Package org.rcsb.cif.schema.core

Class AtomType

java.lang.Object
org.rcsb.cif.schema.DelegatingCategory.DelegatingCifCoreCategory
org.rcsb.cif.schema.core.AtomType
All Implemented Interfaces:
Category
@Generated("org.rcsb.cif.schema.generator.SchemaGenerator")
public class AtomType
extends DelegatingCategory.DelegatingCifCoreCategory
The CATEGORY of data items used to describe atomic type information used in crystallographic structure studies.

  • Constructor Details

  • Method Details

    • getAtomicMass

      public FloatColumn getAtomicMass()
      Mass of this atom type.
      Returns:
      FloatColumn

    • getAtomicNumber

      public IntColumn getAtomicNumber()
      Atomic number of this atom type.
      Returns:
      IntColumn

    • getDescription

      public StrColumn getDescription()
      A description of the atom(s) designated by this atom type. In most cases this will be the element name and oxidation state of a single atom species. For disordered or nonstoichiometric structures it will describe a combination of atom species.
      Returns:
      StrColumn

    • getDisplayColour

      public StrColumn getDisplayColour()
      The display colour assigned to this atom type. Note that the possible colours are enumerated in the display_colour list category of items.
      Returns:
      StrColumn

    • getElectronCount

      public IntColumn getElectronCount()
      Number of electrons in this atom type.
      Returns:
      IntColumn

    • getElementSymbol

      public StrColumn getElementSymbol()
      Element symbol for of this atom type. The default value is extracted from the ion-to-element enumeration_default list using the index value of _atom_type.symbol.
      Returns:
      StrColumn

    • getKey

      public StrColumn getKey()
      Value is a unique key to a set of ATOM_TYPE items in a looped list.
      Returns:
      StrColumn

    • getNumberInCell

      public FloatColumn getNumberInCell()
      Total number of atoms of this atom type in the unit cell.
      Returns:
      FloatColumn

    • getOxidationNumber

      public IntColumn getOxidationNumber()
      Formal oxidation state of this atom type in the structure.
      Returns:
      IntColumn

    • getRadiusBond

      public FloatColumn getRadiusBond()
      The effective intra-molecular bonding radius of this atom type.
      Returns:
      FloatColumn

    • getRadiusContact

      public FloatColumn getRadiusContact()
      The effective inter-molecular bonding radius of this atom type.
      Returns:
      FloatColumn

    • getSymbol

      public StrColumn getSymbol()
      The identity of the atom specie(s) representing this atom type. Normally this code is the element symbol followed by the charge if there is one. The symbol may be composed of any character except an underline or a blank, with the proviso that digits designate an oxidation state and must be followed by a + or - character.
      Returns:
      StrColumn

    • getAnalyticalMass

      public FloatColumn getAnalyticalMass()
      Mass percentage of this atom type derived from chemical analysis.
      Returns:
      FloatColumn

    • getAnalyticalMassPercent

      public FloatColumn getAnalyticalMassPercent()
      Mass percentage of this atom type derived from chemical analysis.
      Returns:
      FloatColumn

    • getScatCromerMannA1

      public FloatColumn getScatCromerMannA1()
      The set of data items used to define Cromer-Mann coefficients for generation of X-ray scattering factors. Ref: International Tables for X-ray Crystallography, Vol. IV (1974) Table 2.2B or International Tables for Crystallography, Vol. C (1991) Tables 6.1.1.4 and 6.1.1.5
      Returns:
      FloatColumn

    • getCromerMannA1

      public FloatColumn getCromerMannA1()
      The set of data items used to define Cromer-Mann coefficients for generation of X-ray scattering factors. Ref: International Tables for X-ray Crystallography, Vol. IV (1974) Table 2.2B or International Tables for Crystallography, Vol. C (1991) Tables 6.1.1.4 and 6.1.1.5
      Returns:
      FloatColumn

    • getScatCromerMannA2

      public FloatColumn getScatCromerMannA2()
      The set of data items used to define Cromer-Mann coefficients for generation of X-ray scattering factors. Ref: International Tables for X-ray Crystallography, Vol. IV (1974) Table 2.2B or International Tables for Crystallography, Vol. C (1991) Tables 6.1.1.4 and 6.1.1.5
      Returns:
      FloatColumn

    • getCromerMannA2

      public FloatColumn getCromerMannA2()
      The set of data items used to define Cromer-Mann coefficients for generation of X-ray scattering factors. Ref: International Tables for X-ray Crystallography, Vol. IV (1974) Table 2.2B or International Tables for Crystallography, Vol. C (1991) Tables 6.1.1.4 and 6.1.1.5
      Returns:
      FloatColumn

    • getScatCromerMannA3

      public FloatColumn getScatCromerMannA3()
      The set of data items used to define Cromer-Mann coefficients for generation of X-ray scattering factors. Ref: International Tables for X-ray Crystallography, Vol. IV (1974) Table 2.2B or International Tables for Crystallography, Vol. C (1991) Tables 6.1.1.4 and 6.1.1.5
      Returns:
      FloatColumn

    • getCromerMannA3

      public FloatColumn getCromerMannA3()
      The set of data items used to define Cromer-Mann coefficients for generation of X-ray scattering factors. Ref: International Tables for X-ray Crystallography, Vol. IV (1974) Table 2.2B or International Tables for Crystallography, Vol. C (1991) Tables 6.1.1.4 and 6.1.1.5
      Returns:
      FloatColumn

    • getScatCromerMannA4

      public FloatColumn getScatCromerMannA4()
      The set of data items used to define Cromer-Mann coefficients for generation of X-ray scattering factors. Ref: International Tables for X-ray Crystallography, Vol. IV (1974) Table 2.2B or International Tables for Crystallography, Vol. C (1991) Tables 6.1.1.4 and 6.1.1.5
      Returns:
      FloatColumn

    • getCromerMannA4

      public FloatColumn getCromerMannA4()
      The set of data items used to define Cromer-Mann coefficients for generation of X-ray scattering factors. Ref: International Tables for X-ray Crystallography, Vol. IV (1974) Table 2.2B or International Tables for Crystallography, Vol. C (1991) Tables 6.1.1.4 and 6.1.1.5
      Returns:
      FloatColumn

    • getScatCromerMannB1

      public FloatColumn getScatCromerMannB1()
      The set of data items used to define Cromer-Mann coefficients for generation of X-ray scattering factors. Ref: International Tables for X-ray Crystallography, Vol. IV (1974) Table 2.2B or International Tables for Crystallography, Vol. C (1991) Tables 6.1.1.4 and 6.1.1.5
      Returns:
      FloatColumn

    • getCromerMannB1

      public FloatColumn getCromerMannB1()
      The set of data items used to define Cromer-Mann coefficients for generation of X-ray scattering factors. Ref: International Tables for X-ray Crystallography, Vol. IV (1974) Table 2.2B or International Tables for Crystallography, Vol. C (1991) Tables 6.1.1.4 and 6.1.1.5
      Returns:
      FloatColumn

    • getScatCromerMannB2

      public FloatColumn getScatCromerMannB2()
      The set of data items used to define Cromer-Mann coefficients for generation of X-ray scattering factors. Ref: International Tables for X-ray Crystallography, Vol. IV (1974) Table 2.2B or International Tables for Crystallography, Vol. C (1991) Tables 6.1.1.4 and 6.1.1.5
      Returns:
      FloatColumn

    • getCromerMannB2

      public FloatColumn getCromerMannB2()
      The set of data items used to define Cromer-Mann coefficients for generation of X-ray scattering factors. Ref: International Tables for X-ray Crystallography, Vol. IV (1974) Table 2.2B or International Tables for Crystallography, Vol. C (1991) Tables 6.1.1.4 and 6.1.1.5
      Returns:
      FloatColumn

    • getScatCromerMannB3

      public FloatColumn getScatCromerMannB3()
      The set of data items used to define Cromer-Mann coefficients for generation of X-ray scattering factors. Ref: International Tables for X-ray Crystallography, Vol. IV (1974) Table 2.2B or International Tables for Crystallography, Vol. C (1991) Tables 6.1.1.4 and 6.1.1.5
      Returns:
      FloatColumn

    • getCromerMannB3

      public FloatColumn getCromerMannB3()
      The set of data items used to define Cromer-Mann coefficients for generation of X-ray scattering factors. Ref: International Tables for X-ray Crystallography, Vol. IV (1974) Table 2.2B or International Tables for Crystallography, Vol. C (1991) Tables 6.1.1.4 and 6.1.1.5
      Returns:
      FloatColumn

    • getScatCromerMannB4

      public FloatColumn getScatCromerMannB4()
      The set of data items used to define Cromer-Mann coefficients for generation of X-ray scattering factors. Ref: International Tables for X-ray Crystallography, Vol. IV (1974) Table 2.2B or International Tables for Crystallography, Vol. C (1991) Tables 6.1.1.4 and 6.1.1.5
      Returns:
      FloatColumn

    • getCromerMannB4

      public FloatColumn getCromerMannB4()
      The set of data items used to define Cromer-Mann coefficients for generation of X-ray scattering factors. Ref: International Tables for X-ray Crystallography, Vol. IV (1974) Table 2.2B or International Tables for Crystallography, Vol. C (1991) Tables 6.1.1.4 and 6.1.1.5
      Returns:
      FloatColumn

    • getScatCromerMannC

      public FloatColumn getScatCromerMannC()
      The set of data items used to define Cromer-Mann coefficients for generation of X-ray scattering factors. Ref: International Tables for X-ray Crystallography, Vol. IV (1974) Table 2.2B or International Tables for Crystallography, Vol. C (1991) Tables 6.1.1.4 and 6.1.1.5
      Returns:
      FloatColumn

    • getCromerMannC

      public FloatColumn getCromerMannC()
      The set of data items used to define Cromer-Mann coefficients for generation of X-ray scattering factors. Ref: International Tables for X-ray Crystallography, Vol. IV (1974) Table 2.2B or International Tables for Crystallography, Vol. C (1991) Tables 6.1.1.4 and 6.1.1.5
      Returns:
      FloatColumn

    • getScatDispersionImag

      public FloatColumn getScatDispersionImag()
      The imaginary component of the anomalous dispersion scattering factors for this atom type and radiation by _diffrn_radiation_wavelength.value
      Returns:
      FloatColumn

    • getDispersionImag

      public FloatColumn getDispersionImag()
      The imaginary component of the anomalous dispersion scattering factors for this atom type and radiation by _diffrn_radiation_wavelength.value
      Returns:
      FloatColumn

    • getScatDispersionReal

      public FloatColumn getScatDispersionReal()
      The real component of the anomalous dispersion scattering factors for this atom type and radiation by _diffrn_radiation_wavelength.value
      Returns:
      FloatColumn

    • getDispersionReal

      public FloatColumn getDispersionReal()
      The real component of the anomalous dispersion scattering factors for this atom type and radiation by _diffrn_radiation_wavelength.value
      Returns:
      FloatColumn

    • getScatDispersionSource

      public StrColumn getScatDispersionSource()
      Reference to source of real and imaginary dispersion corrections for scattering factors used for this atom type.
      Returns:
      StrColumn

    • getDispersionSource

      public StrColumn getDispersionSource()
      Reference to source of real and imaginary dispersion corrections for scattering factors used for this atom type.
      Returns:
      StrColumn

    • getScatLengthNeutron

      public FloatColumn getScatLengthNeutron()
      The bound coherent scattering length for the atom type at the isotopic composition used for the diffraction experiment.
      Returns:
      FloatColumn

    • getLengthNeutron

      public FloatColumn getLengthNeutron()
      The bound coherent scattering length for the atom type at the isotopic composition used for the diffraction experiment.
      Returns:
      FloatColumn

    • getScatSource

      public StrColumn getScatSource()
      Reference to source of scattering factors used for this atom type.
      Returns:
      StrColumn

    • getSource

      public StrColumn getSource()
      Reference to source of scattering factors used for this atom type.
      Returns:
      StrColumn

    • getScatVersusStolList

      public StrColumn getScatVersusStolList()
      List of scattering factors as a function of sin theta on lambda. List has the form [[<stol value 1> <scatfac 1>] [<stol value 2> <scatfac 2>] ....] in increments of 0.01, increasing from 0.0.
      Returns:
      StrColumn

    • getVersusStolList

      public StrColumn getVersusStolList()
      List of scattering factors as a function of sin theta on lambda. List has the form [[<stol value 1> <scatfac 1>] [<stol value 2> <scatfac 2>] ....] in increments of 0.01, increasing from 0.0.
      Returns:
      StrColumn