Package ffx.xray

Class DiffractionData

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

  • Constructor Details

    • DiffractionData

      public DiffractionData(MolecularAssembly[] molecularAssemblies, org.apache.commons.configuration2.CompositeConfiguration properties, SolventModel solventModel, DiffractionFile... dataFiles)
      construct a diffraction data assembly
      Parameters:
      molecularAssemblies - molecular assembly object array (typically containing alternate conformer assemblies), used as the atomic model for comparison against the data
      properties - system properties file
      solventModel - the type of solvent model desired - see bulk solvent model selections
      dataFiles - one or more DiffractionFile to be refined against

  • Method Details

    • AverageFc

      public void AverageFc(MolecularAssembly[] assembly, int index)
      read in a different assembly to average in structure factors
      Parameters:
      assembly - the molecular assembly object array (typically containing alternate conformer assemblies), used as the atomic model to average in with previous assembly
      index - the current data index (for cumulative average purposes)

    • computeAtomicDensity

      public void computeAtomicDensity()
      Parallelized call to compute atomic density on a grid, followed by FFT to compute structure factors.
      See Also:
      • CrystalReciprocalSpace.computeDensity(double[][], boolean)

    • destroy

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

    • getAssembly

      public MolecularAssembly[] getAssembly()
      Getter for the field assembly.
      Returns:
      the assembly

    • getCrystal

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

    • getCrystalReciprocalSpacesFc

      public CrystalReciprocalSpace[] getCrystalReciprocalSpacesFc()
      Getter for the field crs_fc.
      Returns:
      the crs_fc

    • getCrystalReciprocalSpacesFs

      public CrystalReciprocalSpace[] getCrystalReciprocalSpacesFs()
      Getter for the field crs_fs.
      Returns:
      the crs_fs

    • getN

      public int getN()
      Getter for the field n.
      Returns:
      the n

    • getParallelTeam

      public ParallelTeam getParallelTeam()
      Getter for the field parallelTeam.
      Returns:
      the parallelTeam

    • getRefinementData

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

    • getRefinementModel

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

    • getReflectionList

      public ReflectionList[] getReflectionList()
      Getter for the field reflectionList.
      Returns:
      the reflectionList

    • getResolution

      public Resolution[] getResolution()
      Getter for the field resolution.
      Returns:
      the resolution

    • getScaled

      public boolean[] getScaled()
      Getter for the field scaled.
      Returns:
      the scaled

    • 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.

    • printStats

      public void printStats()
      Print all statistics for all datasets associated with the model.

    • scaleBulkFit

      public void scaleBulkFit()
      Scale model and fit bulk solvent to all data.

    • scaleBulkFit

      public void scaleBulkFit(int i)
      Scale model and fit bulk solvent to dataset i of n.
      Parameters:
      i - a int.

    • timings

      public void timings()
      Perform 10 Fc calculations for the purposes of timings.

    • writeData

      public void writeData(String filename)
      write current datasets to MTZ files
      Parameters:
      filename - output filename, or filename root for multiple datasets
      See Also:

    • writeData

      public void writeData(String filename, int i)
      write dataset i to MTZ file
      Parameters:
      filename - output filename
      i - dataset to write out
      See Also:

    • writeMaps

      public void writeMaps(String filename, boolean normalize)
      write 2Fo-Fc and Fo-Fc maps for all datasets
      Parameters:
      filename - output root filename for Fo-Fc and 2Fo-Fc maps

    • writeModel

      public void writeModel(String filename)
      Write current model to PDB file.
      Parameters:
      filename - output PDB filename

    • writeModel

      public void writeModel(String filename, Set<Atom> excludeAtoms, double pH)
      Write current model to PDB file.
      Parameters:
      filename - output PDB filename

    • writeSolventMask

      public void writeSolventMask(String filename)
      Write bulk solvent mask for all datasets to a CCP4 map file.
      Parameters:
      filename - output filename, or output root filename for multiple datasets
      See Also:

    • writeSolventMaskCNS

      public void writeSolventMaskCNS(String filename)
      Write bulk solvent mask for all datasets to a CNS map file.
      Parameters:
      filename - output filename, or output root filename for multiple datasets