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package org.rcsb.cif.schema.mm;
import org.rcsb.cif.model.*;
import org.rcsb.cif.schema.*;
import javax.annotation.Generated;
/**
* 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.
*
* wwPDB recommends wwPDB-assigned residue number, residue ID,
* and chain ID, _atom_site.auth_seq_id _atom_site.auth_comp_id, and
* _atom_site.auth_asym_id, respectively, to be used for publication
* materials.
*/
@Generated("org.rcsb.cif.schema.generator.SchemaGenerator")
public class AtomSite extends DelegatingCategory {
public AtomSite(Category delegate) {
super(delegate);
}
@Override
protected Column createDelegate(String columnName, Column column) {
switch (columnName) {
case "aniso_B[1][1]":
return getAnisoB11();
case "aniso_B[1][1]_esd":
return getAnisoB11Esd();
case "aniso_B[1][2]":
return getAnisoB12();
case "aniso_B[1][2]_esd":
return getAnisoB12Esd();
case "aniso_B[1][3]":
return getAnisoB13();
case "aniso_B[1][3]_esd":
return getAnisoB13Esd();
case "aniso_B[2][2]":
return getAnisoB22();
case "aniso_B[2][2]_esd":
return getAnisoB22Esd();
case "aniso_B[2][3]":
return getAnisoB23();
case "aniso_B[2][3]_esd":
return getAnisoB23Esd();
case "aniso_B[3][3]":
return getAnisoB33();
case "aniso_B[3][3]_esd":
return getAnisoB33Esd();
case "aniso_ratio":
return getAnisoRatio();
case "aniso_U[1][1]":
return getAnisoU11();
case "aniso_U[1][1]_esd":
return getAnisoU11Esd();
case "aniso_U[1][2]":
return getAnisoU12();
case "aniso_U[1][2]_esd":
return getAnisoU12Esd();
case "aniso_U[1][3]":
return getAnisoU13();
case "aniso_U[1][3]_esd":
return getAnisoU13Esd();
case "aniso_U[2][2]":
return getAnisoU22();
case "aniso_U[2][2]_esd":
return getAnisoU22Esd();
case "aniso_U[2][3]":
return getAnisoU23();
case "aniso_U[2][3]_esd":
return getAnisoU23Esd();
case "aniso_U[3][3]":
return getAnisoU33();
case "aniso_U[3][3]_esd":
return getAnisoU33Esd();
case "attached_hydrogens":
return getAttachedHydrogens();
case "auth_asym_id":
return getAuthAsymId();
case "auth_atom_id":
return getAuthAtomId();
case "auth_comp_id":
return getAuthCompId();
case "auth_seq_id":
return getAuthSeqId();
case "B_equiv_geom_mean":
return getBEquivGeomMean();
case "B_equiv_geom_mean_esd":
return getBEquivGeomMeanEsd();
case "B_iso_or_equiv":
return getBIsoOrEquiv();
case "B_iso_or_equiv_esd":
return getBIsoOrEquivEsd();
case "calc_attached_atom":
return getCalcAttachedAtom();
case "calc_flag":
return getCalcFlag();
case "Cartn_x":
return getCartnX();
case "Cartn_x_esd":
return getCartnXEsd();
case "Cartn_y":
return getCartnY();
case "Cartn_y_esd":
return getCartnYEsd();
case "Cartn_z":
return getCartnZ();
case "Cartn_z_esd":
return getCartnZEsd();
case "chemical_conn_number":
return getChemicalConnNumber();
case "constraints":
return getConstraints();
case "details":
return getDetails();
case "disorder_assembly":
return getDisorderAssembly();
case "disorder_group":
return getDisorderGroup();
case "footnote_id":
return getFootnoteId();
case "fract_x":
return getFractX();
case "fract_x_esd":
return getFractXEsd();
case "fract_y":
return getFractY();
case "fract_y_esd":
return getFractYEsd();
case "fract_z":
return getFractZ();
case "fract_z_esd":
return getFractZEsd();
case "group_PDB":
return getGroupPDB();
case "id":
return getId();
case "label_alt_id":
return getLabelAltId();
case "label_asym_id":
return getLabelAsymId();
case "label_atom_id":
return getLabelAtomId();
case "label_comp_id":
return getLabelCompId();
case "label_entity_id":
return getLabelEntityId();
case "label_seq_id":
return getLabelSeqId();
case "occupancy":
return getOccupancy();
case "occupancy_esd":
return getOccupancyEsd();
case "restraints":
return getRestraints();
case "symmetry_multiplicity":
return getSymmetryMultiplicity();
case "thermal_displace_type":
return getThermalDisplaceType();
case "type_symbol":
return getTypeSymbol();
case "U_equiv_geom_mean":
return getUEquivGeomMean();
case "U_equiv_geom_mean_esd":
return getUEquivGeomMeanEsd();
case "U_iso_or_equiv":
return getUIsoOrEquiv();
case "U_iso_or_equiv_esd":
return getUIsoOrEquivEsd();
case "Wyckoff_symbol":
return getWyckoffSymbol();
case "pdbx_atom_ambiguity":
return getPdbxAtomAmbiguity();
case "adp_type":
return getAdpType();
case "refinement_flags":
return getRefinementFlags();
case "refinement_flags_adp":
return getRefinementFlagsAdp();
case "refinement_flags_occupancy":
return getRefinementFlagsOccupancy();
case "refinement_flags_posn":
return getRefinementFlagsPosn();
case "pdbx_auth_alt_id":
return getPdbxAuthAltId();
case "pdbx_PDB_ins_code":
return getPdbxPDBInsCode();
case "pdbx_PDB_model_num":
return getPdbxPDBModelNum();
case "pdbx_PDB_residue_no":
return getPdbxPDBResidueNo();
case "pdbx_PDB_residue_name":
return getPdbxPDBResidueName();
case "pdbx_PDB_strand_id":
return getPdbxPDBStrandId();
case "pdbx_PDB_atom_name":
return getPdbxPDBAtomName();
case "pdbx_auth_atom_name":
return getPdbxAuthAtomName();
case "pdbx_formal_charge":
return getPdbxFormalCharge();
case "pdbx_auth_comp_id":
return getPdbxAuthCompId();
case "pdbx_auth_asym_id":
return getPdbxAuthAsymId();
case "pdbx_auth_seq_id":
return getPdbxAuthSeqId();
case "pdbx_tls_group_id":
return getPdbxTlsGroupId();
case "pdbx_ncs_dom_id":
return getPdbxNcsDomId();
case "pdbx_struct_group_id":
return getPdbxStructGroupId();
case "pdbx_group_NDB":
return getPdbxGroupNDB();
case "pdbx_atom_group":
return getPdbxAtomGroup();
case "pdbx_label_seq_num":
return getPdbxLabelSeqNum();
case "pdbx_not_in_asym":
return getPdbxNotInAsym();
case "pdbx_label_index":
return getPdbxLabelIndex();
case "pdbx_sifts_xref_db_name":
return getPdbxSiftsXrefDbName();
case "pdbx_sifts_xref_db_acc":
return getPdbxSiftsXrefDbAcc();
case "pdbx_sifts_xref_db_num":
return getPdbxSiftsXrefDbNum();
case "pdbx_sifts_xref_db_res":
return getPdbxSiftsXrefDbRes();
case "ihm_model_id":
return getIhmModelId();
default:
return new DelegatingColumn(column);
}
}
/**
* 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.
* @return FloatColumn
*/
public FloatColumn getAnisoB11() {
return delegate.getColumn("aniso_B[1][1]", DelegatingFloatColumn::new);
}
/**
* The standard uncertainty (estimated standard deviation)
* of _atom_site.aniso_B.
* @return FloatColumn
*/
public FloatColumn getAnisoB11Esd() {
return delegate.getColumn("aniso_B[1][1]_esd", DelegatingFloatColumn::new);
}
/**
* 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.
* @return FloatColumn
*/
public FloatColumn getAnisoB12() {
return delegate.getColumn("aniso_B[1][2]", DelegatingFloatColumn::new);
}
/**
* The standard uncertainty (estimated standard deviation)
* of _atom_site.aniso_B.
* @return FloatColumn
*/
public FloatColumn getAnisoB12Esd() {
return delegate.getColumn("aniso_B[1][2]_esd", DelegatingFloatColumn::new);
}
/**
* 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.
* @return FloatColumn
*/
public FloatColumn getAnisoB13() {
return delegate.getColumn("aniso_B[1][3]", DelegatingFloatColumn::new);
}
/**
* The standard uncertainty (estimated standard deviation)
* of _atom_site.aniso_B.
* @return FloatColumn
*/
public FloatColumn getAnisoB13Esd() {
return delegate.getColumn("aniso_B[1][3]_esd", DelegatingFloatColumn::new);
}
/**
* 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.
* @return FloatColumn
*/
public FloatColumn getAnisoB22() {
return delegate.getColumn("aniso_B[2][2]", DelegatingFloatColumn::new);
}
/**
* The standard uncertainty (estimated standard deviation)
* of _atom_site.aniso_B.
* @return FloatColumn
*/
public FloatColumn getAnisoB22Esd() {
return delegate.getColumn("aniso_B[2][2]_esd", DelegatingFloatColumn::new);
}
/**
* 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.
* @return FloatColumn
*/
public FloatColumn getAnisoB23() {
return delegate.getColumn("aniso_B[2][3]", DelegatingFloatColumn::new);
}
/**
* The standard uncertainty (estimated standard deviation)
* of _atom_site.aniso_B.
* @return FloatColumn
*/
public FloatColumn getAnisoB23Esd() {
return delegate.getColumn("aniso_B[2][3]_esd", DelegatingFloatColumn::new);
}
/**
* 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.
* @return FloatColumn
*/
public FloatColumn getAnisoB33() {
return delegate.getColumn("aniso_B[3][3]", DelegatingFloatColumn::new);
}
/**
* The standard uncertainty (estimated standard deviation)
* of _atom_site.aniso_B.
* @return FloatColumn
*/
public FloatColumn getAnisoB33Esd() {
return delegate.getColumn("aniso_B[3][3]_esd", DelegatingFloatColumn::new);
}
/**
* Ratio of the maximum to minimum principal axes of
* displacement (thermal) ellipsoids.
* @return FloatColumn
*/
public FloatColumn getAnisoRatio() {
return delegate.getColumn("aniso_ratio", DelegatingFloatColumn::new);
}
/**
* 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.
* @return FloatColumn
*/
public FloatColumn getAnisoU11() {
return delegate.getColumn("aniso_U[1][1]", DelegatingFloatColumn::new);
}
/**
* The standard uncertainty (estimated standard deviation)
* of _atom_site.aniso_U.
* @return FloatColumn
*/
public FloatColumn getAnisoU11Esd() {
return delegate.getColumn("aniso_U[1][1]_esd", DelegatingFloatColumn::new);
}
/**
* 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.
* @return FloatColumn
*/
public FloatColumn getAnisoU12() {
return delegate.getColumn("aniso_U[1][2]", DelegatingFloatColumn::new);
}
/**
* The standard uncertainty (estimated standard deviation)
* of _atom_site.aniso_U.
* @return FloatColumn
*/
public FloatColumn getAnisoU12Esd() {
return delegate.getColumn("aniso_U[1][2]_esd", DelegatingFloatColumn::new);
}
/**
* 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.
* @return FloatColumn
*/
public FloatColumn getAnisoU13() {
return delegate.getColumn("aniso_U[1][3]", DelegatingFloatColumn::new);
}
/**
* The standard uncertainty (estimated standard deviation)
* of _atom_site.aniso_U.
* @return FloatColumn
*/
public FloatColumn getAnisoU13Esd() {
return delegate.getColumn("aniso_U[1][3]_esd", DelegatingFloatColumn::new);
}
/**
* 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.
* @return FloatColumn
*/
public FloatColumn getAnisoU22() {
return delegate.getColumn("aniso_U[2][2]", DelegatingFloatColumn::new);
}
/**
* The standard uncertainty (estimated standard deviation)
* of _atom_site.aniso_U.
* @return FloatColumn
*/
public FloatColumn getAnisoU22Esd() {
return delegate.getColumn("aniso_U[2][2]_esd", DelegatingFloatColumn::new);
}
/**
* 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.
* @return FloatColumn
*/
public FloatColumn getAnisoU23() {
return delegate.getColumn("aniso_U[2][3]", DelegatingFloatColumn::new);
}
/**
* The standard uncertainty (estimated standard deviation)
* of _atom_site.aniso_U.
* @return FloatColumn
*/
public FloatColumn getAnisoU23Esd() {
return delegate.getColumn("aniso_U[2][3]_esd", DelegatingFloatColumn::new);
}
/**
* 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.
* @return FloatColumn
*/
public FloatColumn getAnisoU33() {
return delegate.getColumn("aniso_U[3][3]", DelegatingFloatColumn::new);
}
/**
* The standard uncertainty (estimated standard deviation)
* of _atom_site.aniso_U.
* @return FloatColumn
*/
public FloatColumn getAnisoU33Esd() {
return delegate.getColumn("aniso_U[3][3]_esd", DelegatingFloatColumn::new);
}
/**
* The number of hydrogen atoms attached to the atom at this site
* excluding any hydrogen atoms for which coordinates (measured or
* calculated) are given.
* @return IntColumn
*/
public IntColumn getAttachedHydrogens() {
return delegate.getColumn("attached_hydrogens", DelegatingIntColumn::new);
}
/**
* 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.
* @return StrColumn
*/
public StrColumn getAuthAsymId() {
return delegate.getColumn("auth_asym_id", DelegatingStrColumn::new);
}
/**
* 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.
* @return StrColumn
*/
public StrColumn getAuthAtomId() {
return delegate.getColumn("auth_atom_id", DelegatingStrColumn::new);
}
/**
* 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.
* @return StrColumn
*/
public StrColumn getAuthCompId() {
return delegate.getColumn("auth_comp_id", DelegatingStrColumn::new);
}
/**
* 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.
* @return IntColumn
*/
public IntColumn getAuthSeqId() {
return delegate.getColumn("auth_seq_id", DelegatingIntColumn::new);
}
/**
* 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.
* @return FloatColumn
*/
public FloatColumn getBEquivGeomMean() {
return delegate.getColumn("B_equiv_geom_mean", DelegatingFloatColumn::new);
}
/**
* The standard uncertainty (estimated standard deviation)
* of _atom_site.B_equiv_geom_mean.
* @return FloatColumn
*/
public FloatColumn getBEquivGeomMeanEsd() {
return delegate.getColumn("B_equiv_geom_mean_esd", DelegatingFloatColumn::new);
}
/**
* 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.
* @return FloatColumn
*/
public FloatColumn getBIsoOrEquiv() {
return delegate.getColumn("B_iso_or_equiv", DelegatingFloatColumn::new);
}
/**
* The standard uncertainty (estimated standard deviation)
* of _atom_site.B_iso_or_equiv.
* @return FloatColumn
*/
public FloatColumn getBIsoOrEquivEsd() {
return delegate.getColumn("B_iso_or_equiv_esd", DelegatingFloatColumn::new);
}
/**
* The _atom_site.id of the atom site to which the
* 'geometry-calculated' atom site is attached.
* @return StrColumn
*/
public StrColumn getCalcAttachedAtom() {
return delegate.getColumn("calc_attached_atom", DelegatingStrColumn::new);
}
/**
* 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'.
* @return StrColumn
*/
public StrColumn getCalcFlag() {
return delegate.getColumn("calc_flag", DelegatingStrColumn::new);
}
/**
* 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.
* @return FloatColumn
*/
public FloatColumn getCartnX() {
return delegate.getColumn("Cartn_x", DelegatingFloatColumn::new);
}
/**
* The standard uncertainty (estimated standard deviation)
* of _atom_site.Cartn_x.
* @return FloatColumn
*/
public FloatColumn getCartnXEsd() {
return delegate.getColumn("Cartn_x_esd", DelegatingFloatColumn::new);
}
/**
* 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.
* @return FloatColumn
*/
public FloatColumn getCartnY() {
return delegate.getColumn("Cartn_y", DelegatingFloatColumn::new);
}
/**
* The standard uncertainty (estimated standard deviation)
* of _atom_site.Cartn_y.
* @return FloatColumn
*/
public FloatColumn getCartnYEsd() {
return delegate.getColumn("Cartn_y_esd", DelegatingFloatColumn::new);
}
/**
* 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.
* @return FloatColumn
*/
public FloatColumn getCartnZ() {
return delegate.getColumn("Cartn_z", DelegatingFloatColumn::new);
}
/**
* The standard uncertainty (estimated standard deviation)
* of _atom_site.Cartn_z.
* @return FloatColumn
*/
public FloatColumn getCartnZEsd() {
return delegate.getColumn("Cartn_z_esd", DelegatingFloatColumn::new);
}
/**
* This data item is a pointer to _chemical_conn_atom.number in the
* CHEMICAL_CONN_ATOM category.
* @return IntColumn
*/
public IntColumn getChemicalConnNumber() {
return delegate.getColumn("chemical_conn_number", DelegatingIntColumn::new);
}
/**
* A description of the constraints applied to parameters at this
* site during refinement. See also _atom_site.refinement_flags
* and _refine.ls_number_constraints.
* @return StrColumn
*/
public StrColumn getConstraints() {
return delegate.getColumn("constraints", DelegatingStrColumn::new);
}
/**
* A description of special aspects of this site. See also
* _atom_site.refinement_flags.
* @return StrColumn
*/
public StrColumn getDetails() {
return delegate.getColumn("details", DelegatingStrColumn::new);
}
/**
* 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. ***
* @return StrColumn
*/
public StrColumn getDisorderAssembly() {
return delegate.getColumn("disorder_assembly", DelegatingStrColumn::new);
}
/**
* 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. ***
* @return StrColumn
*/
public StrColumn getDisorderGroup() {
return delegate.getColumn("disorder_group", DelegatingStrColumn::new);
}
/**
* The value of _atom_site.footnote_id must match an ID
* specified by _atom_sites_footnote.id in the
* ATOM_SITES_FOOTNOTE list.
* @return StrColumn
*/
public StrColumn getFootnoteId() {
return delegate.getColumn("footnote_id", DelegatingStrColumn::new);
}
/**
* The x coordinate of the atom-site position specified as a
* fraction of _cell.length_a.
* @return FloatColumn
*/
public FloatColumn getFractX() {
return delegate.getColumn("fract_x", DelegatingFloatColumn::new);
}
/**
* The standard uncertainty (estimated standard deviation)
* of _atom_site.fract_x.
* @return FloatColumn
*/
public FloatColumn getFractXEsd() {
return delegate.getColumn("fract_x_esd", DelegatingFloatColumn::new);
}
/**
* The y coordinate of the atom-site position specified as a
* fraction of _cell.length_b.
* @return FloatColumn
*/
public FloatColumn getFractY() {
return delegate.getColumn("fract_y", DelegatingFloatColumn::new);
}
/**
* The standard uncertainty (estimated standard deviation)
* of _atom_site.fract_y.
* @return FloatColumn
*/
public FloatColumn getFractYEsd() {
return delegate.getColumn("fract_y_esd", DelegatingFloatColumn::new);
}
/**
* The z coordinate of the atom-site position specified as a
* fraction of _cell.length_c.
* @return FloatColumn
*/
public FloatColumn getFractZ() {
return delegate.getColumn("fract_z", DelegatingFloatColumn::new);
}
/**
* The standard uncertainty (estimated standard deviation)
* of _atom_site.fract_z.
* @return FloatColumn
*/
public FloatColumn getFractZEsd() {
return delegate.getColumn("fract_z_esd", DelegatingFloatColumn::new);
}
/**
* 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.
* @return StrColumn
*/
public StrColumn getGroupPDB() {
return delegate.getColumn("group_PDB", DelegatingStrColumn::new);
}
/**
* 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.
*
* In general, this aggregate identifier does not uniquely
* identify an atom site as for non-polymers _atom_site.label_seq_id
* is '.'.
* @return IntColumn
*/
public IntColumn getId() {
return delegate.getColumn("id", DelegatingIntColumn::new);
}
/**
* 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.
* @return StrColumn
*/
public StrColumn getLabelAltId() {
return delegate.getColumn("label_alt_id", DelegatingStrColumn::new);
}
/**
* 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.
* @return StrColumn
*/
public StrColumn getLabelAsymId() {
return delegate.getColumn("label_asym_id", DelegatingStrColumn::new);
}
/**
* 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.
* @return StrColumn
*/
public StrColumn getLabelAtomId() {
return delegate.getColumn("label_atom_id", DelegatingStrColumn::new);
}
/**
* A component of the identifier for this atom site.
*
* This data item is a pointer to _chem_comp.id in the CHEM_COMP
* category.
* @return StrColumn
*/
public StrColumn getLabelCompId() {
return delegate.getColumn("label_comp_id", DelegatingStrColumn::new);
}
/**
* This data item is a pointer to _entity.id in the ENTITY category.
* @return StrColumn
*/
public StrColumn getLabelEntityId() {
return delegate.getColumn("label_entity_id", DelegatingStrColumn::new);
}
/**
* This data item is a pointer to _entity_poly_seq.num in the
* ENTITY_POLY_SEQ category.
* @return IntColumn
*/
public IntColumn getLabelSeqId() {
return delegate.getColumn("label_seq_id", DelegatingIntColumn::new);
}
/**
* 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.
* @return FloatColumn
*/
public FloatColumn getOccupancy() {
return delegate.getColumn("occupancy", DelegatingFloatColumn::new);
}
/**
* The standard uncertainty (estimated standard deviation)
* of _atom_site.occupancy.
* @return FloatColumn
*/
public FloatColumn getOccupancyEsd() {
return delegate.getColumn("occupancy_esd", DelegatingFloatColumn::new);
}
/**
* A description of restraints applied to specific parameters at
* this site during refinement. See also _atom_site.refinement_flags
* and _refine.ls_number_restraints.
* @return StrColumn
*/
public StrColumn getRestraints() {
return delegate.getColumn("restraints", DelegatingStrColumn::new);
}
/**
* The multiplicity of a site due to the space-group symmetry as is
* given in International Tables for Crystallography Vol. A (2002).
* @return IntColumn
*/
public IntColumn getSymmetryMultiplicity() {
return delegate.getColumn("symmetry_multiplicity", DelegatingIntColumn::new);
}
/**
* A standard code used to describe the type of atomic displacement
* parameters used for the site.
* @return StrColumn
*/
public StrColumn getThermalDisplaceType() {
return delegate.getColumn("thermal_displace_type", DelegatingStrColumn::new);
}
/**
* This data item is a pointer to _atom_type.symbol in the
* ATOM_TYPE category.
* @return StrColumn
*/
public StrColumn getTypeSymbol() {
return delegate.getColumn("type_symbol", DelegatingStrColumn::new);
}
/**
* 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^
* @return FloatColumn
*/
public FloatColumn getUEquivGeomMean() {
return delegate.getColumn("U_equiv_geom_mean", DelegatingFloatColumn::new);
}
/**
* The standard uncertainty (estimated standard deviation)
* of _atom_site.U_equiv_geom_mean.
* @return FloatColumn
*/
public FloatColumn getUEquivGeomMeanEsd() {
return delegate.getColumn("U_equiv_geom_mean_esd", DelegatingFloatColumn::new);
}
/**
* 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.
* @return FloatColumn
*/
public FloatColumn getUIsoOrEquiv() {
return delegate.getColumn("U_iso_or_equiv", DelegatingFloatColumn::new);
}
/**
* The standard uncertainty (estimated standard deviation)
* of _atom_site.U_iso_or_equiv.
* @return FloatColumn
*/
public FloatColumn getUIsoOrEquivEsd() {
return delegate.getColumn("U_iso_or_equiv_esd", DelegatingFloatColumn::new);
}
/**
* The Wyckoff symbol (letter) as listed in the space-group tables
* of International Tables for Crystallography, Vol. A (2002).
* @return StrColumn
*/
public StrColumn getWyckoffSymbol() {
return delegate.getColumn("Wyckoff_symbol", DelegatingStrColumn::new);
}
/**
* The optional value of _atom_site.pdbx_atom_ambiguity atoms that differ only by stereochemistry but
* are not stereospecifically assigned by the experiment.
* @return StrColumn
*/
public StrColumn getPdbxAtomAmbiguity() {
return delegate.getColumn("pdbx_atom_ambiguity", DelegatingStrColumn::new);
}
/**
* A standard code used to describe the type of atomic displacement
* parameters used for the site.
* @return StrColumn
*/
public StrColumn getAdpType() {
return delegate.getColumn("adp_type", DelegatingStrColumn::new);
}
/**
* 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.
* @return StrColumn
*/
public StrColumn getRefinementFlags() {
return delegate.getColumn("refinement_flags", DelegatingStrColumn::new);
}
/**
* A code which indicates the refinement restraints or constraints
* applied to the atomic displacement parameters of this site.
* @return StrColumn
*/
public StrColumn getRefinementFlagsAdp() {
return delegate.getColumn("refinement_flags_adp", DelegatingStrColumn::new);
}
/**
* A code which indicates that refinement restraints or
* constraints were applied to the occupancy of this site.
* @return StrColumn
*/
public StrColumn getRefinementFlagsOccupancy() {
return delegate.getColumn("refinement_flags_occupancy", DelegatingStrColumn::new);
}
/**
* A code which indicates the refinement restraints or constraints
* applied to the positional coordinates of this site.
* @return StrColumn
*/
public StrColumn getRefinementFlagsPosn() {
return delegate.getColumn("refinement_flags_posn", DelegatingStrColumn::new);
}
/**
* Author's alternate location identifier.
* @return StrColumn
*/
public StrColumn getPdbxAuthAltId() {
return delegate.getColumn("pdbx_auth_alt_id", DelegatingStrColumn::new);
}
/**
* PDB insertion code.
* @return StrColumn
*/
public StrColumn getPdbxPDBInsCode() {
return delegate.getColumn("pdbx_PDB_ins_code", DelegatingStrColumn::new);
}
/**
* PDB model number.
* @return IntColumn
*/
public IntColumn getPdbxPDBModelNum() {
return delegate.getColumn("pdbx_PDB_model_num", DelegatingIntColumn::new);
}
/**
* PDB residue number.
* @return StrColumn
*/
public StrColumn getPdbxPDBResidueNo() {
return delegate.getColumn("pdbx_PDB_residue_no", DelegatingStrColumn::new);
}
/**
* PDB residue name.
* @return StrColumn
*/
public StrColumn getPdbxPDBResidueName() {
return delegate.getColumn("pdbx_PDB_residue_name", DelegatingStrColumn::new);
}
/**
* PDB strand id.
* @return StrColumn
*/
public StrColumn getPdbxPDBStrandId() {
return delegate.getColumn("pdbx_PDB_strand_id", DelegatingStrColumn::new);
}
/**
* PDB atom name.
* @return StrColumn
*/
public StrColumn getPdbxPDBAtomName() {
return delegate.getColumn("pdbx_PDB_atom_name", DelegatingStrColumn::new);
}
/**
* Author's atom name.
* @return StrColumn
*/
public StrColumn getPdbxAuthAtomName() {
return delegate.getColumn("pdbx_auth_atom_name", DelegatingStrColumn::new);
}
/**
* The net integer charge assigned to this atom. This is the
* formal charge assignment normally found in chemical diagrams.
* @return IntColumn
*/
public IntColumn getPdbxFormalCharge() {
return delegate.getColumn("pdbx_formal_charge", DelegatingIntColumn::new);
}
/**
* Author's residue name.
* @return StrColumn
*/
public StrColumn getPdbxAuthCompId() {
return delegate.getColumn("pdbx_auth_comp_id", DelegatingStrColumn::new);
}
/**
* Author's strand id.
* @return StrColumn
*/
public StrColumn getPdbxAuthAsymId() {
return delegate.getColumn("pdbx_auth_asym_id", DelegatingStrColumn::new);
}
/**
* Author's sequence identifier.
* @return StrColumn
*/
public StrColumn getPdbxAuthSeqId() {
return delegate.getColumn("pdbx_auth_seq_id", DelegatingStrColumn::new);
}
/**
* 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.
* @return StrColumn
*/
public StrColumn getPdbxTlsGroupId() {
return delegate.getColumn("pdbx_tls_group_id", DelegatingStrColumn::new);
}
/**
* 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.
* @return StrColumn
*/
public StrColumn getPdbxNcsDomId() {
return delegate.getColumn("pdbx_ncs_dom_id", DelegatingStrColumn::new);
}
/**
* 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.
* @return StrColumn
*/
public StrColumn getPdbxStructGroupId() {
return delegate.getColumn("pdbx_struct_group_id", DelegatingStrColumn::new);
}
/**
* The ATOM group code used by the NDB.
* @return StrColumn
*/
public StrColumn getPdbxGroupNDB() {
return delegate.getColumn("pdbx_group_NDB", DelegatingStrColumn::new);
}
/**
* The ATOM group code used by the NDB.
* @return StrColumn
*/
public StrColumn getPdbxAtomGroup() {
return delegate.getColumn("pdbx_atom_group", DelegatingStrColumn::new);
}
/**
* Sequential residue number used by NDB.
* @return StrColumn
*/
public StrColumn getPdbxLabelSeqNum() {
return delegate.getColumn("pdbx_label_seq_num", DelegatingStrColumn::new);
}
/**
* Will identify with a 'Y' that this strand got generated.
* @return StrColumn
*/
public StrColumn getPdbxNotInAsym() {
return delegate.getColumn("pdbx_not_in_asym", DelegatingStrColumn::new);
}
/**
* This data item is an ordinal which identifies distinct chemical components in the atom_site category, both
* polymeric and non-polymeric.
* @return IntColumn
*/
public IntColumn getPdbxLabelIndex() {
return delegate.getColumn("pdbx_label_index", DelegatingIntColumn::new);
}
/**
* The name of additional external databases with residue level mapping.
* @return StrColumn
*/
public StrColumn getPdbxSiftsXrefDbName() {
return delegate.getColumn("pdbx_sifts_xref_db_name", DelegatingStrColumn::new);
}
/**
* The accession code related to the additional external database entry.
* @return StrColumn
*/
public StrColumn getPdbxSiftsXrefDbAcc() {
return delegate.getColumn("pdbx_sifts_xref_db_acc", DelegatingStrColumn::new);
}
/**
* The sequence position of the external database entry that corresponds
* to the residue mapping defined by the SIFTS process.
* @return StrColumn
*/
public StrColumn getPdbxSiftsXrefDbNum() {
return delegate.getColumn("pdbx_sifts_xref_db_num", DelegatingStrColumn::new);
}
/**
* Describes the residue type of the given UniProt match
* @return StrColumn
*/
public StrColumn getPdbxSiftsXrefDbRes() {
return delegate.getColumn("pdbx_sifts_xref_db_res", DelegatingStrColumn::new);
}
/**
* 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.
* @return IntColumn
*/
public IntColumn getIhmModelId() {
return delegate.getColumn("ihm_model_id", DelegatingIntColumn::new);
}
}
