Package org.rcsb.strucmotif.domain.query

Class QueryBuilder.MandatoryBuilder

java.lang.Object
org.rcsb.strucmotif.domain.query.QueryBuilder.MandatoryBuilder
Enclosing class:
QueryBuilder
public class QueryBuilder.MandatoryBuilder extends Object
Parameters are considered mandatory arguments (in the sense that some value has to be given - nonetheless, default values will be used). But internally these values are strictly required. No input validation is performed whatsoever.

  • Method Details

    • backboneDistanceTolerance

      public QueryBuilder.MandatoryBuilder backboneDistanceTolerance(int backboneDistanceTolerance)
      Specify the backbone distance tolerance (default: 1).
      Parameters:
      backboneDistanceTolerance - the tolerance to use
      Returns:
      this builder

    • sideChainDistanceTolerance

      public QueryBuilder.MandatoryBuilder sideChainDistanceTolerance(int sideChainDistanceTolerance)
      Specify the side-chain distance tolerance (default: 1).
      Parameters:
      sideChainDistanceTolerance - the tolerance to use
      Returns:
      this builder

    • angleTolerance

      public QueryBuilder.MandatoryBuilder angleTolerance(int angleTolerance)
      Specify the angle tolerance (default: 1).
      Parameters:
      angleTolerance - the tolerance to use
      Returns:
      this builder

    • rmsdCutoff

      public QueryBuilder.MandatoryBuilder rmsdCutoff(double rmsdCutoff)
      Filter hits based on RMSD. Only relevant when scoring strategy involves alignment.
      Parameters:
      rmsdCutoff - the RMSD cutoff above which hits are filtered
      Returns:
      this builder

    • atomPairingScheme

      public QueryBuilder.MandatoryBuilder atomPairingScheme(AtomPairingScheme atomPairingScheme)
      Controls which atoms will be considered for alignment. Only relevant when scoring scheme is alignment-based.
      Parameters:
      atomPairingScheme - how to pair atoms for alignment routine
      Returns:
      this builder

    • motifPruningStrategy

      public QueryBuilder.MandatoryBuilder motifPruningStrategy(MotifPruner motifPruner)
      Specify the motif pruning strategy.
      Parameters:
      motifPruner - the implementation to prune motifs
      Returns:
      this builder

    • motifPruningStrategy

      public QueryBuilder.MandatoryBuilder motifPruningStrategy(MotifPruningStrategy motifPruningStrategy)
      Specify the motif pruning strategy.
      Parameters:
      motifPruningStrategy - the strategy to prune motifs
      Returns:
      this builder

    • limitResults

      public QueryBuilder.MandatoryBuilder limitResults(int limit)
      Stop after a certain number of accepted hits.
      Parameters:
      limit - the maximum number of hits below the RMSD threshold
      Returns:
      this builder

    • buildParameters

      public QueryBuilder.OptionalStepBuilder buildParameters()
      Creates a Parameters instance based on all values. Proceeds to the next step.
      Returns:
      the optional argument step