Package org.rcsb.cif.schema.mm

Class EmMap

java.lang.Object
org.rcsb.cif.schema.DelegatingCategory
org.rcsb.cif.schema.mm.EmMap
All Implemented Interfaces:
Category
@Generated("org.rcsb.cif.schema.generator.SchemaGenerator")
public class EmMap
extends DelegatingCategory
Data items in the EMD_MAP category record parameters of the CCP4 binary-format map file header (see ftp://ftp.wwpdb.org/pub/emdb/doc/map_format/EMDB_mapFormat_v1.0.pdf), parameters derived from the map header, pixel size, contour level, and annotation details from the depositor. The map is a three-dimensional array of data-values of the same data-type. Important parameters are data-type and array size in three dimensions (i.e. the number of columns, rows and sections). Columns are the fastest changing, followed by rows and sections.

  • Constructor Details

  • Method Details

    • createDelegate

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

    • getAnnotationDetails

      public StrColumn getAnnotationDetails()
      map annotation details
      Returns:
      StrColumn

    • getAxisOrderFast

      public StrColumn getAxisOrderFast()
      The map axis that corresponds to Columns. (CCP4 HEADER WORD 17 MAPC 1=x, 2=y, 3=z)
      Returns:
      StrColumn

    • getAxisOrderMedium

      public StrColumn getAxisOrderMedium()
      The map axis that corresponds to Rows. (CCP4 map header word 18 MAPR 1=x, 2=y, 3=z)
      Returns:
      StrColumn

    • getAxisOrderSlow

      public StrColumn getAxisOrderSlow()
      The map axis that corresponds to Sections. (CCP4 map header word 19 MAPS 1=x, 2=y, 3=z)
      Returns:
      StrColumn

    • getCellA

      public FloatColumn getCellA()
      Map unit cell length parameter a. (CCP4 map header word 11)
      Returns:
      FloatColumn

    • getCellB

      public FloatColumn getCellB()
      Map unit cell length parameter b. (CCP4 map header word 12)
      Returns:
      FloatColumn

    • getCellC

      public FloatColumn getCellC()
      Map unit cell length parameter c. (CCP4 map header word 13)
      Returns:
      FloatColumn

    • getCellAlpha

      public FloatColumn getCellAlpha()
      Value of map unit cell angle parameter alpha in degrees. (CCP4 map header word 14)
      Returns:
      FloatColumn

    • getCellBeta

      public FloatColumn getCellBeta()
      Value of map unit cell angle parameter beta in degrees. (CCP4 map header word 15)
      Returns:
      FloatColumn

    • getCellGamma

      public FloatColumn getCellGamma()
      Value of map unit cell angle parameter gamma in degrees. (CCP4 map header word 16)
      Returns:
      FloatColumn

    • getContourLevel

      public FloatColumn getContourLevel()
      recommended contour level for viewing the map
      Returns:
      FloatColumn

    • getContourLevelSource

      public StrColumn getContourLevelSource()
      source of the recommended contour level
      Returns:
      StrColumn

    • getDataType

      public StrColumn getDataType()
      The map data_type describes the data structure of the map voxels. (CCP4 map header word 4 MODE) EMDB currently holds MODE=0,1,and 2 maps; the majority are MODE=2. MAPS with MODES other than 2 and 0 may not work in CCP4 programs. MODE = 0: 8 bits, density stored as a signed byte (-128 to 127, ISO/IEC 10967) MODE = 1: 16 bits, density stored as a signed integer (-32768 to 32767, ISO/IEC 10967) MODE = 2: 32 bits, density stored as a floating point number (IEEE 754)
      Returns:
      StrColumn

    • getDimensionsCol

      public IntColumn getDimensionsCol()
      The number of columns in the map. (CCP4 map header word 1 NC)
      Returns:
      IntColumn

    • getDimensionsRow

      public IntColumn getDimensionsRow()
      The number of rows in the map. (CCP4 map header word 2 NR)
      Returns:
      IntColumn

    • getDimensionsSec

      public IntColumn getDimensionsSec()
      The number of sections in the map. (CCP4 map header word 3 NS)
      Returns:
      IntColumn

    • getEndianType

      public StrColumn getEndianType()
      map file endian type
      Returns:
      StrColumn

    • getFile

      public StrColumn getFile()
      Map file name.
      Returns:
      StrColumn

    • getFormat

      public StrColumn getFormat()
      map format
      Returns:
      StrColumn

    • getId

      public IntColumn getId()
      Unique id for the EMD_MAP category.
      Returns:
      IntColumn

    • getPartition

      public IntColumn getPartition()
      Identifies the archive file partition number of a primary map, half map, additional map, or mask.
      Returns:
      IntColumn

    • getEntryId

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

    • getLabel

      public StrColumn getLabel()
      text stored in the label field of the CCP4 map header (WORDS 57-256)
      Returns:
      StrColumn

    • getLimitCol

      public IntColumn getLimitCol()
      The final column position of the map relative to the Cartesian coordinate origin in voxel grid units. (derived = .origin_col + .dimensions_col -1)
      Returns:
      IntColumn

    • getLimitRow

      public IntColumn getLimitRow()
      The final row position of the map relative to the Cartesian coordinate origin in voxel grid units. (derived = .origin_row + .dimensions_row -1)
      Returns:
      IntColumn

    • getLimitSec

      public IntColumn getLimitSec()
      The final section position of the map relative to the Cartesian coordinate origin in voxel grid units. (derived -- .origin_sec + .dimensions_sec -1)
      Returns:
      IntColumn

    • getOriginCol

      public IntColumn getOriginCol()
      The position of the first column of the map relative to the Cartesian coordinate origin in voxel grid units. (CCP4 map header word 5 NCSTART)
      Returns:
      IntColumn

    • getOriginRow

      public IntColumn getOriginRow()
      The position of the first row of the map relative to the Cartesian coordinate origin in voxel grid units. (CCP4 map header word 6 NRSTART)
      Returns:
      IntColumn

    • getOriginSec

      public IntColumn getOriginSec()
      The position of the first section of the map relative to the Cartesian coordinate origin in voxel grid units. (CCP4 map header word 7 NSSTART)
      Returns:
      IntColumn

    • getPixelSpacingX

      public FloatColumn getPixelSpacingX()
      The length in Angstroms of one voxel along the X axis.
      Returns:
      FloatColumn

    • getPixelSpacingY

      public FloatColumn getPixelSpacingY()
      The length in Angstroms of one voxel along the Y axis.
      Returns:
      FloatColumn

    • getPixelSpacingZ

      public FloatColumn getPixelSpacingZ()
      The length in Angstroms of one voxel along the Z axis.
      Returns:
      FloatColumn

    • getSizeKb

      public IntColumn getSizeKb()
      map storage size in Kilobytes (before compression)
      Returns:
      IntColumn

    • getSpacingX

      public IntColumn getSpacingX()
      The number of intervals per cell repeat in X. (CCP4 map header word 8 NX)
      Returns:
      IntColumn

    • getSpacingY

      public IntColumn getSpacingY()
      The number of intervals per cell repeat in Y. (CCP4 map header word 9 NY)
      Returns:
      IntColumn

    • getSpacingZ

      public IntColumn getSpacingZ()
      The number of intervals per cell repeat in Z. (CCP4 map header word 10 NZ)
      Returns:
      IntColumn

    • getStatisticsAverage

      public FloatColumn getStatisticsAverage()
      Mean (average) density value of the map.
      Returns:
      FloatColumn

    • getStatisticsMaximum

      public FloatColumn getStatisticsMaximum()
      Maximum density value of the map.
      Returns:
      FloatColumn

    • getStatisticsMinimum

      public FloatColumn getStatisticsMinimum()
      Minimum density value of the map.
      Returns:
      FloatColumn

    • getStatisticsStd

      public FloatColumn getStatisticsStd()
      The standard deviation of the map density values.
      Returns:
      FloatColumn

    • getSymmetrySpaceGroup

      public StrColumn getSymmetrySpaceGroup()
      The space group number for the map. The value is 1 unless the sample is crystalline. (CCP4 map header word 23 ISPG)
      Returns:
      StrColumn

    • getType

      public StrColumn getType()
      map format
      Returns:
      StrColumn