Package org.rcsb.strucmotif.core

Class HitScorer

java.lang.Object

org.rcsb.strucmotif.core.HitScorer

public class HitScorer
extends Object

Scores hits by computing the RMSD with respect to the reference motif.

Constructor Summary

Constructors

Constructor	Description
HitScorer(List<Map<LabelAtomId,float[]>> queryResidues, AtomPairingScheme atomPairingScheme, AlignmentService alignmentService)	Construct a query-specific hit scorer.

Method Summary

Modifier and Type	Method	Description
AlignmentResult	alignToReference(List<Map<LabelAtomId,float[]>> targetResidues)	Align a set of residues to the reference.
AtomPairingScheme	getAtomPairingScheme()	Returns the used atom pairing scheme (e.g., all-atoms, side-chain, ...)

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Constructor Details

HitScorer

public HitScorer(List<Map<LabelAtomId,float[]>> queryResidues,
 AtomPairingScheme atomPairingScheme,
 AlignmentService alignmentService)

Construct a query-specific hit scorer.

Parameters:

queryResidues - the reference structure

atomPairingScheme - how to pair atoms?

alignmentService - alignment service

Method Details

getAtomPairingScheme

public AtomPairingScheme getAtomPairingScheme()

Returns the used atom pairing scheme (e.g., all-atoms, side-chain, ...)

Returns:

an AtomPairingScheme value

alignToReference

public AlignmentResult alignToReference(List<Map<LabelAtomId,float[]>> targetResidues)

Align a set of residues to the reference.

Parameters:

targetResidues - collection of residues

Returns:

an AlignmentResult