BALL::FlexibleMolecule Class Reference

#include <BALL/DOCKING/COMMON/flexibleMolecule.h>

Inheritance diagram for BALL::FlexibleMolecule:

Public Member Functions
	FlexibleMolecule (Molecule *mol)
	FlexibleMolecule (const FlexibleMolecule &flexmol)
virtual	~FlexibleMolecule ()
virtual void	addConformation (Conformation *conf)
void	clearConformations ()
Size	getNumberOfConformations ()
const vector< Conformation * > &	getConformations () const
String	getConformationId (Position i)
Conformation *	getConformation (Position i)
Molecule *	getConformer (Position i)
Molecule *	getConformerById (String id)
Conformation *	getConformationById (String id)
bool	hasConformation (String id)
Molecule *	getParent ()
String	getId () const
void	setId (String id)
void	removeMoleculeOwnership ()

Static Public Member Functions
static void	generateTopologyHash (const AtomContainer *mol, String &hash, bool ignore_hydrogen=false)

Protected Member Functions
bool	checkCompatibility (Conformation *conf)

Protected Attributes
String	id
Molecule *	molecule
vector< Conformation * >	conformations
HashMap< String, Conformation * >	conf_ids_
bool	molecule_ownership_

Detailed Description

FlexibleMolecule class. This class represents any molecule having multiple conformers.

Definition at line 22 of file flexibleMolecule.h.

Constructor & Destructor Documentation

FlexibleMolecule() [1/2]

BALL::FlexibleMolecule::FlexibleMolecule

(

Molecule *

mol

)

FlexibleMolecule() [2/2]

BALL::FlexibleMolecule::FlexibleMolecule

(

const FlexibleMolecule &

flexmol

)

Copy constructor.

~FlexibleMolecule()

virtual BALL::FlexibleMolecule::~FlexibleMolecule ( )

virtual

Destructor.

Member Function Documentation

addConformation()

virtual void BALL::FlexibleMolecule::addConformation ( Conformation *  conf )

virtual

Add a conformation

Parameters

conformation

pointer

Reimplemented in BALL::Receptor.

checkCompatibility()

bool BALL::FlexibleMolecule::checkCompatibility ( Conformation *  conf )

protected

clearConformations()

void BALL::FlexibleMolecule::clearConformations

(

)

Removes and destroyes all conformations of this FlexibleMolecule

generateTopologyHash()

static void BALL::FlexibleMolecule::generateTopologyHash ( const AtomContainer *  mol, String &  hash, bool  ignore_hydrogen = false  )

static

Generate a hashkey for the topology of the given molecule.
This hashkey uses information about all atoms, bonds and bond-orders and generates a cryptographic hashkey from this data.
Note that the atom positions are not taken into account by this function; if you need a hashkey for a conformation, please you Conformation::generateHash() instead.

Parameters

ignore_hydrogen

if set to true, hydrogen atom are ignore during creation of the hashkey. This is useful for searching molecules regardless of the exact protonation state.

getConformation()

Conformation * BALL::FlexibleMolecule::getConformation

(

Position

i

)

Get a pointer to the i-th conformation.

Returns

pointer to i-th conformation

getConformationById()

Conformation * BALL::FlexibleMolecule::getConformationById

(

String

id

)

Get a pointer to a conformation by specifying its ID.

Returns

pointer to Conformation having the specified ID

getConformationId()

String BALL::FlexibleMolecule::getConformationId

(

Position

i

)

Get the ID of the i-th conformation.

Returns

ID of i-th conformation

getConformations()

const vector< Conformation * > & BALL::FlexibleMolecule::getConformations

(

)

const

Get a vector of all stored conformations.

Returns

vector of conformation pointers

getConformer()

Molecule * BALL::FlexibleMolecule::getConformer

(

Position

i

)

Get a pointer to the i-th conformer ( = conformation applied to parent molecule).

Returns

pointer to i-th conformer

getConformerById()

Molecule * BALL::FlexibleMolecule::getConformerById

(

String

id

)

Get a pointer to the conformer by ID ( = conformation applied to parent molecule).

Returns

pointer to conformer having the specified ID

getId()

String BALL::FlexibleMolecule::getId

(

)

const

Get the ID of the Flexible Molecule

Returns

ID of Flexible Molecule

getNumberOfConformations()

Size BALL::FlexibleMolecule::getNumberOfConformations

(

)

Get the number of stored conformations.

Returns

number of conformations

getParent()

Molecule * BALL::FlexibleMolecule::getParent

(

)

Get a pointer to the parent molecule supplied in the constructor

Returns

pointer to parent molecule

hasConformation()

bool BALL::FlexibleMolecule::hasConformation

(

String

id

)

Has the Flexible Molecule an associated conformation with given ID.

Returns

bool

removeMoleculeOwnership()

void BALL::FlexibleMolecule::removeMoleculeOwnership

(

)

setId()

void BALL::FlexibleMolecule::setId

(

String

id

)

Set the ID of the Flexible Molecule

Parameters

id	of Flexible Molecule

Member Data Documentation

conf_ids_

HashMap< String, Conformation* > BALL::FlexibleMolecule::conf_ids_

protected

Definition at line 114 of file flexibleMolecule.h.

conformations

vector< Conformation* > BALL::FlexibleMolecule::conformations

protected

Definition at line 113 of file flexibleMolecule.h.

id

String BALL::FlexibleMolecule::id

protected

Definition at line 110 of file flexibleMolecule.h.

molecule

Molecule* BALL::FlexibleMolecule::molecule

protected

Definition at line 112 of file flexibleMolecule.h.

molecule_ownership_

bool BALL::FlexibleMolecule::molecule_ownership_

protected

Definition at line 115 of file flexibleMolecule.h.