Class AtomSite

  • All Implemented Interfaces:
    Category

    @Generated("org.rcsb.cif.generator.SchemaGenerator")
    public class AtomSite
    extends BaseCategory
    Data items in the ATOM_SITE category record details about the atom sites in a macromolecular crystal structure, such as the positional coordinates, atomic displacement parameters, magnetic moments and directions. The data items for describing anisotropic atomic displacement factors are only used if the corresponding items are not given in the ATOM_SITE_ANISOTROP category.
    • Method Summary

      All Methods Instance Methods Concrete Methods 
      Modifier and Type Method Description
      StrColumn getAdpType()
      A standard code used to describe the type of atomic displacement parameters used for the site.
      FloatColumn getAnisoB11()
      The elements of the anisotropic atomic displacement matrix B, which appears in the structure-factor term as: T = exp{-1/4 sum~i~[sum~j~(B^ij^ h~i~ h~j~ a*~i~ a*~j~)]} h = the Miller indices a* = the reciprocal space cell lengths These matrix elements may appear with atomic coordinates in the ATOM_SITE category, or they may appear in the separate ATOM_SITE_ANISOTROP category, but they may not appear in both places.
      FloatColumn getAnisoB11Esd()
      The standard uncertainty (estimated standard deviation) of _atom_site.aniso_B.
      FloatColumn getAnisoB12()
      The elements of the anisotropic atomic displacement matrix B, which appears in the structure-factor term as: T = exp{-1/4 sum~i~[sum~j~(B^ij^ h~i~ h~j~ a*~i~ a*~j~)]} h = the Miller indices a* = the reciprocal space cell lengths These matrix elements may appear with atomic coordinates in the ATOM_SITE category, or they may appear in the separate ATOM_SITE_ANISOTROP category, but they may not appear in both places.
      FloatColumn getAnisoB12Esd()
      The standard uncertainty (estimated standard deviation) of _atom_site.aniso_B.
      FloatColumn getAnisoB13()
      The elements of the anisotropic atomic displacement matrix B, which appears in the structure-factor term as: T = exp{-1/4 sum~i~[sum~j~(B^ij^ h~i~ h~j~ a*~i~ a*~j~)]} h = the Miller indices a* = the reciprocal space cell lengths These matrix elements may appear with atomic coordinates in the ATOM_SITE category, or they may appear in the separate ATOM_SITE_ANISOTROP category, but they may not appear in both places.
      FloatColumn getAnisoB13Esd()
      The standard uncertainty (estimated standard deviation) of _atom_site.aniso_B.
      FloatColumn getAnisoB22()
      The elements of the anisotropic atomic displacement matrix B, which appears in the structure-factor term as: T = exp{-1/4 sum~i~[sum~j~(B^ij^ h~i~ h~j~ a*~i~ a*~j~)]} h = the Miller indices a* = the reciprocal space cell lengths These matrix elements may appear with atomic coordinates in the ATOM_SITE category, or they may appear in the separate ATOM_SITE_ANISOTROP category, but they may not appear in both places.
      FloatColumn getAnisoB22Esd()
      The standard uncertainty (estimated standard deviation) of _atom_site.aniso_B.
      FloatColumn getAnisoB23()
      The elements of the anisotropic atomic displacement matrix B, which appears in the structure-factor term as: T = exp{-1/4 sum~i~[sum~j~(B^ij^ h~i~ h~j~ a*~i~ a*~j~)]} h = the Miller indices a* = the reciprocal space cell lengths These matrix elements may appear with atomic coordinates in the ATOM_SITE category, or they may appear in the separate ATOM_SITE_ANISOTROP category, but they may not appear in both places.
      FloatColumn getAnisoB23Esd()
      The standard uncertainty (estimated standard deviation) of _atom_site.aniso_B.
      FloatColumn getAnisoB33()
      The elements of the anisotropic atomic displacement matrix B, which appears in the structure-factor term as: T = exp{-1/4 sum~i~[sum~j~(B^ij^ h~i~ h~j~ a*~i~ a*~j~)]} h = the Miller indices a* = the reciprocal space cell lengths These matrix elements may appear with atomic coordinates in the ATOM_SITE category, or they may appear in the separate ATOM_SITE_ANISOTROP category, but they may not appear in both places.
      FloatColumn getAnisoB33Esd()
      The standard uncertainty (estimated standard deviation) of _atom_site.aniso_B.
      FloatColumn getAnisoRatio()
      Ratio of the maximum to minimum principal axes of displacement (thermal) ellipsoids.
      FloatColumn getAnisoU11()
      The elements of the standard anisotropic atomic displacement matrix U, which appears in the structure-factor term as: T = exp{-2 pi^2^ sum~i~[sum~j~(U^ij^ h~i~ h~j~ a*~i~ a*~j~)]} h = the Miller indices a* = the reciprocal space cell lengths These matrix elements may appear with atomic coordinates in the ATOM_SITE category, or they may appear in the separate ATOM_SITE_ANISOTROP category, but they may not appear in both places.
      FloatColumn getAnisoU11Esd()
      The standard uncertainty (estimated standard deviation) of _atom_site.aniso_U.
      FloatColumn getAnisoU12()
      The elements of the standard anisotropic atomic displacement matrix U, which appears in the structure-factor term as: T = exp{-2 pi^2^ sum~i~[sum~j~(U^ij^ h~i~ h~j~ a*~i~ a*~j~)]} h = the Miller indices a* = the reciprocal space cell lengths These matrix elements may appear with atomic coordinates in the ATOM_SITE category, or they may appear in the separate ATOM_SITE_ANISOTROP category, but they may not appear in both places.
      FloatColumn getAnisoU12Esd()
      The standard uncertainty (estimated standard deviation) of _atom_site.aniso_U.
      FloatColumn getAnisoU13()
      The elements of the standard anisotropic atomic displacement matrix U, which appears in the structure-factor term as: T = exp{-2 pi^2^ sum~i~[sum~j~(U^ij^ h~i~ h~j~ a*~i~ a*~j~)]} h = the Miller indices a* = the reciprocal space cell lengths These matrix elements may appear with atomic coordinates in the ATOM_SITE category, or they may appear in the separate ATOM_SITE_ANISOTROP category, but they may not appear in both places.
      FloatColumn getAnisoU13Esd()
      The standard uncertainty (estimated standard deviation) of _atom_site.aniso_U.
      FloatColumn getAnisoU22()
      The elements of the standard anisotropic atomic displacement matrix U, which appears in the structure-factor term as: T = exp{-2 pi^2^ sum~i~[sum~j~(U^ij^ h~i~ h~j~ a*~i~ a*~j~)]} h = the Miller indices a* = the reciprocal space cell lengths These matrix elements may appear with atomic coordinates in the ATOM_SITE category, or they may appear in the separate ATOM_SITE_ANISOTROP category, but they may not appear in both places.
      FloatColumn getAnisoU22Esd()
      The standard uncertainty (estimated standard deviation) of _atom_site.aniso_U.
      FloatColumn getAnisoU23()
      The elements of the standard anisotropic atomic displacement matrix U, which appears in the structure-factor term as: T = exp{-2 pi^2^ sum~i~[sum~j~(U^ij^ h~i~ h~j~ a*~i~ a*~j~)]} h = the Miller indices a* = the reciprocal space cell lengths These matrix elements may appear with atomic coordinates in the ATOM_SITE category, or they may appear in the separate ATOM_SITE_ANISOTROP category, but they may not appear in both places.
      FloatColumn getAnisoU23Esd()
      The standard uncertainty (estimated standard deviation) of _atom_site.aniso_U.
      FloatColumn getAnisoU33()
      The elements of the standard anisotropic atomic displacement matrix U, which appears in the structure-factor term as: T = exp{-2 pi^2^ sum~i~[sum~j~(U^ij^ h~i~ h~j~ a*~i~ a*~j~)]} h = the Miller indices a* = the reciprocal space cell lengths These matrix elements may appear with atomic coordinates in the ATOM_SITE category, or they may appear in the separate ATOM_SITE_ANISOTROP category, but they may not appear in both places.
      FloatColumn getAnisoU33Esd()
      The standard uncertainty (estimated standard deviation) of _atom_site.aniso_U.
      IntColumn getAttachedHydrogens()
      The number of hydrogen atoms attached to the atom at this site excluding any hydrogen atoms for which coordinates (measured or calculated) are given.
      StrColumn getAuthAsymId()
      An alternative identifier for _atom_site.label_asym_id that may be provided by an author in order to match the identification used in the publication that describes the structure.
      StrColumn getAuthAtomId()
      An alternative identifier for _atom_site.label_atom_id that may be provided by an author in order to match the identification used in the publication that describes the structure.
      StrColumn getAuthCompId()
      An alternative identifier for _atom_site.label_comp_id that may be provided by an author in order to match the identification used in the publication that describes the structure.
      IntColumn getAuthSeqId()
      An alternative identifier for _atom_site.label_seq_id that may be provided by an author in order to match the identification used in the publication that describes the structure.
      FloatColumn getBEquivGeomMean()
      Equivalent isotropic atomic displacement parameter, B~eq~, in angstroms squared, calculated as the geometric mean of the anisotropic atomic displacement parameters.
      FloatColumn getBEquivGeomMeanEsd()
      The standard uncertainty (estimated standard deviation) of _atom_site.B_equiv_geom_mean.
      FloatColumn getBIsoOrEquiv()
      Isotropic atomic displacement parameter, or equivalent isotropic atomic displacement parameter, B~eq~, calculated from the anisotropic displacement parameters.
      FloatColumn getBIsoOrEquivEsd()
      The standard uncertainty (estimated standard deviation) of _atom_site.B_iso_or_equiv.
      StrColumn getCalcAttachedAtom()
      The _atom_site.id of the atom site to which the 'geometry-calculated' atom site is attached.
      StrColumn getCalcFlag()
      A standard code to signal whether the site coordinates have been determined from the intensities or calculated from the geometry of surrounding sites, or have been assigned dummy values.
      FloatColumn getCartnX()
      The x atom-site coordinate in angstroms specified according to a set of orthogonal Cartesian axes related to the cell axes as specified by the description given in _atom_sites.Cartn_transform_axes.
      FloatColumn getCartnXEsd()
      The standard uncertainty (estimated standard deviation) of _atom_site.Cartn_x.
      FloatColumn getCartnY()
      The y atom-site coordinate in angstroms specified according to a set of orthogonal Cartesian axes related to the cell axes as specified by the description given in _atom_sites.Cartn_transform_axes.
      FloatColumn getCartnYEsd()
      The standard uncertainty (estimated standard deviation) of _atom_site.Cartn_y.
      FloatColumn getCartnZ()
      The z atom-site coordinate in angstroms specified according to a set of orthogonal Cartesian axes related to the cell axes as specified by the description given in _atom_sites.Cartn_transform_axes.
      FloatColumn getCartnZEsd()
      The standard uncertainty (estimated standard deviation) of _atom_site.Cartn_z.
      IntColumn getChemicalConnNumber()
      This data item is a pointer to _chemical_conn_atom.number in the CHEMICAL_CONN_ATOM category.
      StrColumn getConstraints()
      A description of the constraints applied to parameters at this site during refinement.
      StrColumn getDetails()
      A description of special aspects of this site.
      StrColumn getDisorderAssembly()
      A code which identifies a cluster of atoms that show long-range positional disorder but are locally ordered.
      StrColumn getDisorderGroup()
      A code which identifies a group of positionally disordered atom sites that are locally simultaneously occupied.
      StrColumn getFootnoteId()
      The value of _atom_site.footnote_id must match an ID specified by _atom_sites_footnote.id in the ATOM_SITES_FOOTNOTE list.
      FloatColumn getFractX()
      The x coordinate of the atom-site position specified as a fraction of _cell.length_a.
      FloatColumn getFractXEsd()
      The standard uncertainty (estimated standard deviation) of _atom_site.fract_x.
      FloatColumn getFractY()
      The y coordinate of the atom-site position specified as a fraction of _cell.length_b.
      FloatColumn getFractYEsd()
      The standard uncertainty (estimated standard deviation) of _atom_site.fract_y.
      FloatColumn getFractZ()
      The z coordinate of the atom-site position specified as a fraction of _cell.length_c.
      FloatColumn getFractZEsd()
      The standard uncertainty (estimated standard deviation) of _atom_site.fract_z.
      StrColumn getGroupPDB()
      The group of atoms to which the atom site belongs.
      IntColumn getId()
      The value of _atom_site.id must uniquely identify a record in the ATOM_SITE list.
      IntColumn getIhmModelId()
      The model id corresponding to the atom site.
      StrColumn getLabelAltId()
      A component of the identifier for this atom site.
      StrColumn getLabelAsymId()
      A component of the identifier for this atom site.
      StrColumn getLabelAtomId()
      A component of the identifier for this atom site.
      StrColumn getLabelCompId()
      A component of the identifier for this atom site.
      StrColumn getLabelEntityId()
      This data item is a pointer to _entity.id in the ENTITY category.
      IntColumn getLabelSeqId()
      This data item is a pointer to _entity_poly_seq.num in the ENTITY_POLY_SEQ category.
      FloatColumn getOccupancy()
      The fraction of the atom type present at this site.
      FloatColumn getOccupancyEsd()
      The standard uncertainty (estimated standard deviation) of _atom_site.occupancy.
      StrColumn getPdbxAtomGroup()
      The ATOM group code used by the NDB.
      StrColumn getPdbxAuthAltId()
      Author's alternate location identifier.
      StrColumn getPdbxAuthAsymId()
      Author's strand id.
      StrColumn getPdbxAuthAtomName()
      Author's atom name.
      StrColumn getPdbxAuthCompId()
      Author's residue name.
      StrColumn getPdbxAuthSeqId()
      Author's sequence identifier.
      IntColumn getPdbxFormalCharge()
      The net integer charge assigned to this atom.
      StrColumn getPdbxGroupNDB()
      The ATOM group code used by the NDB.
      StrColumn getPdbxLabelSeqNum()
      Sequential residue number used by NDB.
      StrColumn getPdbxNcsDomId()
      The NCS domain to which the atom position is assigned.
      StrColumn getPdbxNotInAsym()
      Will identify with a 'Y' that this strand got generated.
      StrColumn getPdbxPDBAtomName()
      PDB atom name.
      StrColumn getPdbxPDBInsCode()
      PDB insertion code.
      IntColumn getPdbxPDBModelNum()
      PDB model number.
      StrColumn getPdbxPDBResidueName()
      PDB residue name.
      StrColumn getPdbxPDBResidueNo()
      PDB residue number.
      StrColumn getPdbxPDBStrandId()
      PDB strand id.
      StrColumn getPdbxStructGroupId()
      The value of _atom_site.pdbx_struct_group_id identifies the group or groups assigned to this atom.
      StrColumn getPdbxTlsGroupId()
      The TLS group to which the atom position is assigned.
      StrColumn getRefinementFlags()
      A concatenated series of single-letter codes which indicate the refinement restraints or constraints applied to this site.
      StrColumn getRefinementFlagsAdp()
      A code which indicates the refinement restraints or constraints applied to the atomic displacement parameters of this site.
      StrColumn getRefinementFlagsOccupancy()
      A code which indicates that refinement restraints or constraints were applied to the occupancy of this site.
      StrColumn getRefinementFlagsPosn()
      A code which indicates the refinement restraints or constraints applied to the positional coordinates of this site.
      StrColumn getRestraints()
      A description of restraints applied to specific parameters at this site during refinement.
      IntColumn getSymmetryMultiplicity()
      The multiplicity of a site due to the space-group symmetry as is given in International Tables for Crystallography Vol.
      StrColumn getThermalDisplaceType()
      A standard code used to describe the type of atomic displacement parameters used for the site.
      StrColumn getTypeSymbol()
      This data item is a pointer to _atom_type.symbol in the ATOM_TYPE category.
      FloatColumn getUEquivGeomMean()
      Equivalent isotropic atomic displacement parameter, U~eq~, in angstroms squared, calculated as the geometric mean of the anisotropic atomic displacement parameters.
      FloatColumn getUEquivGeomMeanEsd()
      The standard uncertainty (estimated standard deviation) of _atom_site.U_equiv_geom_mean.
      FloatColumn getUIsoOrEquiv()
      Isotropic atomic displacement parameter, or equivalent isotropic atomic displacement parameter, U~eq~, calculated from anisotropic atomic displacement parameters.
      FloatColumn getUIsoOrEquivEsd()
      The standard uncertainty (estimated standard deviation) of _atom_site.U_iso_or_equiv.
      StrColumn getWyckoffSymbol()
      The Wyckoff symbol (letter) as listed in the space-group tables of International Tables for Crystallography, Vol.
    • Constructor Detail

      • AtomSite

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

        public AtomSite​(String name)
    • Method Detail

      • getAnisoB11

        public FloatColumn getAnisoB11()
        The elements of the anisotropic atomic displacement matrix B, which appears in the structure-factor term as: T = exp{-1/4 sum~i~[sum~j~(B^ij^ h~i~ h~j~ a*~i~ a*~j~)]} h = the Miller indices a* = the reciprocal space cell lengths These matrix elements may appear with atomic coordinates in the ATOM_SITE category, or they may appear in the separate ATOM_SITE_ANISOTROP category, but they may not appear in both places. Similarly, anisotropic displacements may appear as either B's or U's, but not as both. The unique elements of the real symmetric matrix are entered by row. The IUCr Commission on Nomenclature recommends against the use of B for reporting atomic displacement parameters. U, being directly proportional to B, is preferred.
        Returns:
        FloatColumn
      • getAnisoB11Esd

        public FloatColumn getAnisoB11Esd()
        The standard uncertainty (estimated standard deviation) of _atom_site.aniso_B.
        Returns:
        FloatColumn
      • getAnisoB12

        public FloatColumn getAnisoB12()
        The elements of the anisotropic atomic displacement matrix B, which appears in the structure-factor term as: T = exp{-1/4 sum~i~[sum~j~(B^ij^ h~i~ h~j~ a*~i~ a*~j~)]} h = the Miller indices a* = the reciprocal space cell lengths These matrix elements may appear with atomic coordinates in the ATOM_SITE category, or they may appear in the separate ATOM_SITE_ANISOTROP category, but they may not appear in both places. Similarly, anisotropic displacements may appear as either B's or U's, but not as both. The unique elements of the real symmetric matrix are entered by row. The IUCr Commission on Nomenclature recommends against the use of B for reporting atomic displacement parameters. U, being directly proportional to B, is preferred.
        Returns:
        FloatColumn
      • getAnisoB12Esd

        public FloatColumn getAnisoB12Esd()
        The standard uncertainty (estimated standard deviation) of _atom_site.aniso_B.
        Returns:
        FloatColumn
      • getAnisoB13

        public FloatColumn getAnisoB13()
        The elements of the anisotropic atomic displacement matrix B, which appears in the structure-factor term as: T = exp{-1/4 sum~i~[sum~j~(B^ij^ h~i~ h~j~ a*~i~ a*~j~)]} h = the Miller indices a* = the reciprocal space cell lengths These matrix elements may appear with atomic coordinates in the ATOM_SITE category, or they may appear in the separate ATOM_SITE_ANISOTROP category, but they may not appear in both places. Similarly, anisotropic displacements may appear as either B's or U's, but not as both. The unique elements of the real symmetric matrix are entered by row. The IUCr Commission on Nomenclature recommends against the use of B for reporting atomic displacement parameters. U, being directly proportional to B, is preferred.
        Returns:
        FloatColumn
      • getAnisoB13Esd

        public FloatColumn getAnisoB13Esd()
        The standard uncertainty (estimated standard deviation) of _atom_site.aniso_B.
        Returns:
        FloatColumn
      • getAnisoB22

        public FloatColumn getAnisoB22()
        The elements of the anisotropic atomic displacement matrix B, which appears in the structure-factor term as: T = exp{-1/4 sum~i~[sum~j~(B^ij^ h~i~ h~j~ a*~i~ a*~j~)]} h = the Miller indices a* = the reciprocal space cell lengths These matrix elements may appear with atomic coordinates in the ATOM_SITE category, or they may appear in the separate ATOM_SITE_ANISOTROP category, but they may not appear in both places. Similarly, anisotropic displacements may appear as either B's or U's, but not as both. The unique elements of the real symmetric matrix are entered by row. The IUCr Commission on Nomenclature recommends against the use of B for reporting atomic displacement parameters. U, being directly proportional to B, is preferred.
        Returns:
        FloatColumn
      • getAnisoB22Esd

        public FloatColumn getAnisoB22Esd()
        The standard uncertainty (estimated standard deviation) of _atom_site.aniso_B.
        Returns:
        FloatColumn
      • getAnisoB23

        public FloatColumn getAnisoB23()
        The elements of the anisotropic atomic displacement matrix B, which appears in the structure-factor term as: T = exp{-1/4 sum~i~[sum~j~(B^ij^ h~i~ h~j~ a*~i~ a*~j~)]} h = the Miller indices a* = the reciprocal space cell lengths These matrix elements may appear with atomic coordinates in the ATOM_SITE category, or they may appear in the separate ATOM_SITE_ANISOTROP category, but they may not appear in both places. Similarly, anisotropic displacements may appear as either B's or U's, but not as both. The unique elements of the real symmetric matrix are entered by row. The IUCr Commission on Nomenclature recommends against the use of B for reporting atomic displacement parameters. U, being directly proportional to B, is preferred.
        Returns:
        FloatColumn
      • getAnisoB23Esd

        public FloatColumn getAnisoB23Esd()
        The standard uncertainty (estimated standard deviation) of _atom_site.aniso_B.
        Returns:
        FloatColumn
      • getAnisoB33

        public FloatColumn getAnisoB33()
        The elements of the anisotropic atomic displacement matrix B, which appears in the structure-factor term as: T = exp{-1/4 sum~i~[sum~j~(B^ij^ h~i~ h~j~ a*~i~ a*~j~)]} h = the Miller indices a* = the reciprocal space cell lengths These matrix elements may appear with atomic coordinates in the ATOM_SITE category, or they may appear in the separate ATOM_SITE_ANISOTROP category, but they may not appear in both places. Similarly, anisotropic displacements may appear as either B's or U's, but not as both. The unique elements of the real symmetric matrix are entered by row. The IUCr Commission on Nomenclature recommends against the use of B for reporting atomic displacement parameters. U, being directly proportional to B, is preferred.
        Returns:
        FloatColumn
      • getAnisoB33Esd

        public FloatColumn getAnisoB33Esd()
        The standard uncertainty (estimated standard deviation) of _atom_site.aniso_B.
        Returns:
        FloatColumn
      • getAnisoRatio

        public FloatColumn getAnisoRatio()
        Ratio of the maximum to minimum principal axes of displacement (thermal) ellipsoids.
        Returns:
        FloatColumn
      • getAnisoU11

        public FloatColumn getAnisoU11()
        The elements of the standard anisotropic atomic displacement matrix U, which appears in the structure-factor term as: T = exp{-2 pi^2^ sum~i~[sum~j~(U^ij^ h~i~ h~j~ a*~i~ a*~j~)]} h = the Miller indices a* = the reciprocal space cell lengths These matrix elements may appear with atomic coordinates in the ATOM_SITE category, or they may appear in the separate ATOM_SITE_ANISOTROP category, but they may not appear in both places. Similarly, anisotropic displacements may appear as either B's or U's, but not as both. The unique elements of the real symmetric matrix are entered by row.
        Returns:
        FloatColumn
      • getAnisoU11Esd

        public FloatColumn getAnisoU11Esd()
        The standard uncertainty (estimated standard deviation) of _atom_site.aniso_U.
        Returns:
        FloatColumn
      • getAnisoU12

        public FloatColumn getAnisoU12()
        The elements of the standard anisotropic atomic displacement matrix U, which appears in the structure-factor term as: T = exp{-2 pi^2^ sum~i~[sum~j~(U^ij^ h~i~ h~j~ a*~i~ a*~j~)]} h = the Miller indices a* = the reciprocal space cell lengths These matrix elements may appear with atomic coordinates in the ATOM_SITE category, or they may appear in the separate ATOM_SITE_ANISOTROP category, but they may not appear in both places. Similarly, anisotropic displacements may appear as either B's or U's, but not as both. The unique elements of the real symmetric matrix are entered by row.
        Returns:
        FloatColumn
      • getAnisoU12Esd

        public FloatColumn getAnisoU12Esd()
        The standard uncertainty (estimated standard deviation) of _atom_site.aniso_U.
        Returns:
        FloatColumn
      • getAnisoU13

        public FloatColumn getAnisoU13()
        The elements of the standard anisotropic atomic displacement matrix U, which appears in the structure-factor term as: T = exp{-2 pi^2^ sum~i~[sum~j~(U^ij^ h~i~ h~j~ a*~i~ a*~j~)]} h = the Miller indices a* = the reciprocal space cell lengths These matrix elements may appear with atomic coordinates in the ATOM_SITE category, or they may appear in the separate ATOM_SITE_ANISOTROP category, but they may not appear in both places. Similarly, anisotropic displacements may appear as either B's or U's, but not as both. The unique elements of the real symmetric matrix are entered by row.
        Returns:
        FloatColumn
      • getAnisoU13Esd

        public FloatColumn getAnisoU13Esd()
        The standard uncertainty (estimated standard deviation) of _atom_site.aniso_U.
        Returns:
        FloatColumn
      • getAnisoU22

        public FloatColumn getAnisoU22()
        The elements of the standard anisotropic atomic displacement matrix U, which appears in the structure-factor term as: T = exp{-2 pi^2^ sum~i~[sum~j~(U^ij^ h~i~ h~j~ a*~i~ a*~j~)]} h = the Miller indices a* = the reciprocal space cell lengths These matrix elements may appear with atomic coordinates in the ATOM_SITE category, or they may appear in the separate ATOM_SITE_ANISOTROP category, but they may not appear in both places. Similarly, anisotropic displacements may appear as either B's or U's, but not as both. The unique elements of the real symmetric matrix are entered by row.
        Returns:
        FloatColumn
      • getAnisoU22Esd

        public FloatColumn getAnisoU22Esd()
        The standard uncertainty (estimated standard deviation) of _atom_site.aniso_U.
        Returns:
        FloatColumn
      • getAnisoU23

        public FloatColumn getAnisoU23()
        The elements of the standard anisotropic atomic displacement matrix U, which appears in the structure-factor term as: T = exp{-2 pi^2^ sum~i~[sum~j~(U^ij^ h~i~ h~j~ a*~i~ a*~j~)]} h = the Miller indices a* = the reciprocal space cell lengths These matrix elements may appear with atomic coordinates in the ATOM_SITE category, or they may appear in the separate ATOM_SITE_ANISOTROP category, but they may not appear in both places. Similarly, anisotropic displacements may appear as either B's or U's, but not as both. The unique elements of the real symmetric matrix are entered by row.
        Returns:
        FloatColumn
      • getAnisoU23Esd

        public FloatColumn getAnisoU23Esd()
        The standard uncertainty (estimated standard deviation) of _atom_site.aniso_U.
        Returns:
        FloatColumn
      • getAnisoU33

        public FloatColumn getAnisoU33()
        The elements of the standard anisotropic atomic displacement matrix U, which appears in the structure-factor term as: T = exp{-2 pi^2^ sum~i~[sum~j~(U^ij^ h~i~ h~j~ a*~i~ a*~j~)]} h = the Miller indices a* = the reciprocal space cell lengths These matrix elements may appear with atomic coordinates in the ATOM_SITE category, or they may appear in the separate ATOM_SITE_ANISOTROP category, but they may not appear in both places. Similarly, anisotropic displacements may appear as either B's or U's, but not as both. The unique elements of the real symmetric matrix are entered by row.
        Returns:
        FloatColumn
      • getAnisoU33Esd

        public FloatColumn getAnisoU33Esd()
        The standard uncertainty (estimated standard deviation) of _atom_site.aniso_U.
        Returns:
        FloatColumn
      • getAttachedHydrogens

        public IntColumn getAttachedHydrogens()
        The number of hydrogen atoms attached to the atom at this site excluding any hydrogen atoms for which coordinates (measured or calculated) are given.
        Returns:
        IntColumn
      • getAuthAsymId

        public StrColumn getAuthAsymId()
        An alternative identifier for _atom_site.label_asym_id that may be provided by an author in order to match the identification used in the publication that describes the structure.
        Returns:
        StrColumn
      • getAuthAtomId

        public StrColumn getAuthAtomId()
        An alternative identifier for _atom_site.label_atom_id that may be provided by an author in order to match the identification used in the publication that describes the structure.
        Returns:
        StrColumn
      • getAuthCompId

        public StrColumn getAuthCompId()
        An alternative identifier for _atom_site.label_comp_id that may be provided by an author in order to match the identification used in the publication that describes the structure.
        Returns:
        StrColumn
      • getAuthSeqId

        public IntColumn getAuthSeqId()
        An alternative identifier for _atom_site.label_seq_id that may be provided by an author in order to match the identification used in the publication that describes the structure. Note that this is not necessarily a number, that the values do not have to be positive, and that the value does not have to correspond to the value of _atom_site.label_seq_id. The value of _atom_site.label_seq_id is required to be a sequential list of positive integers. The author may assign values to _atom_site.auth_seq_id in any desired way. For instance, the values may be used to relate this structure to a numbering scheme in a homologous structure, including sequence gaps or insertion codes. Alternatively, a scheme may be used for a truncated polymer that maintains the numbering scheme of the full length polymer. In all cases, the scheme used here must match the scheme used in the publication that describes the structure.
        Returns:
        IntColumn
      • getBEquivGeomMean

        public FloatColumn getBEquivGeomMean()
        Equivalent isotropic atomic displacement parameter, B~eq~, in angstroms squared, calculated as the geometric mean of the anisotropic atomic displacement parameters. B~eq~ = (B~i~ B~j~ B~k~)^1/3^ B~n~ = the principal components of the orthogonalized B^ij^ The IUCr Commission on Nomenclature recommends against the use of B for reporting atomic displacement parameters. U, being directly proportional to B, is preferred.
        Returns:
        FloatColumn
      • getBEquivGeomMeanEsd

        public FloatColumn getBEquivGeomMeanEsd()
        The standard uncertainty (estimated standard deviation) of _atom_site.B_equiv_geom_mean.
        Returns:
        FloatColumn
      • getBIsoOrEquiv

        public FloatColumn getBIsoOrEquiv()
        Isotropic atomic displacement parameter, or equivalent isotropic atomic displacement parameter, B~eq~, calculated from the anisotropic displacement parameters. B~eq~ = (1/3) sum~i~[sum~j~(B^ij^ A~i~ A~j~ a*~i~ a*~j~)] A = the real space cell lengths a* = the reciprocal space cell lengths B^ij^ = 8 pi^2^ U^ij^ Ref: Fischer, R. X. & Tillmanns, E. (1988). Acta Cryst. C44, 775-776. The IUCr Commission on Nomenclature recommends against the use of B for reporting atomic displacement parameters. U, being directly proportional to B, is preferred. Note - The particular type of ADP stored in this item is qualified by item _refine.pdbx_adp_type.
        Returns:
        FloatColumn
      • getBIsoOrEquivEsd

        public FloatColumn getBIsoOrEquivEsd()
        The standard uncertainty (estimated standard deviation) of _atom_site.B_iso_or_equiv.
        Returns:
        FloatColumn
      • getCalcAttachedAtom

        public StrColumn getCalcAttachedAtom()
        The _atom_site.id of the atom site to which the 'geometry-calculated' atom site is attached.
        Returns:
        StrColumn
      • getCalcFlag

        public StrColumn getCalcFlag()
        A standard code to signal whether the site coordinates have been determined from the intensities or calculated from the geometry of surrounding sites, or have been assigned dummy values. The abbreviation 'c' may be used in place of 'calc'.
        Returns:
        StrColumn
      • getCartnX

        public FloatColumn getCartnX()
        The x atom-site coordinate in angstroms specified according to a set of orthogonal Cartesian axes related to the cell axes as specified by the description given in _atom_sites.Cartn_transform_axes.
        Returns:
        FloatColumn
      • getCartnXEsd

        public FloatColumn getCartnXEsd()
        The standard uncertainty (estimated standard deviation) of _atom_site.Cartn_x.
        Returns:
        FloatColumn
      • getCartnY

        public FloatColumn getCartnY()
        The y atom-site coordinate in angstroms specified according to a set of orthogonal Cartesian axes related to the cell axes as specified by the description given in _atom_sites.Cartn_transform_axes.
        Returns:
        FloatColumn
      • getCartnYEsd

        public FloatColumn getCartnYEsd()
        The standard uncertainty (estimated standard deviation) of _atom_site.Cartn_y.
        Returns:
        FloatColumn
      • getCartnZ

        public FloatColumn getCartnZ()
        The z atom-site coordinate in angstroms specified according to a set of orthogonal Cartesian axes related to the cell axes as specified by the description given in _atom_sites.Cartn_transform_axes.
        Returns:
        FloatColumn
      • getCartnZEsd

        public FloatColumn getCartnZEsd()
        The standard uncertainty (estimated standard deviation) of _atom_site.Cartn_z.
        Returns:
        FloatColumn
      • getChemicalConnNumber

        public IntColumn getChemicalConnNumber()
        This data item is a pointer to _chemical_conn_atom.number in the CHEMICAL_CONN_ATOM category.
        Returns:
        IntColumn
      • getConstraints

        public StrColumn getConstraints()
        A description of the constraints applied to parameters at this site during refinement. See also _atom_site.refinement_flags and _refine.ls_number_constraints.
        Returns:
        StrColumn
      • getDetails

        public StrColumn getDetails()
        A description of special aspects of this site. See also _atom_site.refinement_flags.
        Returns:
        StrColumn
      • getDisorderAssembly

        public StrColumn getDisorderAssembly()
        A code which identifies a cluster of atoms that show long-range positional disorder but are locally ordered. Within each such cluster of atoms, _atom_site.disorder_group is used to identify the sites that are simultaneously occupied. This field is only needed if there is more than one cluster of disordered atoms showing independent local order. *** This data item would not in general be used in a macromolecular data block. ***
        Returns:
        StrColumn
      • getDisorderGroup

        public StrColumn getDisorderGroup()
        A code which identifies a group of positionally disordered atom sites that are locally simultaneously occupied. Atoms that are positionally disordered over two or more sites (e.g. the hydrogen atoms of a methyl group that exists in two orientations) can be assigned to two or more groups. Sites belonging to the same group are simultaneously occupied, but those belonging to different groups are not. A minus prefix (e.g. '-1') is used to indicate sites disordered about a special position. *** This data item would not in general be used in a macromolecular data block. ***
        Returns:
        StrColumn
      • getFootnoteId

        public StrColumn getFootnoteId()
        The value of _atom_site.footnote_id must match an ID specified by _atom_sites_footnote.id in the ATOM_SITES_FOOTNOTE list.
        Returns:
        StrColumn
      • getFractX

        public FloatColumn getFractX()
        The x coordinate of the atom-site position specified as a fraction of _cell.length_a.
        Returns:
        FloatColumn
      • getFractXEsd

        public FloatColumn getFractXEsd()
        The standard uncertainty (estimated standard deviation) of _atom_site.fract_x.
        Returns:
        FloatColumn
      • getFractY

        public FloatColumn getFractY()
        The y coordinate of the atom-site position specified as a fraction of _cell.length_b.
        Returns:
        FloatColumn
      • getFractYEsd

        public FloatColumn getFractYEsd()
        The standard uncertainty (estimated standard deviation) of _atom_site.fract_y.
        Returns:
        FloatColumn
      • getFractZ

        public FloatColumn getFractZ()
        The z coordinate of the atom-site position specified as a fraction of _cell.length_c.
        Returns:
        FloatColumn
      • getFractZEsd

        public FloatColumn getFractZEsd()
        The standard uncertainty (estimated standard deviation) of _atom_site.fract_z.
        Returns:
        FloatColumn
      • getGroupPDB

        public StrColumn getGroupPDB()
        The group of atoms to which the atom site belongs. This data item is provided for compatibility with the original Protein Data Bank format, and only for that purpose.
        Returns:
        StrColumn
      • getId

        public IntColumn getId()
        The value of _atom_site.id must uniquely identify a record in the ATOM_SITE list. Note that this item need not be a number; it can be any unique identifier. This data item was introduced to provide compatibility between small-molecule and macromolecular CIFs. In a small-molecule CIF, _atom_site_label is the identifier for the atom. In a macromolecular CIF, the atom identifier is the aggregate of _atom_site.label_alt_id, _atom_site.label_asym_id, _atom_site.label_atom_id, _atom_site.label_comp_id and _atom_site.label_seq_id. For the two types of files to be compatible, a formal identifier for the category had to be introduced that was independent of the different modes of identifying the atoms. For compatibility with older CIFs, _atom_site_label is aliased to _atom_site.id.
        Returns:
        IntColumn
      • getLabelAltId

        public StrColumn getLabelAltId()
        A component of the identifier for this atom site. For further details, see the definition of the ATOM_SITE_ALT category. This data item is a pointer to _atom_sites_alt.id in the ATOM_SITES_ALT category.
        Returns:
        StrColumn
      • getLabelAsymId

        public StrColumn getLabelAsymId()
        A component of the identifier for this atom site. For further details, see the definition of the STRUCT_ASYM category. This data item is a pointer to _struct_asym.id in the STRUCT_ASYM category.
        Returns:
        StrColumn
      • getLabelAtomId

        public StrColumn getLabelAtomId()
        A component of the identifier for this atom site. This data item is a pointer to _chem_comp_atom.atom_id in the CHEM_COMP_ATOM category.
        Returns:
        StrColumn
      • getLabelCompId

        public StrColumn getLabelCompId()
        A component of the identifier for this atom site. This data item is a pointer to _chem_comp.id in the CHEM_COMP category.
        Returns:
        StrColumn
      • getLabelEntityId

        public StrColumn getLabelEntityId()
        This data item is a pointer to _entity.id in the ENTITY category.
        Returns:
        StrColumn
      • getLabelSeqId

        public IntColumn getLabelSeqId()
        This data item is a pointer to _entity_poly_seq.num in the ENTITY_POLY_SEQ category.
        Returns:
        IntColumn
      • getOccupancy

        public FloatColumn getOccupancy()
        The fraction of the atom type present at this site. The sum of the occupancies of all the atom types at this site may not significantly exceed 1.0 unless it is a dummy site.
        Returns:
        FloatColumn
      • getOccupancyEsd

        public FloatColumn getOccupancyEsd()
        The standard uncertainty (estimated standard deviation) of _atom_site.occupancy.
        Returns:
        FloatColumn
      • getRestraints

        public StrColumn getRestraints()
        A description of restraints applied to specific parameters at this site during refinement. See also _atom_site.refinement_flags and _refine.ls_number_restraints.
        Returns:
        StrColumn
      • getSymmetryMultiplicity

        public IntColumn getSymmetryMultiplicity()
        The multiplicity of a site due to the space-group symmetry as is given in International Tables for Crystallography Vol. A (2002).
        Returns:
        IntColumn
      • getThermalDisplaceType

        public StrColumn getThermalDisplaceType()
        A standard code used to describe the type of atomic displacement parameters used for the site.
        Returns:
        StrColumn
      • getTypeSymbol

        public StrColumn getTypeSymbol()
        This data item is a pointer to _atom_type.symbol in the ATOM_TYPE category.
        Returns:
        StrColumn
      • getUEquivGeomMean

        public FloatColumn getUEquivGeomMean()
        Equivalent isotropic atomic displacement parameter, U~eq~, in angstroms squared, calculated as the geometric mean of the anisotropic atomic displacement parameters. U~eq~ = (U~i~ U~j~ U~k~)^1/3^ U~n~ = the principal components of the orthogonalized U^ij^
        Returns:
        FloatColumn
      • getUEquivGeomMeanEsd

        public FloatColumn getUEquivGeomMeanEsd()
        The standard uncertainty (estimated standard deviation) of _atom_site.U_equiv_geom_mean.
        Returns:
        FloatColumn
      • getUIsoOrEquiv

        public FloatColumn getUIsoOrEquiv()
        Isotropic atomic displacement parameter, or equivalent isotropic atomic displacement parameter, U~eq~, calculated from anisotropic atomic displacement parameters. U~eq~ = (1/3) sum~i~[sum~j~(U^ij^ A~i~ A~j~ a*~i~ a*~j~)] A = the real space cell lengths a* = the reciprocal space cell lengths Ref: Fischer, R. X. & Tillmanns, E. (1988). Acta Cryst. C44, 775-776.
        Returns:
        FloatColumn
      • getUIsoOrEquivEsd

        public FloatColumn getUIsoOrEquivEsd()
        The standard uncertainty (estimated standard deviation) of _atom_site.U_iso_or_equiv.
        Returns:
        FloatColumn
      • getWyckoffSymbol

        public StrColumn getWyckoffSymbol()
        The Wyckoff symbol (letter) as listed in the space-group tables of International Tables for Crystallography, Vol. A (2002).
        Returns:
        StrColumn
      • getAdpType

        public StrColumn getAdpType()
        A standard code used to describe the type of atomic displacement parameters used for the site.
        Returns:
        StrColumn
      • getRefinementFlags

        public StrColumn getRefinementFlags()
        A concatenated series of single-letter codes which indicate the refinement restraints or constraints applied to this site. This item should not be used. It has been replaced by _atom_site.refinement_flags_posn, *_adp and *_occupancy. It is retained in this dictionary only to provide compatibility with old CIFs.
        Returns:
        StrColumn
      • getRefinementFlagsAdp

        public StrColumn getRefinementFlagsAdp()
        A code which indicates the refinement restraints or constraints applied to the atomic displacement parameters of this site.
        Returns:
        StrColumn
      • getRefinementFlagsOccupancy

        public StrColumn getRefinementFlagsOccupancy()
        A code which indicates that refinement restraints or constraints were applied to the occupancy of this site.
        Returns:
        StrColumn
      • getRefinementFlagsPosn

        public StrColumn getRefinementFlagsPosn()
        A code which indicates the refinement restraints or constraints applied to the positional coordinates of this site.
        Returns:
        StrColumn
      • getPdbxAuthAltId

        public StrColumn getPdbxAuthAltId()
        Author's alternate location identifier.
        Returns:
        StrColumn
      • getPdbxPDBInsCode

        public StrColumn getPdbxPDBInsCode()
        PDB insertion code.
        Returns:
        StrColumn
      • getPdbxPDBModelNum

        public IntColumn getPdbxPDBModelNum()
        PDB model number.
        Returns:
        IntColumn
      • getPdbxPDBResidueNo

        public StrColumn getPdbxPDBResidueNo()
        PDB residue number.
        Returns:
        StrColumn
      • getPdbxPDBResidueName

        public StrColumn getPdbxPDBResidueName()
        PDB residue name.
        Returns:
        StrColumn
      • getPdbxPDBStrandId

        public StrColumn getPdbxPDBStrandId()
        PDB strand id.
        Returns:
        StrColumn
      • getPdbxPDBAtomName

        public StrColumn getPdbxPDBAtomName()
        PDB atom name.
        Returns:
        StrColumn
      • getPdbxAuthAtomName

        public StrColumn getPdbxAuthAtomName()
        Author's atom name.
        Returns:
        StrColumn
      • getPdbxFormalCharge

        public IntColumn getPdbxFormalCharge()
        The net integer charge assigned to this atom. This is the formal charge assignment normally found in chemical diagrams.
        Returns:
        IntColumn
      • getPdbxAuthCompId

        public StrColumn getPdbxAuthCompId()
        Author's residue name.
        Returns:
        StrColumn
      • getPdbxAuthAsymId

        public StrColumn getPdbxAuthAsymId()
        Author's strand id.
        Returns:
        StrColumn
      • getPdbxAuthSeqId

        public StrColumn getPdbxAuthSeqId()
        Author's sequence identifier.
        Returns:
        StrColumn
      • getPdbxTlsGroupId

        public StrColumn getPdbxTlsGroupId()
        The TLS group to which the atom position is assigned. The TLS group is defined in category pdbx_refine_tls. This item is a reference to _pdbx_refine_tls.id.
        Returns:
        StrColumn
      • getPdbxNcsDomId

        public StrColumn getPdbxNcsDomId()
        The NCS domain to which the atom position is assigned. The NCS group is defined in category struct_ncs_dom. This item is a reference to _struct_ncs_dom.id.
        Returns:
        StrColumn
      • getPdbxStructGroupId

        public StrColumn getPdbxStructGroupId()
        The value of _atom_site.pdbx_struct_group_id identifies the group or groups assigned to this atom. This is a reference to the identifier for group definition in category PDBX_STRUCT_GROUP_LIST. Multiple groups identifiers are encoded as a comma separated list.
        Returns:
        StrColumn
      • getPdbxGroupNDB

        public StrColumn getPdbxGroupNDB()
        The ATOM group code used by the NDB.
        Returns:
        StrColumn
      • getPdbxAtomGroup

        public StrColumn getPdbxAtomGroup()
        The ATOM group code used by the NDB.
        Returns:
        StrColumn
      • getPdbxLabelSeqNum

        public StrColumn getPdbxLabelSeqNum()
        Sequential residue number used by NDB.
        Returns:
        StrColumn
      • getPdbxNotInAsym

        public StrColumn getPdbxNotInAsym()
        Will identify with a 'Y' that this strand got generated.
        Returns:
        StrColumn
      • getIhmModelId

        public IntColumn getIhmModelId()
        The model id corresponding to the atom site. This data item is a pointer to _ihm_model_list.model_id in the IHM_MODEL_LIST category.
        Returns:
        IntColumn