Package org.rcsb.cif.schema.mm

Class PdbxDccGeometry

java.lang.Object

org.rcsb.cif.schema.DelegatingCategory

org.rcsb.cif.schema.mm.PdbxDccGeometry

All Implemented Interfaces:

Category

@Generated("org.rcsb.cif.schema.generator.SchemaGenerator")
public class PdbxDccGeometry
extends DelegatingCategory

Data items in the category record the overall deviations about geometry (such as bond length, angle, dihedral, chirality, planarity). These data are calculated with the phenix module model_vs_data.

Nested Class Summary

Nested classes/interfaces inherited from class org.rcsb.cif.schema.DelegatingCategory

DelegatingCategory.DelegatingCifCoreCategory

Nested classes/interfaces inherited from interface org.rcsb.cif.model.Category

Category.EmptyCategory

Field Summary

Fields inherited from class org.rcsb.cif.schema.DelegatingCategory

delegate

Constructor Summary

Constructors

Constructor	Description
PdbxDccGeometry(Category delegate)

Method Summary

Modifier and Type	Method	Description
protected Column	createDelegate(String columnName, Column column)
FloatColumn	getAllAtomClashscore()	All atom score is determined by steric overlaps >0.4A per 1000 atoms.
FloatColumn	getAngleLigandMax()	The maximum root mean square deviation for bond angles (ligand only).
FloatColumn	getAngleLigandRms()	The overall root mean square deviation for bond angles (ligand only).
FloatColumn	getAngleOverallMax()	The maximum root mean square deviation for bond angles (all atoms).
FloatColumn	getAngleOverallRms()	The overall root mean square deviation for bond angles (all atoms).
FloatColumn	getBondLigandMax()	The maximum root mean square deviation for bond lengths (ligand only).
FloatColumn	getBondLigandRms()	The overall root mean square deviation for bond lengths (ligand only).
FloatColumn	getBondOverallMax()	The maximum root mean square deviation for bond lengths (all atoms).
FloatColumn	getBondOverallRms()	The overall root mean square deviation for bond lengths (all atoms).
IntColumn	getCbetaDeviations()	Number of Cbeta deviations >0.25A.
FloatColumn	getChiralityOverallMax()	The maximum root mean square deviation for chirality (all atoms).
FloatColumn	getChiralityOverallRms()	The overall root mean square deviation for chirality (all atoms).
FloatColumn	getDihedralOverallMax()	The maximum root mean square deviation for dihedrals (all atoms).
FloatColumn	getDihedralOverallRms()	The overall root mean square deviation for dihedrals (all atoms).
FloatColumn	getNon_bondedRms()	The overall on-bonded distance (all atoms).
FloatColumn	getOverallScore()	The overall score for the geometry (the smaller the better).
StrColumn	getPdbid()	The PDB id code.
FloatColumn	getPlanarityOverallMax()	The maximum root mean square deviation for planarity (all atoms).
FloatColumn	getPlanarityOverallRms()	The overall root mean square deviation for planarity (all atoms).
IntColumn	getRamachandranAllowedNumber()	Number of allowed residues in Ramachandran plot.
FloatColumn	getRamachandranAllowedPercent()	Percentage of allowed residues in Ramachandran plot.
IntColumn	getRamachandranFavoredNumber()	Number of favored residues in Ramachandran plot.
FloatColumn	getRamachandranFavoredPercent()	Percentage of favored residues in Ramachandran plot.
IntColumn	getRamachandranOutlierNumber()	Number of outliers in Ramachandran plot.
FloatColumn	getRamachandranOutlierPercent()	Percentage of outliers in Ramachandran plot.
IntColumn	getRotamerOutliersNumber()	Number of rotamer outliers.
FloatColumn	getRotamerOutliersPercent()	Percentage of rotamer outliers.

Methods inherited from class org.rcsb.cif.schema.DelegatingCategory

getCategoryName, getColumn, getColumns, getRowCount

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

columns, getColumn, isDefined

Constructor Details

PdbxDccGeometry

public PdbxDccGeometry(Category delegate)

Method Details

createDelegate

protected Column createDelegate(String columnName, Column column)

Overrides:

createDelegate in class DelegatingCategory

getPdbid

public StrColumn getPdbid()

The PDB id code.

Returns:

StrColumn

getRamachandranOutlierPercent

public FloatColumn getRamachandranOutlierPercent()

Percentage of outliers in Ramachandran plot.

Returns:

FloatColumn

getRamachandranOutlierNumber

public IntColumn getRamachandranOutlierNumber()

Number of outliers in Ramachandran plot.

Returns:

IntColumn

getRamachandranAllowedPercent

public FloatColumn getRamachandranAllowedPercent()

Percentage of allowed residues in Ramachandran plot.

Returns:

FloatColumn

getRamachandranAllowedNumber

public IntColumn getRamachandranAllowedNumber()

Number of allowed residues in Ramachandran plot.

Returns:

IntColumn

getRamachandranFavoredPercent

public FloatColumn getRamachandranFavoredPercent()

Percentage of favored residues in Ramachandran plot.

Returns:

FloatColumn

getRamachandranFavoredNumber

public IntColumn getRamachandranFavoredNumber()

Number of favored residues in Ramachandran plot.

Returns:

IntColumn

getRotamerOutliersPercent

public FloatColumn getRotamerOutliersPercent()

Percentage of rotamer outliers.

Returns:

FloatColumn

getRotamerOutliersNumber

public IntColumn getRotamerOutliersNumber()

Number of rotamer outliers.

Returns:

IntColumn

getCbetaDeviations

public IntColumn getCbetaDeviations()

Number of Cbeta deviations >0.25A.

Returns:

IntColumn

getAllAtomClashscore

public FloatColumn getAllAtomClashscore()

All atom score is determined by steric overlaps >0.4A per 1000 atoms.

Returns:

FloatColumn

getOverallScore

public FloatColumn getOverallScore()

The overall score for the geometry (the smaller the better).

Returns:

FloatColumn

getBondOverallRms

public FloatColumn getBondOverallRms()

The overall root mean square deviation for bond lengths (all atoms).

Returns:

FloatColumn

getBondOverallMax

public FloatColumn getBondOverallMax()

The maximum root mean square deviation for bond lengths (all atoms).

Returns:

FloatColumn

getBondLigandRms

public FloatColumn getBondLigandRms()

The overall root mean square deviation for bond lengths (ligand only).

Returns:

FloatColumn

getBondLigandMax

public FloatColumn getBondLigandMax()

The maximum root mean square deviation for bond lengths (ligand only).

Returns:

FloatColumn

getAngleOverallRms

public FloatColumn getAngleOverallRms()

The overall root mean square deviation for bond angles (all atoms).

Returns:

FloatColumn

getAngleOverallMax

public FloatColumn getAngleOverallMax()

The maximum root mean square deviation for bond angles (all atoms).

Returns:

FloatColumn

getAngleLigandRms

public FloatColumn getAngleLigandRms()

The overall root mean square deviation for bond angles (ligand only).

Returns:

FloatColumn

getAngleLigandMax

public FloatColumn getAngleLigandMax()

The maximum root mean square deviation for bond angles (ligand only).

Returns:

FloatColumn

getDihedralOverallRms

public FloatColumn getDihedralOverallRms()

The overall root mean square deviation for dihedrals (all atoms).

Returns:

FloatColumn

getDihedralOverallMax

public FloatColumn getDihedralOverallMax()

The maximum root mean square deviation for dihedrals (all atoms).

Returns:

FloatColumn

getChiralityOverallRms

public FloatColumn getChiralityOverallRms()

The overall root mean square deviation for chirality (all atoms).

Returns:

FloatColumn

getChiralityOverallMax

public FloatColumn getChiralityOverallMax()

The maximum root mean square deviation for chirality (all atoms).

Returns:

FloatColumn

getPlanarityOverallRms

public FloatColumn getPlanarityOverallRms()

The overall root mean square deviation for planarity (all atoms).

Returns:

FloatColumn

getPlanarityOverallMax

public FloatColumn getPlanarityOverallMax()

The maximum root mean square deviation for planarity (all atoms).

Returns:

FloatColumn

getNon_bondedRms

public FloatColumn getNon_bondedRms()

The overall on-bonded distance (all atoms).

Returns:

FloatColumn