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 assembly, org.apache.commons.configuration2.CompositeConfiguration properties)
      construct a diffraction data assembly, assumes an X-ray data set with a weight of 1.0 using the same name as the molecular assembly
      Parameters:
      assembly - molecular assembly object, used as the atomic model for comparison against the data
      properties - system properties file

    • DiffractionData

      public DiffractionData(MolecularAssembly assembly, org.apache.commons.configuration2.CompositeConfiguration properties, DiffractionFile... datafile)
      construct a diffraction data assembly
      Parameters:
      assembly - molecular assembly object, used as the atomic model for comparison against the data
      properties - system properties file
      datafile - one or more DiffractionFile to be refined against

    • DiffractionData

      public DiffractionData(MolecularAssembly assembly, org.apache.commons.configuration2.CompositeConfiguration properties, CrystalReciprocalSpace.SolventModel solventmodel)
      construct a diffraction data assembly, assumes an X-ray data set with a weight of 1.0 using the same name as the molecular assembly
      Parameters:
      assembly - molecular assembly object, 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

    • DiffractionData

      public DiffractionData(MolecularAssembly assembly, org.apache.commons.configuration2.CompositeConfiguration properties, CrystalReciprocalSpace.SolventModel solventmodel, DiffractionFile... datafile)
      construct a diffraction data assembly
      Parameters:
      assembly - molecular assembly object, 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
      datafile - one or more DiffractionFile to be refined against

    • DiffractionData

      public DiffractionData(MolecularAssembly[] assembly, org.apache.commons.configuration2.CompositeConfiguration properties)
      construct a diffraction data assembly, assumes an X-ray data set with a weight of 1.0 using the same name as the molecular assembly
      Parameters:
      assembly - molecular assembly object array (typically containing alternate conformer assemblies), used as the atomic model for comparison against the data
      properties - system properties file

    • DiffractionData

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

    • DiffractionData

      public DiffractionData(MolecularAssembly[] assembly, org.apache.commons.configuration2.CompositeConfiguration properties, CrystalReciprocalSpace.SolventModel solventmodel, DiffractionFile... datafile)
      construct a diffraction data assembly
      Parameters:
      assembly - 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
      datafile - 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.

    • 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.

    • getAssembly

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

    • getAtomArray

      public Atom[] getAtomArray()
      getAtomArray

      return the atom array for the model associated with this data

      Specified by:
      getAtomArray in interface DataContainer
      Returns:
      an array of Atom objects.

    • 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

    • getCrystalStats

      public CrystalStats[] getCrystalStats()
      Getter for the field crystalStats.
      Returns:
      the crystalStats

    • getDataFiles

      public DiffractionFile[] getDataFiles()
      Getter for the field dataFiles.
      Returns:
      the dataFiles

    • getFsigfCutoff

      public double getFsigfCutoff()
      Getter for the field fsigfCutoff.
      Returns:
      the fsigfCutoff

    • getModelName

      public String getModelName()
      Getter for the field modelName.
      Returns:
      the modelName

    • getMolecularAssemblies

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

    • getN

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

    • getParallelTeam

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

    • getRCrystalStat

      public double getRCrystalStat()
      Return R value for OST x-ray minimization.
      Returns:
      a double.

    • 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

    • getScaleBulkMinimize

      public ScaleBulkMinimize[] getScaleBulkMinimize()
      Getter for the field scaleBulkMinimize.
      Returns:
      the scaleBulkMinimize

    • getScaled

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

    • getSigmaAMinimize

      public SigmaAMinimize[] getSigmaAMinimize()
      Getter for the field sigmaAMinimize.
      Returns:
      the sigmaAMinimize

    • getSigmaATol

      public double getSigmaATol()
      Getter for the field sigmaATol.
      Returns:
      the sigmaATol

    • getSolventModel

      public CrystalReciprocalSpace.SolventModel getSolventModel()
      Getter for the field solventModel.
      Returns:
      the solventModel

    • getSplineMinimize

      public SplineMinimize[] getSplineMinimize()
      Getter for the field splineMinimize.
      Returns:
      the splineMinimize

    • 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.

    • getXrayScaleTol

      public double getXrayScaleTol()
      Getter for the field xrayScaleTol.
      Returns:
      the xrayScaleTol

    • getaRadBuff

      public double getaRadBuff()
      Getter for the field aRadBuff.
      Returns:
      the aRadBuff

    • getxWeight

      public double getxWeight()
      Getter for the field xWeight.
      Returns:
      the xWeight

    • isRefineMolOcc

      public boolean isRefineMolOcc()
      isRefineMolOcc.
      Returns:
      the refineMolOcc

    • isUse_3g

      public boolean isUse_3g()
      isUse_3g.
      Returns:
      the use_3g

    • 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.

    • printScaleAndR

      public void printScaleAndR()
      Print scale and R statistics for all datasets associated with the model.

    • 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.

    • setSolventAB

      public void setSolventAB(double a, double b)
      set the bulk solvent parameters for a given bulk solvent model
      Parameters:
      a - typically the width of the atom
      b - typically the rate with which the atom transitions to bulk
      See Also:
      • CrystalReciprocalSpace.setSolventAB(double, double)

    • 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)
      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