Package org.rcsb.cif.schema.mm

Class Em3dReconstruction

java.lang.Object
org.rcsb.cif.schema.DelegatingCategory
org.rcsb.cif.schema.mm.Em3dReconstruction
All Implemented Interfaces:
Category
@Generated("org.rcsb.cif.schema.generator.SchemaGenerator")
public class Em3dReconstruction
extends DelegatingCategory
Data items in the EM_3D_RECONSTRUCTION category record details of the 3D reconstruction procedure from 2D projections.

  • Constructor Details

  • Method Details

    • createDelegate

      protected Column createDelegate​(String columnName, Column column)
      Overrides:
      createDelegate in class DelegatingCategory

    • getEntryId

      public StrColumn getEntryId()
      This data item is a pointer to _entry.id in the ENTRY category.
      Returns:
      StrColumn

    • getId

      public StrColumn getId()
      The value of _em_3d_reconstruction.id must uniquely identify the 3d reconstruction.
      Returns:
      StrColumn

    • getMethod

      public StrColumn getMethod()
      The algorithm method used for the 3d-reconstruction.
      Returns:
      StrColumn

    • getAlgorithm

      public StrColumn getAlgorithm()
      The algorithm used project from 2D orientations to 3D map.
      Returns:
      StrColumn

    • getCitationId

      public StrColumn getCitationId()
      This data item is a pointer to _citation.id in the CITATION category.
      Returns:
      StrColumn

    • getDetails

      public StrColumn getDetails()
      Any additional details used in the 3d reconstruction.
      Returns:
      StrColumn

    • getResolution

      public FloatColumn getResolution()
      The final resolution (in Angstroms)of the 3D reconstruction.
      Returns:
      FloatColumn

    • getResolutionMethod

      public StrColumn getResolutionMethod()
      The method used to determine the final resolution of the 3d reconstruction. The Fourier Shell Correlation criterion as a measure of resolution is based on the concept of splitting the (2D) data set into two halves; averaging each and comparing them using the Fourier Ring Correlation (FRC) technique.
      Returns:
      StrColumn

    • getMagnificationCalibration

      public StrColumn getMagnificationCalibration()
      The magnification calibration method for the 3d reconstruction.
      Returns:
      StrColumn

    • getCtfCorrectionMethod

      public StrColumn getCtfCorrectionMethod()
      The CTF-correction method. The Contrast Transfer Function CTF compensation for low contrast specimens (e.g. frozen-hydrated), for which phase contrast is the only significant mechanism, then higher defocus levels must be used to achieve any significant transfer, and several images at different focus levels must be combined to complete the information lost from the transfer gaps of any one image. The CTF correction can be applied to each extracted particle separately or to the whole micrograph after digitisation. The simplest level of compensation is to reverse phases at the negative lobes of the CTF.
      Returns:
      StrColumn

    • getNominalPixelSize

      public FloatColumn getNominalPixelSize()
      The nominal pixel size of the projection set of images.
      Returns:
      FloatColumn

    • getActualPixelSize

      public FloatColumn getActualPixelSize()
      The actual pixel size of projection set of images.
      Returns:
      FloatColumn

    • getNumParticles

      public IntColumn getNumParticles()
      The number of 2D projections or 3D subtomograms used in the 3d reconstruction
      Returns:
      IntColumn

    • getEulerAnglesDetails

      public StrColumn getEulerAnglesDetails()
      euler angles details
      Returns:
      StrColumn

    • getNumClassAverages

      public IntColumn getNumClassAverages()
      This item was correspondence to two type of em dataset processing_emDataSet_singleParticle.numClassAverages processing_emDataSet_icosahedral.numClassAverages
      Returns:
      IntColumn

    • getSoftware

      public StrColumn getSoftware()
      software name
      Returns:
      StrColumn

    • getFscType

      public StrColumn getFscType()
      type of FSC curve used to determine map resolution
      Returns:
      StrColumn

    • getRefinementType

      public StrColumn getRefinementType()
      type of refinement performed in order to determine map resolution
      Returns:
      StrColumn

    • getImageProcessingId

      public StrColumn getImageProcessingId()
      Foreign key to the EM_IMAGE_PROCESSING category
      Returns:
      StrColumn

    • getSymmetryType

      public StrColumn getSymmetryType()
      The type of symmetry applied to the reconstruction
      Returns:
      StrColumn