BALL::ScoringFunction Class Reference

#include <BALL/SCORING/COMMON/scoringFunction.h>

Inheritance diagram for BALL::ScoringFunction:

Classes
struct	Default
struct	Option
struct	Result

Public Member Functions
	ScoringFunction ()
	ScoringFunction (const ScoringFunction &sf)
	ScoringFunction (AtomContainer &receptor, AtomContainer &ligand)
	ScoringFunction (AtomContainer &receptor, AtomContainer &ligand, const Options &options)
	ScoringFunction (AtomContainer &receptor, AtomContainer &ligand, Options &options)
	ScoringFunction (AtomContainer &receptor, Vector3 &hashgrid_origin, Options &options)
virtual	~ScoringFunction ()
virtual void	clear ()
ScoringFunction &	operator= (const ScoringFunction &sf)
bool	setup ()
bool	setup (AtomContainer &receptor, AtomContainer &ligand)
bool	setup (AtomContainer &receptor, AtomContainer &ligand, const Options &options)
void	setMaximumNumberOfErrors (Size nr)
Size	getMaximumNumberOfErrors () const
void	setFirstMolecule (AtomContainer &molecule1)
AtomContainer *	getFirstMolecule () const
void	setSecondMolecule (AtomContainer &molecule2)
AtomContainer *	getSecondMolecule () const
void	setReceptor (AtomContainer &receptor)
AtomContainer *	getReceptor () const
void	setLigand (AtomContainer &ligand)
AtomContainer *	getLigand () const
void	setIntercept (double intercept)
double	getIntercept () const
void	setBaseFunction (ScoringBaseFunction &base_function)
	Set the instance of BaseFunction for the scoring function. More...
ScoringBaseFunction *	getBaseFunction () const
void	insertComponent (ScoringComponent *component)
void	insertComponent (ScoringComponent *component, float coefficient)
void	removeComponent (const ScoringComponent *component)
void	removeComponent (const String &name)
void	setCoefficient (const ScoringComponent *component, float coefficient)
void	setCoefficient (const String &name, float coefficient)
bool	getCoefficient (const ScoringComponent *component, float &coefficient) const
bool	getCoefficient (const String &name, float &coefficient) const
ScoringComponent *	getComponent (const String &name) const
ScoringComponent *	getComponent (const Size index) const
double	calculateScore ()
const HashSet< const Atom * > &	getUnassignedAtoms () const
HashSet< const Atom * > &	getUnassignedAtoms ()
double	getExpEnergyStddev ()
void	enableStoreInteractionsOnlyForPhContraints ()
String	convertTime (double seconds)
virtual void	update ()
virtual double	updateScore ()
virtual void	printResult (bool detail=0)
void	getScoreContributions (vector< double > &score_contributions, vector< String > &names)
String	getEquation ()
void	enableStoreInteractions (bool b=true)
String	getName ()
int	getBurialDepthScale ()
String	valueToString (double value)
void	unsetTrainingParameters ()
void	setNormalizationParameters (double stddev, double mean)
const HashGrid3< Atom * > *	getHashGrid ()
const Vector3 &	getLigandCenter () const
double	getLigandRadius () const
bool	storeInteractionsEnabled ()
virtual int	getNoNeighboringReceptorAtoms ()
int	getNoLigandAtoms ()
Options	getOptions ()
Options *	getOptionsToModify ()
void	createStaticLigandFragments ()
const vector< Bond * > *	getRotatableLigandBonds () const
const vector < StaticLigandFragment * > *	getStaticLigandFragments () const
bool	hasFlexibleResidues ()
void	setFlexibleResidues (const std::set< Residue * > &flexible_residues)
bool	assignRotamer (Residue *residue, ResidueRotamerSet *rotamer_set, const Rotamer *rotamer)
void	resetFlexibleResidues ()
Size	countNeighboringReceptorAtoms (const Atom *atom, double distance_threshold, bool onePerCell=0, int *number_of_overlaps=0) const
void	resetResiduePositions (Residue *residue, list< Vector3 > &old_positions)
double	getScore ()
const std::map< Atom *, int > *	getAtomFragmentMap ()

Static Public Member Functions
static HashGrid3< Atom * > *	initializeHashGrid (AtomContainer *sys, Vector3 &center, double &resolution, int hashgrid_size)
static void	getDefaultOptions (Options &options)

Public Attributes
list< Constraint * >	constraints

Protected Member Functions
void	setName (String name)
void	updateComponent (int id, AtomPairList *)
Vector3	calculateGeometricalCenter (AtomContainer *s, int *no_ligand_atoms=NULL)
double	calculateMoleculeRadius (AtomContainer *sys, Vector3 &center)
void	setupFlexibleResidues_ ()
virtual void	setupReferenceLigand ()
int	checkForAtomOverlaps (const AtomPairVector *pair_vector)
AtomPairVector *	createNonbondedPairVector (HashGrid3< Atom * > *hashgrid, int &overlaps, bool rec_lig, bool check_fragments=0, bool intra_fragment=0)
AtomPairVector *	createLigandNonbondedPairVector (bool intra_fragment, int &overlaps)
bool	hasPharmacophoreConstraints_ ()
void	clearStoredInteractions_ ()
double	calculateConstraintsScore ()
void	enableInteractionComponents_ (const list< String > &type_names)
virtual double	getES ()
void	enableAllComponents_ ()
void	fetchStaticLigandFragment (Atom *a1, int index)
int	countCovalentBonds (const Atom *atom, int threshold=-1)
virtual void	createAllLigandNonBondedPairs ()
virtual double	calculateStaticLigandFragmentEnergy ()
bool	isPeptideBond (const Bond *bond) const

Protected Attributes
String	name_
Options	options_
AtomContainer *	receptor_
AtomContainer *	ligand_
double	score_
double	intercept_
ScoringBaseFunction *	base_function_
vector< ScoringComponent * >	scoring_components_
HashSet< const Atom * >	unassigned_atoms_
Size	max_number_of_errors_
Size	number_of_errors_
double	ligand_radius_
int	ligand_atoms_
Vector3	ligand_center_
HashGrid3< Atom * > *	hashgrid_
HashGrid3< Atom * > *	all_residues_hashgrid_
HashGrid3< Atom * > *	static_residues_hashgrid_
HashGrid3< Atom * > *	flexible_residues_hashgrid_
double	resolution_
std::map< Atom *, int >	atoms_to_fragments_
int	reference_neighbors_
int	neighboring_target_atoms_
int	misplaced_ligand_atoms_
int	hashgrid_search_radius_
double	nonbonded_cutoff_
double	nonbonded_cutoff_2_
bool	ignore_h_clashes_
int	overlaps_
int	ligand_intramol_overlaps_
double	allowed_intermolecular_overlap_
double	allowed_intramolecular_overlap_
double	neighbor_cutoff_2_
vector< StaticLigandFragment * >	static_ligand_fragments_
bool	store_interactions_
bool	store_interactions_phC_only_
AtomPairVector *	all_ligand_nonbonded_
double	conformation_scale_
bool	use_all_lig_nonb_
bool	use_static_lig_fragments_
int	burial_depth_scale_
double	exp_energy_stddev_
double	exp_energy_mean_
std::set< Residue * >	flexible_residues_
Result	result_
double	static_ligand_energy_
vector< Bond * >	rotatable_ligand_bonds_
list< list< Vector3 > >	flexres_org_positions_

Friends
class	PharmacophoreConstraint
class	SideChainOptimizer

Detailed Description

Definition at line 28 of file scoringFunction.h.

Constructor & Destructor Documentation

BALL::ScoringFunction::ScoringFunction

(

)

BALL::ScoringFunction::ScoringFunction

(

const ScoringFunction &

sf

)

BALL::ScoringFunction::ScoringFunction	(	AtomContainer &	receptor,
		AtomContainer &	ligand
	)

BALL::ScoringFunction::ScoringFunction	(	AtomContainer &	receptor,
		AtomContainer &	ligand,
		const Options &	options
	)

BALL::ScoringFunction::ScoringFunction	(	AtomContainer &	receptor,
		AtomContainer &	ligand,
		Options &	options
	)

BALL::ScoringFunction::ScoringFunction	(	AtomContainer &	receptor,
		Vector3 &	hashgrid_origin,
		Options &	options
	)

Constructor for use without reference ligand

Parameters

hashgrid_origin

Origin of the HashGrid that will hold receptor atoms as potential interaction partners.

virtual BALL::ScoringFunction::~ScoringFunction ( )

virtual

Member Function Documentation

bool BALL::ScoringFunction::assignRotamer	(	Residue *	residue,
		ResidueRotamerSet *	rotamer_set,
		const Rotamer *	rotamer
	)

Assign the given rotamer to the specified residue.
After applying the new rotamer, it is checked whether it overlaps with any other receptor residues. If this is the case, the previously used rotamer will re-applied and zero will be returned. Else, one will be returned by this function. The hash_grid_ of this ScoringFunction that keeps track of all receptor atoms will be automatically updated.

double BALL::ScoringFunction::calculateConstraintsScore ( )

protected

Calculates penalty-scores for all defined Contraints and returns the sum.

Vector3 BALL::ScoringFunction::calculateGeometricalCenter ( AtomContainer *  s, int *  no_ligand_atoms = NULL  )

protected

Calculates the geometrical center of the given structure

Parameters

no_ligand_atoms

if specified, the number of atoms of the current ligand candidate is saved here.

double BALL::ScoringFunction::calculateMoleculeRadius ( AtomContainer *  sys, Vector3 &  center  )

protected

Calculates the radius of a given structure, i.e. the maximal distance from its geometrical center.

double BALL::ScoringFunction::calculateScore

(

)

virtual double BALL::ScoringFunction::calculateStaticLigandFragmentEnergy ( )

protectedvirtual

Calculates the energy within the StaticLigandFragments only!
This needs to be done only once for each ligand candidate.

int BALL::ScoringFunction::checkForAtomOverlaps ( const AtomPairVector *  pair_vector )

protected

Check how many of the atom pairs in the given AtomPairVector clash with each other.

virtual void BALL::ScoringFunction::clear ( )

virtual

Reimplemented in BALL::SLICKEnergy, and BALL::SLICKScore.

void BALL::ScoringFunction::clearStoredInteractions_ ( )

protected

Clears the MolecularInteractions saved for each ligand- and receptor-atom.

String BALL::ScoringFunction::convertTime

(

double

seconds

)

Converts the given seconds (e.g. result of BALL::Timer::getClockTime()) into the appropriate unit and output a String containing value and unit.

int BALL::ScoringFunction::countCovalentBonds ( const Atom *  atom, int  threshold = -1  )

protected

Returns the number of covalent bonds of the given atom

Parameters

threshold

if specified, it is only checked whether there are at least so many covalent bonds.

Size BALL::ScoringFunction::countNeighboringReceptorAtoms	(	const Atom *	atom,
		double	distance_threshold,
		bool	onePerCell = 0,
		int *	number_of_overlaps = 0
	)		const

Count the number of receptor atoms that have a distance <= distance_threshold to the specified atom.

Parameters

onePerCell

If true, only one receptor atom within each hashgrid cell will be taken into account, i.e. the number of neighboring nonempty cells is counted.

virtual void BALL::ScoringFunction::createAllLigandNonBondedPairs ( )

protectedvirtual

Calculates all nonbonded pairs of ligand atoms, i.e. without using a cutoff. This way much time can be saved (for small+medium sized ligands) because the pairlist of the nonbonded comformation component will not be changed by future calls of update() for this ligand.

AtomPairVector* BALL::ScoringFunction::createLigandNonbondedPairVector ( bool  intra_fragment, int &  overlaps  )

protected

Creates nonbonded pairs of ligand atoms.
If StaticLigandFragments are used, only atoms that are part of different StaticLigandFragments are searched. This way, time can be saved during updating the ForceFields, since the score/energy within each StaticLigandFragments will not change.

Parameters

intra_fragment	if set to true (and check_fragment == 1), nonbonded interactions between atoms of the same fragment are searched instead. This is used to calculated the energy of all StaticLigandFragments once for each ligand candidate.
overlaps	the number of atom overlaps will be added to this value

AtomPairVector* BALL::ScoringFunction::createNonbondedPairVector ( HashGrid3< Atom * > *  hashgrid, int &  overlaps, bool  rec_lig, bool  check_fragments = 0, bool  intra_fragment = 0  )

protected

Creates a vector of pairs of ligand atoms and receptor atoms (or atoms of additional systems, e.g. water molecules).
The structure to which the interactions of the current ligand are to be search is represented by the given HashGrid.
The vector of nonbonded atom pairs created by this function is to be used to update the ScoringComponents.

Parameters

rec_lig	determines whether interactions between ligand and receptor are sought. If this is the case, the checks that make sure that two atoms chosen as an atompair are no neighbors and are not identical can be skipped. This way, some time can be saved.
check_fragment	if set to true it is is checked whether two atoms are not part of the same StaticLigandFragment
intra_fragment	if set to true (and check_fragment == 1), nonbonded interactions between atoms of the same fragment are searched instead. This is used to calculated the energy of all StaticLigandFragments once for each ligand candidate.
overlaps	the number of atom overlaps will be added to this value.

void BALL::ScoringFunction::createStaticLigandFragments

(

)

Creates StaticLigandFragments for the current ligand candidate. After this function has been called once for the current ligand candidate, conformation energy is only calculated anew between inter-fragment atom-pairs of this ligand candidate. This way, the speed of energy/score computation can be increased.

void BALL::ScoringFunction::enableAllComponents_ ( )

protected

Enables all ScoringComponents.

void BALL::ScoringFunction::enableInteractionComponents_ ( const list< String > &  type_names )

protected

Enabled the ScoringComponents of the given types and disables all other ScoringComponents. Components that evaluate the intramolecular energy of the ligand will be disabled.

void BALL::ScoringFunction::enableStoreInteractions

(

bool

b = true

)

Determines whether interactions calculated by this ScoringFunction should be saved to each ligand atom a in a->interactions. By default storing of interactions is disabled for new ScoringFunctions.

void BALL::ScoringFunction::enableStoreInteractionsOnlyForPhContraints

(

)

void BALL::ScoringFunction::fetchStaticLigandFragment ( Atom *  a1, int  index  )

protected

Fetches the StaticLigandFragments starting with a1.
This function is used by createStaticLigandFragments(), so that is does not need to be called directly.

Parameters

already_processed_atoms

a temporary hashmap that will store already processed atoms.

const std::map<Atom*, int>* BALL::ScoringFunction::getAtomFragmentMap

(

)

ScoringBaseFunction* BALL::ScoringFunction::getBaseFunction

(

)

const

Return a pointer to the instance of BaseFunction used by this scoring function.

int BALL::ScoringFunction::getBurialDepthScale

(

)

bool BALL::ScoringFunction::getCoefficient	(	const ScoringComponent *	component,
		float &	coefficient
	)		const

Get the coefficient of a component. If there was no matching component, return false, ow return true.

bool BALL::ScoringFunction::getCoefficient	(	const String &	name,
		float &	coefficient
	)		const

Get the coefficient of a component. If there was no matching component, return false, ow return true.

ScoringComponent* BALL::ScoringFunction::getComponent

(

const String &

name

)

const

Return a pointer to a component in the components vector.

ScoringComponent* BALL::ScoringFunction::getComponent

(

const Size

index

)

const

Return a pointer to a component in the components vector.

static void BALL::ScoringFunction::getDefaultOptions ( Options &  options )

static

Stores the default options of this ScoringFunction in the given Option object.

String BALL::ScoringFunction::getEquation

(

)

Returns a string containing the equation of this ScoringFunction (as sum of over all ScoringComponents).

virtual double BALL::ScoringFunction::getES ( )

protectedvirtual

Reimplemented in BALL::GridedPLP, BALL::PLPScoring, BALL::GridedMM, BALL::MMScoring, and BALL::PBScoring.

double BALL::ScoringFunction::getExpEnergyStddev

(

)

Returns the standard deviation of the experimentally determined binding free energy of the used training data set

AtomContainer* BALL::ScoringFunction::getFirstMolecule

(

)

const

const HashGrid3<Atom*>* BALL::ScoringFunction::getHashGrid

(

)

double BALL::ScoringFunction::getIntercept

(

)

const

AtomContainer* BALL::ScoringFunction::getLigand

(

)

const

Return the ligand of the complex (which is just the same as molecule2_).

const Vector3& BALL::ScoringFunction::getLigandCenter

(

)

const

Returns geometrical center of the current ligand candidate.

double BALL::ScoringFunction::getLigandRadius

(

)

const

Size BALL::ScoringFunction::getMaximumNumberOfErrors

(

)

const

String BALL::ScoringFunction::getName

(

)

Return the name of this ScoringFunction.

int BALL::ScoringFunction::getNoLigandAtoms

(

)

Return the number of atoms of the current ligand.

virtual int BALL::ScoringFunction::getNoNeighboringReceptorAtoms ( )

virtual

Returns the average number of receptor atoms neighboring each ligand atom as determined by the last call of update().

Reimplemented in BALL::GridBasedScoring.

Options BALL::ScoringFunction::getOptions

(

)

Return the options set for this scoring function.

Options* BALL::ScoringFunction::getOptionsToModify

(

)

Return pointer to the options set for this scoring function.

AtomContainer* BALL::ScoringFunction::getReceptor

(

)

const

Return the receptor of the complex (which is just the same as molecule1_).

const vector<Bond*>* BALL::ScoringFunction::getRotatableLigandBonds

(

)

const

double BALL::ScoringFunction::getScore

(

)

Return the previously calculated score.

void BALL::ScoringFunction::getScoreContributions	(	vector< double > &	score_contributions,
		vector< String > &	names
	)

AtomContainer* BALL::ScoringFunction::getSecondMolecule

(

)

const

const vector<StaticLigandFragment*>* BALL::ScoringFunction::getStaticLigandFragments

(

)

const

const HashSet<const Atom*>& BALL::ScoringFunction::getUnassignedAtoms

(

)

const

HashSet<const Atom*>& BALL::ScoringFunction::getUnassignedAtoms

(

)

bool BALL::ScoringFunction::hasFlexibleResidues

(

)

bool BALL::ScoringFunction::hasPharmacophoreConstraints_ ( )

protected

static HashGrid3<Atom*>* BALL::ScoringFunction::initializeHashGrid ( AtomContainer *  sys, Vector3 &  center, double &  resolution, int  hashgrid_size  )

static

void BALL::ScoringFunction::insertComponent

(

ScoringComponent *

component

)

Add a scoring component to the scoring functions scoring_components_.

Parameters

component

Scoring component to add.

void BALL::ScoringFunction::insertComponent	(	ScoringComponent *	component,
		float	coefficient
	)

Add a scoring component and its coefficient to the scoring functions scoring_components_.

Parameters

component	Scoring component to add.
coefficient	Coefficient associated with the added component.

bool BALL::ScoringFunction::isPeptideBond ( const Bond *  bond ) const

protected

Determines whether the given bond is a peptide bond and thereby not rotatable.

ScoringFunction& BALL::ScoringFunction::operator=

(

const ScoringFunction &

sf

)

virtual void BALL::ScoringFunction::printResult ( bool  detail = 0 )

virtual

Prints an explanation of the score as obtained by the last call of updateScore() to stdout

Parameters

detail

If true, information about inidividual score-contributions is printed as well as the overview.

void BALL::ScoringFunction::removeComponent

(

const ScoringComponent *

component

)

Remove a component from the component list of this scoring function and delete it from memory. If there was no matching component, do nothing. Note that the user will get no feedback if there was no component removed.

void BALL::ScoringFunction::removeComponent

(

const String &

name

)

Remove a component from the component list of this scoring function and delete it from memory. If there was no matching component, do nothing. Note that the user will get no feedback if there was no component removed. Only the first occurrence of a name in the component list will be removed.

void BALL::ScoringFunction::resetFlexibleResidues

(

)

Resets flexible residues to the conformations observed in the input pdb-file.
This does only have any effect if optimization of flexible residues has been used before the call of this function.

void BALL::ScoringFunction::resetResiduePositions	(	Residue *	residue,
		list< Vector3 > &	old_positions
	)

void BALL::ScoringFunction::setBaseFunction

(

ScoringBaseFunction &

base_function

)

Set the instance of BaseFunction for the scoring function.

void BALL::ScoringFunction::setCoefficient	(	const ScoringComponent *	component,
		float	coefficient
	)

Set the coefficient of a component. If there was no matching component, do nothing. Note that the user will get no feedback if there was no coefficient set.

void BALL::ScoringFunction::setCoefficient	(	const String &	name,
		float	coefficient
	)

Set the coefficient of a named component. If there was no matching component, do nothing. Note that the user will get no feedback if there was no coefficient set. Only the first occurrence of a name in the component list will be changed.

void BALL::ScoringFunction::setFirstMolecule

(

AtomContainer &

molecule1

)

void BALL::ScoringFunction::setFlexibleResidues

(

const std::set< Residue * > &

flexible_residues

)

void BALL::ScoringFunction::setIntercept

(

double

intercept

)

void BALL::ScoringFunction::setLigand

(

AtomContainer &

ligand

)

Set the ligand of the complex (which is just the same as molecule2_).

void BALL::ScoringFunction::setMaximumNumberOfErrors

(

Size

nr

)

void BALL::ScoringFunction::setName ( String  name )

protected

Set the name of this ScoringFunction

void BALL::ScoringFunction::setNormalizationParameters	(	double	stddev,
		double	mean
	)

Set mean and standard deviation of the experimentally determined binding free energy of the used training data set.

void BALL::ScoringFunction::setReceptor

(

AtomContainer &

receptor

)

Set the receptor of the complex (which is just the same as molecule1_).

void BALL::ScoringFunction::setSecondMolecule

(

AtomContainer &

molecule2

)

bool BALL::ScoringFunction::setup

(

)

bool BALL::ScoringFunction::setup	(	AtomContainer &	receptor,
		AtomContainer &	ligand
	)

bool BALL::ScoringFunction::setup	(	AtomContainer &	receptor,
		AtomContainer &	ligand,
		const Options &	options
	)

void BALL::ScoringFunction::setupFlexibleResidues_ ( )

protected

virtual void BALL::ScoringFunction::setupReferenceLigand ( )

protectedvirtual

Use the current ligand as reference ligand. Thus, the average number of neighboring target atoms per reference ligand atom is calculated and can later be compared to the value for a ligand candidate, so that its depth of burial is thereby estimated.

Reimplemented in BALL::GridBasedScoring.

bool BALL::ScoringFunction::storeInteractionsEnabled

(

)

Tells whether interactions calculated by this ScoringFunction should be saved to each ligand atom a in a->interactions. By default storing of interactions is disabled for new ScoringFunctions.

void BALL::ScoringFunction::unsetTrainingParameters

(

)

Sets the coefficients of all ScoringComponents to 1 and unsets all transformations. This is necessay if obtained scores are to be used for an optimization via regression.

virtual void BALL::ScoringFunction::update ( )

virtual

Update all nonbonded pair-lists.

Reimplemented in BALL::DiffGridBasedScoring.

void BALL::ScoringFunction::updateComponent ( int  id, AtomPairList *    )

protected

virtual double BALL::ScoringFunction::updateScore ( )

virtual

Calculates the score for the current ligand pose.

Reimplemented in BALL::DiffGridBasedScoring.

String BALL::ScoringFunction::valueToString

(

double

value

)

Friends And Related Function Documentation

friend class PharmacophoreConstraint

friend

Definition at line 31 of file scoringFunction.h.

friend class SideChainOptimizer

friend

Definition at line 32 of file scoringFunction.h.

Member Data Documentation

AtomPairVector* BALL::ScoringFunction::all_ligand_nonbonded_

protected

All nonbonded pairs of the current ligand. Calculated without cutoff by createAllLigandNonBondedPairs().

Definition at line 767 of file scoringFunction.h.

HashGrid3<Atom*>* BALL::ScoringFunction::all_residues_hashgrid_

protected

Definition at line 666 of file scoringFunction.h.

double BALL::ScoringFunction::allowed_intermolecular_overlap_

protected

Allowed overlap in Angstroem for two atoms of two different molecules (used since even in many crystal structures, some atoms overlap minimally).

Definition at line 732 of file scoringFunction.h.

double BALL::ScoringFunction::allowed_intramolecular_overlap_

protected

Allowed overlap in Angstroem for two atoms of the same molecule (used since even in many crystal structures, some atoms overlap minimally).

Definition at line 738 of file scoringFunction.h.

std::map<Atom*, int> BALL::ScoringFunction::atoms_to_fragments_

protected

Maps each ligand atom to its StaticLigandFragments (if StaticLigandFragments have been calculated).

Definition at line 678 of file scoringFunction.h.

ScoringBaseFunction* BALL::ScoringFunction::base_function_

protected

The base funcion for scoring simple terms

Definition at line 623 of file scoringFunction.h.

int BALL::ScoringFunction::burial_depth_scale_

protected

Definition at line 784 of file scoringFunction.h.

double BALL::ScoringFunction::conformation_scale_

protected

Allows scaling down the contribution of the conformational energy of the ligand to the overall score.

Definition at line 772 of file scoringFunction.h.

list<Constraint*> BALL::ScoringFunction::constraints

List holding all ReferenceAreas of the ScoringFunction.
ReferenceAreas can be added/deleted/modified directly by the user and will be used during all future calls of updateScore().

Definition at line 457 of file scoringFunction.h.

double BALL::ScoringFunction::exp_energy_mean_

protected

Mean of the experimentally determined binding free energy of the used training data set.

Definition at line 794 of file scoringFunction.h.

double BALL::ScoringFunction::exp_energy_stddev_

protected

Standard deviation of the experimentally determined binding free energy of the used training data set.

Definition at line 789 of file scoringFunction.h.

std::set<Residue*> BALL::ScoringFunction::flexible_residues_

protected

Definition at line 796 of file scoringFunction.h.

HashGrid3<Atom*>* BALL::ScoringFunction::flexible_residues_hashgrid_

protected

Definition at line 668 of file scoringFunction.h.

list<list<Vector3> > BALL::ScoringFunction::flexres_org_positions_

protected

Original positions of all atoms of all flexible residues, i.e. as they appear in the input receptor object.

Definition at line 818 of file scoringFunction.h.

HashGrid3<Atom*>* BALL::ScoringFunction::hashgrid_

protected

HashGrid used to find potential interaction partners for a ligand atom.

Definition at line 664 of file scoringFunction.h.

int BALL::ScoringFunction::hashgrid_search_radius_

protected

Number of boxes around a ligand atom that are to be searched.

Definition at line 701 of file scoringFunction.h.

bool BALL::ScoringFunction::ignore_h_clashes_

protected

Determines whether an overlap between two Hydrogen atoms should be considered a sterical clash.

Definition at line 716 of file scoringFunction.h.

double BALL::ScoringFunction::intercept_

protected

The intercept necessary for calculating the score

Definition at line 618 of file scoringFunction.h.

AtomContainer* BALL::ScoringFunction::ligand_

protected

Ligand to dock

Definition at line 608 of file scoringFunction.h.

int BALL::ScoringFunction::ligand_atoms_

protected

Number of atoms of the current ligand candidate. Value is set by each call of calculateGeometricalCenter()

Definition at line 654 of file scoringFunction.h.

Vector3 BALL::ScoringFunction::ligand_center_

protected

Geometrical center of the current ligand

Definition at line 659 of file scoringFunction.h.

int BALL::ScoringFunction::ligand_intramol_overlaps_

protected

Number of overlapping ligand atom pairs as determined by the last call of update().

Definition at line 726 of file scoringFunction.h.

double BALL::ScoringFunction::ligand_radius_

protected

Radius of the current ligand, i.e. the maximal distance from its geometrical center

Definition at line 648 of file scoringFunction.h.

Size BALL::ScoringFunction::max_number_of_errors_

protected

Max number of unassigned atoms

Definition at line 638 of file scoringFunction.h.

int BALL::ScoringFunction::misplaced_ligand_atoms_

protected

Number of ligand atoms that were found to be lying outside of hash_grid_, as determined by the last call of createNonBondedPairList().

Definition at line 696 of file scoringFunction.h.

String BALL::ScoringFunction::name_

protected

Name of the scoring function

Definition at line 593 of file scoringFunction.h.

double BALL::ScoringFunction::neighbor_cutoff_2_

protected

Number of target atoms within this squared distance of ligand atoms are used to approximate the depth of burial of the ligand.

Definition at line 744 of file scoringFunction.h.

int BALL::ScoringFunction::neighboring_target_atoms_

protected

Average number of target atoms within a distance of 'neighbor_cutoff' Angstroem of a ligand atom.
the value is calculated during each call of createNonBondedPairList().

Definition at line 690 of file scoringFunction.h.

double BALL::ScoringFunction::nonbonded_cutoff_

protected

Cutoff value for nonbonded energy.

Definition at line 706 of file scoringFunction.h.

double BALL::ScoringFunction::nonbonded_cutoff_2_

protected

Squared cutoff value for nonbonded energy.

Definition at line 711 of file scoringFunction.h.

Size BALL::ScoringFunction::number_of_errors_

protected

Actual number of counted errors

Definition at line 643 of file scoringFunction.h.

Options BALL::ScoringFunction::options_

protected

Scoring function options

Definition at line 598 of file scoringFunction.h.

int BALL::ScoringFunction::overlaps_

protected

Number of overlapping receptor-ligand atom pairs as determined by the last call of update().

Definition at line 721 of file scoringFunction.h.

AtomContainer* BALL::ScoringFunction::receptor_

protected

Receptor to dock in

Definition at line 603 of file scoringFunction.h.

int BALL::ScoringFunction::reference_neighbors_

protected

Average number of interactions per atom of a reference ligand within a small radius. This is used to estimate the depth of burial of the ligand (candidate).

Definition at line 684 of file scoringFunction.h.

double BALL::ScoringFunction::resolution_

protected

Resolution that was specified by use of the Options object in the constructor.

Definition at line 673 of file scoringFunction.h.

Result BALL::ScoringFunction::result_

protected

Saves the final and all intermediate results of the last call of updateScore().

Definition at line 801 of file scoringFunction.h.

vector<Bond*> BALL::ScoringFunction::rotatable_ligand_bonds_

protected

Rotatable bonds of the current ligand molecule. They are calculated by the function createStaticLigandFragments().

Definition at line 812 of file scoringFunction.h.

double BALL::ScoringFunction::score_

protected

Overall score of the scoring function

Definition at line 613 of file scoringFunction.h.

vector<ScoringComponent*> BALL::ScoringFunction::scoring_components_

protected

The scoring components used by a particular scoring function (e.g. HBonds, VDW, etc.)

Definition at line 628 of file scoringFunction.h.

double BALL::ScoringFunction::static_ligand_energy_

protected

Energy of the StaticLigandFragments. Is calculated once for each ligand candidate by createStaticLigandFragments().

Definition at line 806 of file scoringFunction.h.

vector<StaticLigandFragment*> BALL::ScoringFunction::static_ligand_fragments_

protected

contains the static fragments of the current ligand candidate.
The conformation of each ligand is not changed during docking; only the position of fragments in relation to each other is modified.
Thus, if static_ligand_fragments_ is not empty, createNonBondedPairList() will automatically search only for inter-fragment atom-pairs and ligand-receptor pairs, but not for intra-fragment pairs.

Definition at line 753 of file scoringFunction.h.

HashGrid3<Atom*>* BALL::ScoringFunction::static_residues_hashgrid_

protected

Definition at line 667 of file scoringFunction.h.

bool BALL::ScoringFunction::store_interactions_

protected

Determines whether interactions calculated by this ScoringFunction should be saved to each ligand atom a in a->interactions.
By default this is disabled for new ScoringFunctions.

Definition at line 760 of file scoringFunction.h.

bool BALL::ScoringFunction::store_interactions_phC_only_

protected

Definition at line 762 of file scoringFunction.h.

HashSet<const Atom*> BALL::ScoringFunction::unassigned_atoms_

protected

Atoms, for which the setup of the force field fails

Definition at line 633 of file scoringFunction.h.

bool BALL::ScoringFunction::use_all_lig_nonb_

protected

see Default::ALL_LIG_NONB_PAIRS

Definition at line 777 of file scoringFunction.h.

bool BALL::ScoringFunction::use_static_lig_fragments_

protected

see Default::USE_STATIC_LIG_FRAGMENTS

Definition at line 782 of file scoringFunction.h.