org.rcsb.cif.schema.core.ModelSite Maven / Gradle / Ivy
package org.rcsb.cif.schema.core;
import org.rcsb.cif.model.*;
import org.rcsb.cif.schema.*;
import javax.annotation.Generated;
/**
* The CATEGORY of data items used to describe atomic sites and
* connections in the proposed atomic model.
*/
@Generated("org.rcsb.cif.schema.generator.SchemaGenerator")
public class ModelSite extends DelegatingCategory.DelegatingCifCoreCategory {
private static final String NAME = "model_site";
public ModelSite(CifCoreBlock parentBlock) {
super(NAME, parentBlock);
}
/**
* The set of three ADP eigenvalues for the associated eigenvectors
* given by _model_site.ADP_eigenvectors. The eigenvalues are
* sorted in order of magnitude with the largest first.
* @return FloatColumn
*/
public FloatColumn getAdpEigenvalues() {
return new DelegatingFloatColumn(parentBlock.getColumn("model_site_adp_eigenvalues"));
}
/**
* Standard uncertainty of _model_site.ADP_eigenvalues.
* @return FloatColumn
*/
public FloatColumn getAdpEigenvaluesSu() {
return new DelegatingFloatColumn(parentBlock.getColumn("model_site_adp_eigenvalues_su"));
}
/**
* The set of three ADP eigenvectors corresponding to the values
* given in _model_site.ADP_eigenvalues. The eigenvectors are
* contained in the rows of a matrix ordered from top to bottom
* in order largest to smallest corresponding eigenvalue. The
* eigenvector elements are direction cosines to the orthogonal
* axes X,Y,Z.
* @return FloatColumn
*/
public FloatColumn getAdpEigenvectors() {
return new DelegatingFloatColumn(parentBlock.getColumn("model_site_adp_eigenvectors"));
}
/**
* Standard uncertainty of _model_site.ADP_eigenvectors.
* @return FloatColumn
*/
public FloatColumn getAdpEigenvectorsSu() {
return new DelegatingFloatColumn(parentBlock.getColumn("model_site_adp_eigenvectors_su"));
}
/**
* Matrix of dimensionless anisotropic atomic displacement parameters.
* @return FloatColumn
*/
public FloatColumn getAdpMatrixBeta() {
return new DelegatingFloatColumn(parentBlock.getColumn("model_site_adp_matrix_beta"));
}
/**
* Standard uncertainty of _model_site.ADP_matrix_beta.
* @return FloatColumn
*/
public FloatColumn getAdpMatrixBetaSu() {
return new DelegatingFloatColumn(parentBlock.getColumn("model_site_adp_matrix_beta_su"));
}
/**
* Vector of Cartesian (orthogonal angstrom) atom site coordinates.
* @return FloatColumn
*/
public FloatColumn getCartnXyz() {
return new DelegatingFloatColumn(parentBlock.getColumn("model_site_cartn_xyz"));
}
/**
* Standard uncertainty of _model_site.Cartn_xyz.
* @return FloatColumn
*/
public FloatColumn getCartnXyzSu() {
return new DelegatingFloatColumn(parentBlock.getColumn("model_site_cartn_xyz_su"));
}
/**
* Display colour code assigned to this atom site. Note that the
* possible colours are enumerated in the colour_RGB list, and
* the default code is enumerated in the colour_hue list.
* @return StrColumn
*/
public StrColumn getDisplayColour() {
return new DelegatingStrColumn(parentBlock.getColumn("model_site_display_colour"));
}
/**
* Vector of fractional atom site coordinates.
* @return FloatColumn
*/
public FloatColumn getFractXyz() {
return new DelegatingFloatColumn(parentBlock.getColumn("model_site_fract_xyz"));
}
/**
* Standard uncertainty of _model_site.fract_xyz.
* @return FloatColumn
*/
public FloatColumn getFractXyzSu() {
return new DelegatingFloatColumn(parentBlock.getColumn("model_site_fract_xyz_su"));
}
/**
* An identifier for the model site that is unique within its loop.
* @return StrColumn
*/
public StrColumn getId() {
return new DelegatingStrColumn(parentBlock.getColumn("model_site_id"));
}
/**
* Index number of an atomic site in the connected molecule.
* @return IntColumn
*/
public IntColumn getIndex() {
return new DelegatingIntColumn(parentBlock.getColumn("model_site_index"));
}
/**
* Code identifies a site in the atom_site category of data.
* @return StrColumn
*/
public StrColumn getLabel() {
return new DelegatingStrColumn(parentBlock.getColumn("model_site_label"));
}
/**
* Index number of a distinct molecules in the cell, not related by
* symmetry.
* @return IntColumn
*/
public IntColumn getMoleIndex() {
return new DelegatingIntColumn(parentBlock.getColumn("model_site_mole_index"));
}
/**
* Atomic radius of atom located at this site.
* @return FloatColumn
*/
public FloatColumn getRadiusBond() {
return new DelegatingFloatColumn(parentBlock.getColumn("model_site_radius_bond"));
}
/**
* Atomic contact radius of atom specie located at this site.
* @return FloatColumn
*/
public FloatColumn getRadiusContact() {
return new DelegatingFloatColumn(parentBlock.getColumn("model_site_radius_contact"));
}
/**
* The set of data items which specify the symmetry operation codes
* which must be applied to the atom sites involved in the geometry angle.
*
* The symmetry code of each atom site as the symmetry-equivalent position
* number 'n' and the cell translation number 'pqr'. These numbers are
* combined to form the code 'n pqr' or n_pqr.
*
* The character string n_pqr is composed as follows:
*
* n refers to the symmetry operation that is applied to the
* coordinates stored in _atom_site.fract_xyz. It must match a
* number given in _symmetry_equiv.pos_site_id.
*
* p, q and r refer to the translations that are subsequently
* applied to the symmetry transformed coordinates to generate
* the atom used in calculating the angle. These translations
* (x,y,z) are related to (p,q,r) by the relations
* p = 5 + x
* q = 5 + y
* r = 5 + z
* @return StrColumn
*/
public StrColumn getSymop() {
return new DelegatingStrColumn(parentBlock.getColumn("model_site_symop"));
}
/**
* Code to identify the atom specie(s) occupying this site.
* @return StrColumn
*/
public StrColumn getTypeSymbol() {
return new DelegatingStrColumn(parentBlock.getColumn("model_site_type_symbol"));
}
}