Package ffx.realspace

Class RealSpaceData

java.lang.Object
ffx.realspace.RealSpaceData
All Implemented Interfaces:
DataContainer
public class RealSpaceData extends Object implements DataContainer
RealSpaceData class.
Since:
1.0
Author:
Timothy D. Fenn

  • Constructor Details

    • RealSpaceData

      public RealSpaceData(MolecularAssembly molecularAssembly, org.apache.commons.configuration2.CompositeConfiguration properties, ParallelTeam parallelTeam, DiffractionData diffractionData)
      Construct a real space data molecularAssemblies, assumes a real space map with a weight of 1.0 using the same name as the molecular molecularAssemblies.
      Parameters:
      molecularAssembly - molecular molecularAssemblies object, used as the atomic model for comparison against the data
      properties - system properties file
      parallelTeam - a ParallelTeam object.
      diffractionData - diffraction data

    • RealSpaceData

      public RealSpaceData(MolecularAssembly[] molecularAssemblies, org.apache.commons.configuration2.CompositeConfiguration properties, ParallelTeam parallelTeam, DiffractionData diffractionData)
      Construct a real space data molecularAssemblies, assumes a real space map with a weight of 1.0 using the same name as the molecularAssemblies.
      Parameters:
      molecularAssemblies - molecular molecularAssemblies object, used as the atomic model for comparison against the data
      properties - system properties file
      parallelTeam - a ParallelTeam object.
      diffractionData - diffraction data

    • RealSpaceData

      public RealSpaceData(MolecularAssembly assembly, org.apache.commons.configuration2.CompositeConfiguration properties, ParallelTeam parallelTeam)
      Construct a real space data molecularAssemblies, assumes a real space map with a weight of 1.0 using the same name as the molecular molecularAssemblies.
      Parameters:
      assembly - molecular molecularAssemblies object, used as the atomic model for comparison against the data
      properties - system properties file
      parallelTeam - a ParallelTeam object.

    • RealSpaceData

      public RealSpaceData(MolecularAssembly assembly, org.apache.commons.configuration2.CompositeConfiguration properties, ParallelTeam parallelTeam, RealSpaceFile... datafile)
      Construct a real space data molecularAssemblies.
      Parameters:
      assembly - molecular molecularAssemblies object, used as the atomic model for comparison against the data
      properties - system properties file
      parallelTeam - a ParallelTeam object.
      datafile - one or more RealSpaceFile to be refined against

    • RealSpaceData

      public RealSpaceData(MolecularAssembly[] molecularAssemblies, org.apache.commons.configuration2.CompositeConfiguration properties, ParallelTeam parallelTeam, RealSpaceFile... dataFile)
      Construct a real space data molecularAssemblies.
      Parameters:
      molecularAssemblies - molecular molecularAssemblies object array (typically containing alternate conformer assemblies), used as the atomic model for comparison against the data
      properties - system properties file
      parallelTeam - a ParallelTeam object.
      dataFile - one or more RealSpaceFile to be refined against

  • Method Details

    • destroy

      public boolean destroy()
      Similar to Potential.destroy(), frees up resources associated with this RealSpaceData.
      Returns:
      If assets successfully freed.

    • getActiveAtomArray

      public Atom[] getActiveAtomArray()
      getActiveAtomArray
      Specified by:
      getActiveAtomArray in interface DataContainer
      Returns:
      an array of Atom objects.

    • getAltMolecules

      public List<List<Molecule>> getAltMolecules()
      getAltMolecules
      Specified by:
      getAltMolecules in interface DataContainer
      Returns:
      a List object.

    • getAltResidues

      public List<List<Residue>> getAltResidues()
      getAltResidues
      Specified by:
      getAltResidues in interface DataContainer
      Returns:
      a List object.

    • getAtomArray

      public Atom[] getAtomArray()
      getAtomArray
      Specified by:
      getAtomArray in interface DataContainer
      Returns:
      an array of Atom objects.

    • getCrystal

      public Crystal[] getCrystal()
      Getter for the field crystal.
      Returns:
      the crystal

    • setCrystal

      public void setCrystal(Crystal[] crystal)
      Setter for the field crystal.
      Parameters:
      crystal - the crystal to set

    • getLambda

      public double getLambda()
      Getter for the field lambda.
      Returns:
      the lambda

    • setLambda

      public void setLambda(double lambda)
      Set the current value of the state variable.
      Parameters:
      lambda - a double.

    • getMolecularAssemblies

      public MolecularAssembly[] getMolecularAssemblies()
      getMolecularAssemblies
      Specified by:
      getMolecularAssemblies in interface DataContainer
      Returns:
      an array of MolecularAssembly objects.

    • getRealSpaceGradient

      public double[] getRealSpaceGradient(double[] gradient)
      Getter for the field realSpaceGradient.
      Parameters:
      gradient - the gradient array.
      Returns:
      the real space gradient added to the input gradient array, or a new array if the gradient is null or too small.

    • getRefinementData

      public RealSpaceRefinementData[] getRefinementData()
      Getter for the field refinementData.
      Returns:
      the refinementData

    • setRefinementData

      public void setRefinementData(RealSpaceRefinementData[] refinementData)
      Setter for the field refinementData.
      Parameters:
      refinementData - the refinementData to set

    • getRefinementModel

      public RefinementModel getRefinementModel()
      getRefinementModel
      Specified by:
      getRefinementModel in interface DataContainer
      Returns:
      a RefinementModel object.

    • getWeight

      public double getWeight()
      getWeight
      Specified by:
      getWeight in interface DataContainer
      Returns:
      the current data weight.

    • setWeight

      public void setWeight(double weight)
      setWeight
      Specified by:
      setWeight in interface DataContainer
      Parameters:
      weight - set the overall weight of the data.

    • printEnergyUpdate

      public String printEnergyUpdate()
      printEnergyUpdate
      Specified by:
      printEnergyUpdate in interface DataContainer
      Returns:
      a String object.

    • printOptimizationHeader

      public String printOptimizationHeader()
      printOptimizationHeader
      Specified by:
      printOptimizationHeader in interface DataContainer
      Returns:
      a String object.

    • printOptimizationUpdate

      public String printOptimizationUpdate()
      printOptimizationUpdate
      Specified by:
      printOptimizationUpdate in interface DataContainer
      Returns:
      a String object.