Package org.rcsb.cif.schema.mm

Class AtomType

java.lang.Object
org.rcsb.cif.schema.DelegatingCategory
org.rcsb.cif.schema.mm.AtomType
All Implemented Interfaces:
Category
@Generated("org.rcsb.cif.schema.generator.SchemaGenerator")
public class AtomType
extends DelegatingCategory
Data items in the ATOM_TYPE category record details about the properties of the atoms that occupy the atom sites, such as the atomic scattering factors.

  • Constructor Details

  • Method Details

    • createDelegate

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

    • getAnalyticalMassPercent

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

    • getDescription

      public StrColumn getDescription()
      A description of the atom(s) designated by this atom type. In most cases, this is 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

    • getNumberInCell

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

    • getOxidationNumber

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

    • getRadiusBond

      public FloatColumn getRadiusBond()
      The effective intramolecular bonding radius in angstroms of this atom type.
      Returns:
      FloatColumn

    • getRadiusContact

      public FloatColumn getRadiusContact()
      The effective intermolecular bonding radius in angstroms of this atom type.
      Returns:
      FloatColumn

    • getScatCromerMannA1

      public FloatColumn getScatCromerMannA1()
      The Cromer-Mann scattering-factor coefficient a1 used to calculate the scattering factors for this atom type. Ref: International Tables for X-ray Crystallography (1974). Vol. IV, Table 2.2B or: International Tables for Crystallography (2004). Vol. C, Tables 6.1.1.4 and 6.1.1.5.
      Returns:
      FloatColumn

    • getScatCromerMannA2

      public FloatColumn getScatCromerMannA2()
      The Cromer-Mann scattering-factor coefficient a2 used to calculate the scattering factors for this atom type. Ref: International Tables for X-ray Crystallography (1974). Vol. IV, Table 2.2B or: International Tables for Crystallography (2004). Vol. C, Tables 6.1.1.4 and 6.1.1.5.
      Returns:
      FloatColumn

    • getScatCromerMannA3

      public FloatColumn getScatCromerMannA3()
      The Cromer-Mann scattering-factor coefficient a3 used to calculate the scattering factors for this atom type. Ref: International Tables for X-ray Crystallography (1974). Vol. IV, Table 2.2B or: International Tables for Crystallography (2004). Vol. C, Tables 6.1.1.4 and 6.1.1.5.
      Returns:
      FloatColumn

    • getScatCromerMannA4

      public FloatColumn getScatCromerMannA4()
      The Cromer-Mann scattering-factor coefficient a4 used to calculate the scattering factors for this atom type. Ref: International Tables for X-ray Crystallography (1974). Vol. IV, Table 2.2B or: International Tables for Crystallography (2004). Vol. C, Tables 6.1.1.4 and 6.1.1.5.
      Returns:
      FloatColumn

    • getScatCromerMannB1

      public FloatColumn getScatCromerMannB1()
      The Cromer-Mann scattering-factor coefficient b1 used to calculate the scattering factors for this atom type. Ref: International Tables for X-ray Crystallography (1974). Vol. IV, Table 2.2B or: International Tables for Crystallography (2004). Vol. C, Tables 6.1.1.4 and 6.1.1.5.
      Returns:
      FloatColumn

    • getScatCromerMannB2

      public FloatColumn getScatCromerMannB2()
      The Cromer-Mann scattering-factor coefficient b2 used to calculate the scattering factors for this atom type. Ref: International Tables for X-ray Crystallography (1974). Vol. IV, Table 2.2B or: International Tables for Crystallography (2004). Vol. C, Tables 6.1.1.4 and 6.1.1.5.
      Returns:
      FloatColumn

    • getScatCromerMannB3

      public FloatColumn getScatCromerMannB3()
      The Cromer-Mann scattering-factor coefficient b3 used to calculate the scattering factors for this atom type. Ref: International Tables for X-ray Crystallography (1974). Vol. IV, Table 2.2B or: International Tables for Crystallography (2004). Vol. C, Tables 6.1.1.4 and 6.1.1.5.
      Returns:
      FloatColumn

    • getScatCromerMannB4

      public FloatColumn getScatCromerMannB4()
      The Cromer-Mann scattering-factor coefficient b4 used to calculate the scattering factors for this atom type. Ref: International Tables for X-ray Crystallography (1974). Vol. IV, Table 2.2B or: International Tables for Crystallography (2004). Vol. C, Tables 6.1.1.4 and 6.1.1.5.
      Returns:
      FloatColumn

    • getScatCromerMannC

      public FloatColumn getScatCromerMannC()
      The Cromer-Mann scattering-factor coefficient c used to calculate the scattering factors for this atom type. Ref: International Tables for X-ray Crystallography (1974). Vol. IV, Table 2.2B or: International Tables for Crystallography (2004). Vol. C, Tables 6.1.1.4 and 6.1.1.5.
      Returns:
      FloatColumn

    • getScatDispersionImag

      public FloatColumn getScatDispersionImag()
      The imaginary component of the anomalous-dispersion scattering factor, f'', in electrons for this atom type and the radiation identified by _diffrn_radiation_wavelength.id.
      Returns:
      FloatColumn

    • getScatDispersionReal

      public FloatColumn getScatDispersionReal()
      The real component of the anomalous-dispersion scattering factor, f', in electrons for this atom type and the radiation identified by _diffrn_radiation_wavelength.id.
      Returns:
      FloatColumn

    • getScatLengthNeutron

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

    • getScatSource

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

    • getScatVersusStolList

      public StrColumn getScatVersusStolList()
      A table of scattering factors as a function of sin theta over lambda. This table should be well commented to indicate the items present. Regularly formatted lists are strongly recommended.
      Returns:
      StrColumn

    • getSymbol

      public StrColumn getSymbol()
      The code used to identify the atom species (singular or plural) representing this atom type. Normally this code is the element symbol. The code may be composed of any character except an underscore with the additional proviso that digits designate an oxidation state and must be followed by a + or - character.
      Returns:
      StrColumn

    • getScatDispersionSource

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

    • getPdbxScatCromerMannA5

      public FloatColumn getPdbxScatCromerMannA5()
      Scattering-factor coefficient a5, used to calculate electron elastic atomic scattering factors for the defined atom type. Electron Elastic Scattering Factors Ref: International Tables for X-ray Crystallography (2006). Vol. C, Table 4.3.2.2, pp. 282-283. Cromer_Mann equation Ref: International Tables for X-ray Crystallography (1974). Vol. IV, Table 2.2B or: International Tables for Crystallography (2004). Vol. C, Tables 6.1.1.4 and 6.1.1.5.
      Returns:
      FloatColumn

    • getPdbxScatCromerMannB5

      public FloatColumn getPdbxScatCromerMannB5()
      Scattering-factor coefficient b5, used to calculate electron elastic atomic scattering factors for the defined atom type. Electron Elastic Scattering Factors Ref: International Tables for X-ray Crystallography (2006). Vol. C, Table 4.3.2.2, pp. 282-283. Cromer_Mann equation Ref: International Tables for X-ray Crystallography (1974). Vol. IV, Table 2.2B or: International Tables for Crystallography (2004). Vol. C, Tables 6.1.1.4 and 6.1.1.5.
      Returns:
      FloatColumn

    • getPdbxScatCromerMannA6

      public FloatColumn getPdbxScatCromerMannA6()
      Scattering-factor coefficient a6, used to calculate electron elastic atomic scattering factors for the defined atom type. Electron Elastic Scattering Factors Ref: International Tables for X-ray Crystallography (2006). Vol. C, Table 4.3.2.2, pp. 282-283. Cromer_Mann equation Ref: International Tables for X-ray Crystallography (1974). Vol. IV, Table 2.2B or: International Tables for Crystallography (2004). Vol. C, Tables 6.1.1.4 and 6.1.1.5.
      Returns:
      FloatColumn

    • getPdbxScatCromerMannB6

      public FloatColumn getPdbxScatCromerMannB6()
      Scattering-factor coefficient b6, used to calculate electron elastic atomic scattering factors for the defined atom type. Electron Elastic Scattering Factors Ref: International Tables for X-ray Crystallography (2006). Vol. C, Table 4.3.2.2, pp. 282-283. Cromer_Mann equation Ref: International Tables for X-ray Crystallography (1974). Vol. IV, Table 2.2B or: International Tables for Crystallography (2004). Vol. C, Tables 6.1.1.4 and 6.1.1.5.
      Returns:
      FloatColumn

    • getPdbxScatZ

      public IntColumn getPdbxScatZ()
      Atomic number of atom in scattering amplitude.
      Returns:
      IntColumn

    • getPdbxNElectrons

      public IntColumn getPdbxNElectrons()
      Number of electrons in atom used in scattering factor
      Returns:
      IntColumn