector3 BALL::AddHydrogenProcessor::getNormal_ ( const Vector3 &  v ) const

protected

Computes a vector orthogonal to the input. It uses the x-axis as reference. If the input is colinear to the x-axis, the y-axis is used.

Parameters

v	A vector for which an orthogonal vector shoudl be computed

Returns

A vector of unit length orthogonal to the input

Size BALL::AddHydrogenProcessor::getNumberOfAddedHydrogens ( ) const

inline

Returns the number of added hydrogen atoms. This value will accumulate over multiple calls of operator()

Returns

The number of added hydrogens

Definition at line 118 of file addHydrogenProcessor.h.

vector<Atom*> BALL::AddHydrogenProcessor::getPartners_ ( Atom &  atom ) const

protected

Returns a list of atoms bound to the specified Atom

Parameters

atom	the atom for which the binding partners should be determined

Returns

A std::vector containing all Atoms that have a bond to the specified Atom

bool BALL::AddHydrogenProcessor::hasMultipleBond_ ( const Atom &  atom ) const

protected

Determines whether an Atom has a bond that is not a single bond.

Parameters

atom	The Atom that should be checked for non-single bonds.

Returns

true if the atom has a a non-single bond, false otherwise

bool BALL::AddHydrogenProcessor::isRingAtom_ ( const Atom &  atom ) const

protected

Returns whether the atom is in the internal list of ring atoms

See also

AddHydrogenProcessor::setRings

Parameters

atom	The Atom that should be checked

Returns

true if the Atom is in the ring Atom set false otherwise

bool BALL::AddHydrogenProcessor::normalize_ ( Vector3 &  v ) const

protected

Normalizes a vector.

Parameters

v	The vector that should be normalized. Normalization is performed in-place.

Returns

true if the vector is non-zero false otherwise.

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

virtual

Adds hydrogen atoms to the specified composite. If composite is a Residue it uses the peptide bond rule to place hydrogens. Otherwise the placement heuristic based on the modified Schomaker-Stevenson rule is used.

See also

UnaryProcessor::operator()

Parameters

composite

The composite that should be saturated with hydrogens

Returns

Processor::CONTINUE is returned in all cases.

Reimplemented from BALL::UnaryProcessor< Composite >.

Processor::Result BALL::AddHydrogenProcessor::placePeptideBondH_ ( Residue *  res )

protected

Place peptide bond H-atoms according to Kabsch-Sander

Parameters

res	A pointer to a Residue for which a peptide bond hydrogen should be placed

Returns

Processor::CONTINUE in all cases.

void BALL::AddHydrogenProcessor::setRings

(

const vector< vector< Atom * > > &

rings

)

Sets the internal list of ring atoms. This is necessary computing a better estimate of the hydrogen position.

Parameters

rings

A set of rings. A suitable input for this method can be computed by using RingPerceptionProcessor::calculateSSSR

virtual bool BALL::AddHydrogenProcessor::start ( )

virtual

Initialize the processor. Resets the number of added hydrogens.

See also

UnaryProcessor::start()

Returns

true in all cases

Reimplemented from BALL::UnaryProcessor< Composite >.