Package org.rcsb.cif.model.generated

Class Em3dReconstruction

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

    • Constructor Detail

      • Em3dReconstruction

        public Em3dReconstruction​(String name,
                          int rowCount,
                          Object[] encodedColumns)

      • Em3dReconstruction

        public Em3dReconstruction​(String name)

    • Method Detail

      • 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