Package org.rcsb.cif.model.generated

Class PdbxValidateRmsdBond

java.lang.Object

org.rcsb.cif.model.BaseCategory

org.rcsb.cif.model.generated.PdbxValidateRmsdBond

All Implemented Interfaces:

Category

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

Data items in the PDBX_VALIDATE_RMSD_BOND category list the covalent bonds that have values which deviate from expected values by more than 6*rmsd.

Field Summary

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

isText, textFields

Constructor Summary

Constructors

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

Method Summary

Modifier and Type	Method	Description
StrColumn	getAuthAsymId1()	Part of the identifier of the first of the two atom sites that define the covalent bond.
StrColumn	getAuthAsymId2()	Part of the identifier of the second of the two atom sites that define the covalent bond.
StrColumn	getAuthAtomId1()	Part of the identifier of the first of the two atom sites that define the covalent bond.
StrColumn	getAuthAtomId2()	Part of the identifier of the second of the two atom sites that define the covalent bond.
StrColumn	getAuthCompId1()	Part of the identifier of the first of the two atom sites that define the covalent bond.
StrColumn	getAuthCompId2()	Part of the identifier of the second of the two atom sites that define the covalent bond.
StrColumn	getAuthSeqId1()	Part of the identifier of the first of the two atom sites that define the covalent bond.
StrColumn	getAuthSeqId2()	Part of the identifier of the second of the two atom sites that define the covalent bond.
FloatColumn	getBondDeviation()	The value of the deviation from ideal for the defined covalent bond for the two atoms defined.
FloatColumn	getBondStandardDeviation()	The uncertaintiy in target value of the bond length expressed as a standard deviation.
FloatColumn	getBondTargetValue()	The target value of the bond length
FloatColumn	getBondValue()	The value of the bond length
IntColumn	getId()	The value of _pdbx_validate_rmsd_bond.id must uniquely identify each item in the PDBX_VALIDATE_RMSD_BOND list.
StrColumn	getLabelAltId1()	An optional identifier of the first of the two atoms that define the covalent bond.
StrColumn	getLabelAltId2()	An optional identifier of the second of the two atoms that define the covalent bond.
StrColumn	getLinkerFlag()	A flag to indicate if the bond is between two residues
StrColumn	getPDBInsCode1()	Optional identifier of the first of the two atom sites that define the covalent bond.
StrColumn	getPDBInsCode2()	Optional identifier of the second of the two atom sites that define the covalent bond.
IntColumn	getPDBModelNum()	The model number for the given bond

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

PdbxValidateRmsdBond

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

PdbxValidateRmsdBond

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

PdbxValidateRmsdBond

public PdbxValidateRmsdBond(String name)

Method Detail

getId

public IntColumn getId()

The value of _pdbx_validate_rmsd_bond.id must uniquely identify each item in the PDBX_VALIDATE_RMSD_BOND list. This is an integer serial number.

Returns:

IntColumn

getPDBModelNum

public IntColumn getPDBModelNum()

The model number for the given bond

Returns:

IntColumn

getAuthAsymId1

public StrColumn getAuthAsymId1()

Part of the identifier of the first of the two atom sites that define the covalent bond. This data item is a pointer to _atom_site.auth_asym_id in the ATOM_SITE category.

Returns:

StrColumn

getAuthAtomId1

public StrColumn getAuthAtomId1()

Part of the identifier of the first of the two atom sites that define the covalent bond. This data item is a pointer to _atom_site.auth_atom_id in the ATOM_SITE category.

Returns:

StrColumn

getAuthCompId1

public StrColumn getAuthCompId1()

Part of the identifier of the first of the two atom sites that define the covalent bond. This data item is a pointer to _atom_site.auth_comp_id in the ATOM_SITE category.

Returns:

StrColumn

getAuthSeqId1

public StrColumn getAuthSeqId1()

Part of the identifier of the first of the two atom sites that define the covalent bond. This data item is a pointer to _atom_site.auth_seq_id in the ATOM_SITE category.

Returns:

StrColumn

getAuthAtomId2

public StrColumn getAuthAtomId2()

Part of the identifier of the second of the two atom sites that define the covalent bond. This data item is a pointer to _atom_site.auth_atom_id in the ATOM_SITE category.

Returns:

StrColumn

getAuthAsymId2

public StrColumn getAuthAsymId2()

Part of the identifier of the second of the two atom sites that define the covalent bond. This data item is a pointer to _atom_site.auth_asym_id in the ATOM_SITE category.

Returns:

StrColumn

getAuthCompId2

public StrColumn getAuthCompId2()

Part of the identifier of the second of the two atom sites that define the covalent bond. This data item is a pointer to _atom_site.auth_comp_id in the ATOM_SITE category.

Returns:

StrColumn

getAuthSeqId2

public StrColumn getAuthSeqId2()

Part of the identifier of the second of the two atom sites that define the covalent bond. This data item is a pointer to _atom_site.auth_seq_id in the ATOM_SITE category.

Returns:

StrColumn

getPDBInsCode1

public StrColumn getPDBInsCode1()

Optional identifier of the first of the two atom sites that define the covalent bond. This data item is a pointer to _atom_site.pdbx_PDB_ins_code in the ATOM_SITE category.

Returns:

StrColumn

getPDBInsCode2

public StrColumn getPDBInsCode2()

Optional identifier of the second of the two atom sites that define the covalent bond. This data item is a pointer to _atom_site.pdbx_PDB_ins_code in the ATOM_SITE category.

Returns:

StrColumn

getLabelAltId1

public StrColumn getLabelAltId1()

An optional identifier of the first of the two atoms that define the covalent bond. This data item is a pointer to _atom_site.label_alt_id in the ATOM_SITE category.

Returns:

StrColumn

getLabelAltId2

public StrColumn getLabelAltId2()

An optional identifier of the second of the two atoms that define the covalent bond. This data item is a pointer to _atom_site.label_alt_id in the ATOM_SITE category.

Returns:

StrColumn

getBondDeviation

public FloatColumn getBondDeviation()

The value of the deviation from ideal for the defined covalent bond for the two atoms defined.

Returns:

FloatColumn

getBondValue

public FloatColumn getBondValue()

The value of the bond length

Returns:

FloatColumn

getBondTargetValue

public FloatColumn getBondTargetValue()

The target value of the bond length

Returns:

FloatColumn

getBondStandardDeviation

public FloatColumn getBondStandardDeviation()

The uncertaintiy in target value of the bond length expressed as a standard deviation.

Returns:

FloatColumn

getLinkerFlag

public StrColumn getLinkerFlag()

A flag to indicate if the bond is between two residues

Returns:

StrColumn