org.rcsb.cif.schema.core.GeomBond 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 specify the geometry bonds in the
* structural model as derived from the atomic sites.
*/
@Generated("org.rcsb.cif.schema.generator.SchemaGenerator")
public class GeomBond extends DelegatingCategory.DelegatingCifCoreCategory {
private static final String NAME = "geom_bond";
public GeomBond(CifCoreBlock parentBlock) {
super(NAME, parentBlock);
}
/**
* Unique identifier for the bond.
* @return StrColumn
*/
public StrColumn getId() {
return new DelegatingStrColumn(parentBlock.getColumn("geom_bond_id"));
}
/**
* The number of times the given bond appears in the environment
* of the atoms labelled _geom_bond.atom_site_label_1. In cases
* where the full list of bonds is given, one of the series of
* equivalent bonds may be assigned the appropriate multiplicity
* while the others are assigned a value of 0.
* @return IntColumn
*/
public IntColumn getMultiplicity() {
return new DelegatingIntColumn(parentBlock.getColumn("geom_bond_multiplicity"));
}
/**
* This code signals whether the angle is referred to in a
* publication or should be placed in a table of significant angles.
* @return StrColumn
*/
public StrColumn getPublFlag() {
return new DelegatingStrColumn(parentBlock.getColumn("geom_bond_publ_flag"));
}
/**
* 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 getSiteSymmetry1() {
return new DelegatingStrColumn(parentBlock.getColumn("geom_bond_site_symmetry_1"));
}
/**
* 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 getSiteSymmetry2() {
return new DelegatingStrColumn(parentBlock.getColumn("geom_bond_site_symmetry_2"));
}
/**
* Bond valence calculated from the bond distance.
* @return FloatColumn
*/
public FloatColumn getValence() {
return new DelegatingFloatColumn(parentBlock.getColumn("geom_bond_valence"));
}
/**
* Standard uncertainty of _geom_bond.valence.
* @return FloatColumn
*/
public FloatColumn getValenceSu() {
return new DelegatingFloatColumn(parentBlock.getColumn("geom_bond_valence_su"));
}
/**
* This label is a unique identifier for a particular site in the
* asymmetric unit of the crystal unit cell.
* @return StrColumn
*/
public StrColumn getAtomSiteId1() {
return new DelegatingStrColumn(parentBlock.getAliasedColumn("geom_bond_atom_site_id_1", "geom_bond_atom_site_label_1"));
}
/**
* This label is a unique identifier for a particular site in the
* asymmetric unit of the crystal unit cell.
* @return StrColumn
*/
public StrColumn getAtomSiteLabel1() {
return new DelegatingStrColumn(parentBlock.getAliasedColumn("geom_bond_atom_site_id_1", "geom_bond_atom_site_label_1"));
}
/**
* This label is a unique identifier for a particular site in the
* asymmetric unit of the crystal unit cell.
* @return StrColumn
*/
public StrColumn getAtomSiteId2() {
return new DelegatingStrColumn(parentBlock.getAliasedColumn("geom_bond_atom_site_id_2", "geom_bond_atom_site_label_2"));
}
/**
* This label is a unique identifier for a particular site in the
* asymmetric unit of the crystal unit cell.
* @return StrColumn
*/
public StrColumn getAtomSiteLabel2() {
return new DelegatingStrColumn(parentBlock.getAliasedColumn("geom_bond_atom_site_id_2", "geom_bond_atom_site_label_2"));
}
/**
* Intramolecular bond distance between the sites identified
* by _geom_bond.id
* @return FloatColumn
*/
public FloatColumn getDist() {
return new DelegatingFloatColumn(parentBlock.getAliasedColumn("geom_bond_dist", "geom_bond_distance"));
}
/**
* Intramolecular bond distance between the sites identified
* by _geom_bond.id
* @return FloatColumn
*/
public FloatColumn getDistance() {
return new DelegatingFloatColumn(parentBlock.getAliasedColumn("geom_bond_dist", "geom_bond_distance"));
}
/**
* Standard uncertainty of the intramolecular bond distance
* between the sites identified by _geom_bond.id.
* @return FloatColumn
*/
public FloatColumn getDistEsd() {
return new DelegatingFloatColumn(parentBlock.getAliasedColumn("geom_bond_dist_esd", "geom_bond_distance_su"));
}
/**
* Standard uncertainty of the intramolecular bond distance
* between the sites identified by _geom_bond.id.
* @return FloatColumn
*/
public FloatColumn getDistanceSu() {
return new DelegatingFloatColumn(parentBlock.getAliasedColumn("geom_bond_dist_esd", "geom_bond_distance_su"));
}
}