Package org.rcsb.cif.model.generated

Class ChemLinkChir

java.lang.Object

org.rcsb.cif.model.BaseCategory

org.rcsb.cif.model.generated.ChemLinkChir

All Implemented Interfaces:

Category

@Generated("org.rcsb.cif.generator.SchemaGenerator")
public class ChemLinkChir
extends BaseCategory

Data items in the CHEM_LINK_CHIR category provide details about the chiral centres in a link between two chemical components. The atoms bonded to the chiral atom are specified in the CHEM_LINK_CHIR_ATOM category.

Field Summary

Fields inherited from class org.rcsb.cif.model.BaseCategory

isText, textFields

Constructor Summary

Constructors

Constructor	Description
ChemLinkChir(String name)
ChemLinkChir(String name, int rowCount, Object[] encodedColumns)
ChemLinkChir(String name, Map<String,Column> columns)

Method Summary

Modifier and Type	Method	Description
StrColumn	getAtomCompId()	This data item indicates whether the chiral atom is found in the first or the second of the two components connected by the link.
StrColumn	getAtomConfig()	The chiral configuration of the atom that is a chiral centre.
StrColumn	getAtomId()	The ID of the atom that is a chiral centre.
StrColumn	getId()	The value of _chem_link_chir.id must uniquely identify a record in the CHEM_LINK_CHIR list.
StrColumn	getLinkId()	This data item is a pointer to _chem_link.id in the CHEM_LINK category.
IntColumn	getNumberAtomsAll()	The total number of atoms bonded to the atom specified by _chem_link_chir.atom_id.
IntColumn	getNumberAtomsNh()	The number of non-hydrogen atoms bonded to the atom specified by _chem_link_chir.atom_id.
StrColumn	getVolumeFlag()	A flag to indicate whether a chiral volume should match the standard value in both magnitude and sign, or in magnitude only.
FloatColumn	getVolumeThree()	The chiral volume, V(c), for chiral centres that involve a chiral atom bonded to three non-hydrogen atoms and one hydrogen atom.
FloatColumn	getVolumeThreeEsd()	The standard uncertainty (estimated standard deviation) of _chem_link_chir.volume_three.

Methods inherited from class org.rcsb.cif.model.BaseCategory

getBinaryColumn, getCategoryName, getColumn, getColumnNames, getRowCount, isDefined

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

columnNames, columns, get

Constructor Detail

ChemLinkChir

public ChemLinkChir(String name,
                    Map<String,Column> columns)

ChemLinkChir

public ChemLinkChir(String name,
                    int rowCount,
                    Object[] encodedColumns)

ChemLinkChir

public ChemLinkChir(String name)

Method Detail

getAtomCompId

public StrColumn getAtomCompId()

This data item indicates whether the chiral atom is found in the first or the second of the two components connected by the link.

Returns:

StrColumn

getAtomId

public StrColumn getAtomId()

The ID of the atom that is a chiral centre. As this data item does not point to a specific atom in a specific chemical component, it is not a child in the linkage sense.

Returns:

StrColumn

getAtomConfig

public StrColumn getAtomConfig()

The chiral configuration of the atom that is a chiral centre.

Returns:

StrColumn

getId

public StrColumn getId()

The value of _chem_link_chir.id must uniquely identify a record in the CHEM_LINK_CHIR list.

Returns:

StrColumn

getLinkId

public StrColumn getLinkId()

This data item is a pointer to _chem_link.id in the CHEM_LINK category.

Returns:

StrColumn

getNumberAtomsAll

public IntColumn getNumberAtomsAll()

The total number of atoms bonded to the atom specified by _chem_link_chir.atom_id.

Returns:

IntColumn

getNumberAtomsNh

public IntColumn getNumberAtomsNh()

The number of non-hydrogen atoms bonded to the atom specified by _chem_link_chir.atom_id.

Returns:

IntColumn

getVolumeFlag

public StrColumn getVolumeFlag()

A flag to indicate whether a chiral volume should match the standard value in both magnitude and sign, or in magnitude only.

Returns:

StrColumn

getVolumeThree

public FloatColumn getVolumeThree()

The chiral volume, V(c), for chiral centres that involve a chiral atom bonded to three non-hydrogen atoms and one hydrogen atom. V~c~ = V1 * (V2 X V3) V1 = the vector distance from the atom specified by _chem_link_chir.atom_id to the first atom in the CHEM_LINK_CHIR_ATOM list V2 = the vector distance from the atom specified by _chem_link_chir.atom_id to the second atom in the CHEM_LINK_CHIR_ATOM list V3 = the vector distance from the atom specified by _chem_link_chir.atom_id to the third atom in the CHEM_LINK_CHIR_ATOM list * = the vector dot product X = the vector cross product

Returns:

FloatColumn

getVolumeThreeEsd

public FloatColumn getVolumeThreeEsd()

The standard uncertainty (estimated standard deviation) of _chem_link_chir.volume_three.

Returns:

FloatColumn