org.rcsb.cif.schema.mm.AtomSite

All Implemented Interfaces:: Category

@Generated("org.rcsb.cif.schema.generator.SchemaGenerator")
public class AtomSite
extends DelegatingCategory

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.

Nested Class Summary

Nested classes/interfaces inherited from class org.rcsb.cif.schema.DelegatingCategory
DelegatingCategory.DelegatingCifCoreCategory

Nested classes/interfaces inherited from interface org.rcsb.cif.model.Category
Category.EmptyCategory
Field Summary

Fields inherited from class org.rcsb.cif.schema.DelegatingCategory
delegate
Constructor Summary

Constructors

Constructor Description

AtomSite(Category delegate)

Method Summary

Modifier and Type	Method	Description
`protected Column`	`createDelegate(String columnName, Column column)`
`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 place holder to indicate alternate conformation.
`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.

Methods inherited from class org.rcsb.cif.schema.DelegatingCategory

getCategoryName, getColumn, getColumns, getRowCount

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Methods inherited from interface org.rcsb.cif.model.Category

columns, getColumn, isDefined

Constructor Details
- AtomSite
  
  public AtomSite(Category delegate)
Method Details
- createDelegate
  
  protected Column createDelegate(String columnName, Column column)
  
  Overrides:
  
  createDelegate in class DelegatingCategory
- 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 place holder to indicate alternate conformation. The alternate conformation can be an entire polymer chain, or several residues or partial residue (several atoms within one residue). If an atom is provided in more than one position, then a non-blank alternate location indicator must be used for each of the atomic positions.
  
  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 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

Class AtomSite

Nested Class Summary

Nested classes/interfaces inherited from class org.rcsb.cif.schema.DelegatingCategory

Nested classes/interfaces inherited from interface org.rcsb.cif.model.Category

Field Summary

Fields inherited from class org.rcsb.cif.schema.DelegatingCategory

Constructor Summary

Method Summary

Methods inherited from class org.rcsb.cif.schema.DelegatingCategory

Methods inherited from class java.lang.Object

Methods inherited from interface org.rcsb.cif.model.Category

Constructor Details

Method Details