java.lang.Object
- org.rcsb.cif.model.BaseCategory
- - org.rcsb.cif.model.generated.PdbxDccMap

All Implemented Interfaces:

Category
```
@Generated("org.rcsb.cif.generator.SchemaGenerator")
public class PdbxDccMap
extends BaseCategory
```
Data items in the category record residual map properties such as Real Space electron density Correlation Coefficient (RSCC), real space R factors (RSR) and the Zscores for each residue, the main/side chains.

Field Summary
- Fields inherited from class org.rcsb.cif.model.BaseCategory
  isText, textFields

Constructor Summary

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

Method Summary

All Methods Instance Methods Concrete Methods
Modifier and Type	Method	Description
`StrColumn`	`getAuthAsymId()`	The author provided chain id.
`StrColumn`	`getAuthCompId()`	The author provided compound ID (residue name).
`StrColumn`	`getAuthSeqId()`	The author provided residue number.
`FloatColumn`	`getBisoMean()`	The occupancy weighted average isotropic B factors for the residue.
`FloatColumn`	`getBisoMeanMainChain()`	The occupancy weighted average isotropic B factors for the main chain atoms.
`FloatColumn`	`getBisoMeanPhosphateGroup()`	The occupancy weighted average isotropic B factors for the phosphate atoms.
`FloatColumn`	`getBisoMeanSideChain()`	The occupancy weighted average isotropic B factors for the side chain atoms.
`FloatColumn`	`getDensityConnectivity()`	Defined in sfcheck.
`FloatColumn`	`getDensityIndexMainChain()`	Defined in sfcheck.
`FloatColumn`	`getDensityIndexSideChain()`	Defined in sfcheck.
`IntColumn`	`getId()`	The ordered number of residue in the output list.
`StrColumn`	`getLabelAltId()`	Author provided alternate location identifier.
`StrColumn`	`getLabelInsCode()`	The PDB insertion code.
`FloatColumn`	`getLLDF()`	It is the Ligand Local Density Function defined as the (<RsR>_local - RsR_Ligand)/sigma_RsR, where <RsR>_local is the mean RSR of polymer residues in 5 Angstrom (including the crystallographic symmetry) surrounding the ligand, and sigma_RsR is sigma value calculated from the surrounding residues.
`StrColumn`	`getModelId()`	The component model identifier for this analysis.
`FloatColumn`	`getOccupancyMean()`	The averaged occupancy for the residue.
`FloatColumn`	`getOccupancyMeanMainChain()`	The averaged occupancy forthe main chain atoms.
`FloatColumn`	`getOccupancyMeanPhosphateGroup()`	The averaged occupancy forthe phosphate atoms.
`FloatColumn`	`getOccupancyMeanSideChain()`	The averaged occupancy forthe side chain atoms.
`StrColumn`	`getPdbId()`	The PDB id code (four characters).
`StrColumn`	`getQualityIndicator()`	The value indicates any problems with this group of atoms.
`FloatColumn`	`getRSCC()`	The Real Space electron density Correlation Coefficient for the residue.
`FloatColumn`	`getRSCCMainChain()`	The Real Space electron density Correlation Coefficient for the main chain atoms.
`FloatColumn`	`getRSCCPhosphateGroup()`	The Real Space electron density Correlation Coefficient for the phosphate atoms.
`FloatColumn`	`getRSCCSideChain()`	The Real Space electron density Correlation Coefficient for the side chain atoms.
`FloatColumn`	`getRSR()`	The Real space Rfactor (RSR) for the residue.
`FloatColumn`	`getRSRMainChain()`	The Real space Rfactor (RSR) for the main chain atoms.
`FloatColumn`	`getRSRPhosphateGroup()`	The Real space Rfactor (RSR) for the phosphate atoms.
`FloatColumn`	`getRSRSideChain()`	The Real space Rfactor (RSR) for the side chain atoms.
`FloatColumn`	`getRSRZ()`	Zscore of the Real Space Rfactor (RSRZ) for the residue.
`FloatColumn`	`getRSRZMainChain()`	Zscore of the Real Space Rfactor (RSRZ) for the main chain atoms.
`FloatColumn`	`getRSRZPhosphateGroup()`	Zscore of the Real Space Rfactor (RSRZ) for the phosphate atoms.
`FloatColumn`	`getRSRZSideChain()`	Zscore of the Real Space Rfactor (RSRZ) for the side chain atoms.
`FloatColumn`	`getRSZD()`	The real space difference density Z score (defined as Delta_rho/sigma(Delta_rho)) from Tickle (2012).
`FloatColumn`	`getRSZDMainChain()`	The same as _pdbx_dcc_map.RSZD, use for the main chain atoms.
`FloatColumn`	`getRSZDPhosphateGroup()`	The same as _pdbx_dcc_map.RSZD, use for the phosphate atoms of nucleic acids.
`FloatColumn`	`getRSZDSideChain()`	The same as _pdbx_dcc_map.RSZD, use for the side chain atoms.
`FloatColumn`	`getRSZO()`	The real space observed density Z score (defined as <rho_obs>/sigma(Delta_rho)) from Tickle (2012).
`FloatColumn`	`getRSZOMainChain()`	The same as _pdbx_dcc_map.RSZO, use for the main chain atoms.
`FloatColumn`	`getRSZOPhosphateGroup()`	The same as _pdbx_dcc_map.RSZO, use for the phosphate atoms of nucleic acids.
`FloatColumn`	`getRSZOSideChain()`	The same as _pdbx_dcc_map.RSZO, use for the side chain atoms.
`FloatColumn`	`getRSZOZscore()`	The Zscore of RSZO (or the Zscore of <rho_obs>/sigma(Delta_rho)).
`FloatColumn`	`getShift()`	Defined in sfcheck (displacement/sigma_of_displacement).
`FloatColumn`	`getShiftMainChain()`	The same as _pdbx_dcc_map.density_shift, but it is for main chain.
`FloatColumn`	`getShiftSideChain()`	The same as _pdbx_dcc_map.density_shift, but it is for side chain.
`FloatColumn`	`getWeightedRSR()`	The weighted Real Space Rfactor (defined as RSR/RSCC) for the residue.
`FloatColumn`	`getWeightedRSRZ()`	Zscore of weighted Real Space Rfactor for the residue.
`FloatColumn`	`getWRSRMainChain()`	The weighted Real Space Rfactor (RSR/RSCC) for the main chain atoms.
`FloatColumn`	`getWRSRPhosphateGroup()`	The weighted Real Space Rfactor (RSR/RSCC) for the phosphate atoms.
`FloatColumn`	`getWRSRSideChain()`	The weighted Real Space Rfactor (RSR/RSCC) for the side chain atoms.
`FloatColumn`	`getWRSRZMainChain()`	Zscore of weighted Real Space Rfactor (RSR/RSCC) for the main chain atoms.
`FloatColumn`	`getWRSRZPhosphateGroup()`	Zscore of weighted Real Space Rfactor (RSR/RSCC) for the phosphate atoms.
`FloatColumn`	`getWRSRZSideChain()`	Zscore of weighted Real Space Rfactor (RSR/RSCC) for the side chain atoms.

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
  - PdbxDccMap
```
public PdbxDccMap(String name,
                  Map<String,Column> columns)
```
  - PdbxDccMap
```
public PdbxDccMap(String name,
                  int rowCount,
                  Object[] encodedColumns)
```
  - PdbxDccMap
```
public PdbxDccMap(String name)
```
- Method Detail
  - getId
```
public IntColumn getId()
```
    The ordered number of residue in the output list.
    
    Returns:
    
    IntColumn
  - getModelId
```
public StrColumn getModelId()
```
    The component model identifier for this analysis.
    
    Returns:
    
    StrColumn
  - getPdbId
```
public StrColumn getPdbId()
```
    The PDB id code (four characters).
    
    Returns:
    
    StrColumn
  - getAuthAsymId
```
public StrColumn getAuthAsymId()
```
    The author provided chain id.
    
    Returns:
    
    StrColumn
  - getAuthCompId
```
public StrColumn getAuthCompId()
```
    The author provided compound ID (residue name).
    
    Returns:
    
    StrColumn
  - getAuthSeqId
```
public StrColumn getAuthSeqId()
```
    The author provided residue number.
    
    Returns:
    
    StrColumn
  - getLabelAltId
```
public StrColumn getLabelAltId()
```
    Author provided alternate location identifier.
    
    Returns:
    
    StrColumn
  - getLabelInsCode
```
public StrColumn getLabelInsCode()
```
    The PDB insertion code.
    
    Returns:
    
    StrColumn
  - getRSCC
```
public FloatColumn getRSCC()
```
    The Real Space electron density Correlation Coefficient for the residue. It is defined as RSCC=(<xy>-<x><y>)/[sqrt(<x**2>-<x>**2)*sqrt(<y**2>-<y>**2)] where x is the observed density from the (2mFo-DFc) map and y is the calculated density from the Fc map
    
    Returns:
    
    FloatColumn
  - getRSR
```
public FloatColumn getRSR()
```
    The Real space Rfactor (RSR) for the residue. It is defined as RSR=sum(|x-y|/x+y|) which is the summation over all grid points around the residue, where x is the observed density from the (2mFo-DFc) map and y is the calculated density from the Fc map.
    
    Returns:
    
    FloatColumn
  - getWeightedRSR
```
public FloatColumn getWeightedRSR()
```
    The weighted Real Space Rfactor (defined as RSR/RSCC) for the residue.
    
    Returns:
    
    FloatColumn
  - getRSRZ
```
public FloatColumn getRSRZ()
```
    Zscore of the Real Space Rfactor (RSRZ) for the residue. It is defined as (RSR-<RSR>)/sigma_RSR, where <RSR> and sigma_RSR are for the whole map, RSR is for the residue.
    
    Returns:
    
    FloatColumn
  - getWeightedRSRZ
```
public FloatColumn getWeightedRSRZ()
```
    Zscore of weighted Real Space Rfactor for the residue. It is defined as (wRSR-<wRSR>)/sigma_wRSR, where <wRSR> and sigma_wRSR are for the whole map, wRSR is for the residue.
    
    Returns:
    
    FloatColumn
  - getBisoMean
```
public FloatColumn getBisoMean()
```
    The occupancy weighted average isotropic B factors for the residue. It is defined as (SUM B*Q)/(SUM Q), where B is the isotropic B factor for each atom and Q is the occupancy.
    
    Returns:
    
    FloatColumn
  - getOccupancyMean
```
public FloatColumn getOccupancyMean()
```
    The averaged occupancy for the residue.
    
    Returns:
    
    FloatColumn
  - getRSCCMainChain
```
public FloatColumn getRSCCMainChain()
```
    The Real Space electron density Correlation Coefficient for the main chain atoms.
    
    Returns:
    
    FloatColumn
  - getRSRMainChain
```
public FloatColumn getRSRMainChain()
```
    The Real space Rfactor (RSR) for the main chain atoms.
    
    Returns:
    
    FloatColumn
  - getWRSRMainChain
```
public FloatColumn getWRSRMainChain()
```
    The weighted Real Space Rfactor (RSR/RSCC) for the main chain atoms.
    
    Returns:
    
    FloatColumn
  - getRSRZMainChain
```
public FloatColumn getRSRZMainChain()
```
    Zscore of the Real Space Rfactor (RSRZ) for the main chain atoms.
    
    Returns:
    
    FloatColumn
  - getWRSRZMainChain
```
public FloatColumn getWRSRZMainChain()
```
    Zscore of weighted Real Space Rfactor (RSR/RSCC) for the main chain atoms.
    
    Returns:
    
    FloatColumn
  - getBisoMeanMainChain
```
public FloatColumn getBisoMeanMainChain()
```
    The occupancy weighted average isotropic B factors for the main chain atoms.
    
    Returns:
    
    FloatColumn
  - getOccupancyMeanMainChain
```
public FloatColumn getOccupancyMeanMainChain()
```
    The averaged occupancy forthe main chain atoms.
    
    Returns:
    
    FloatColumn
  - getRSCCSideChain
```
public FloatColumn getRSCCSideChain()
```
    The Real Space electron density Correlation Coefficient for the side chain atoms.
    
    Returns:
    
    FloatColumn
  - getRSRSideChain
```
public FloatColumn getRSRSideChain()
```
    The Real space Rfactor (RSR) for the side chain atoms.
    
    Returns:
    
    FloatColumn
  - getWRSRSideChain
```
public FloatColumn getWRSRSideChain()
```
    The weighted Real Space Rfactor (RSR/RSCC) for the side chain atoms.
    
    Returns:
    
    FloatColumn
  - getRSRZSideChain
```
public FloatColumn getRSRZSideChain()
```
    Zscore of the Real Space Rfactor (RSRZ) for the side chain atoms.
    
    Returns:
    
    FloatColumn
  - getWRSRZSideChain
```
public FloatColumn getWRSRZSideChain()
```
    Zscore of weighted Real Space Rfactor (RSR/RSCC) for the side chain atoms.
    
    Returns:
    
    FloatColumn
  - getBisoMeanSideChain
```
public FloatColumn getBisoMeanSideChain()
```
    The occupancy weighted average isotropic B factors for the side chain atoms.
    
    Returns:
    
    FloatColumn
  - getOccupancyMeanSideChain
```
public FloatColumn getOccupancyMeanSideChain()
```
    The averaged occupancy forthe side chain atoms.
    
    Returns:
    
    FloatColumn
  - getRSCCPhosphateGroup
```
public FloatColumn getRSCCPhosphateGroup()
```
    The Real Space electron density Correlation Coefficient for the phosphate atoms.
    
    Returns:
    
    FloatColumn
  - getRSRPhosphateGroup
```
public FloatColumn getRSRPhosphateGroup()
```
    The Real space Rfactor (RSR) for the phosphate atoms.
    
    Returns:
    
    FloatColumn
  - getWRSRPhosphateGroup
```
public FloatColumn getWRSRPhosphateGroup()
```
    The weighted Real Space Rfactor (RSR/RSCC) for the phosphate atoms.
    
    Returns:
    
    FloatColumn
  - getRSRZPhosphateGroup
```
public FloatColumn getRSRZPhosphateGroup()
```
    Zscore of the Real Space Rfactor (RSRZ) for the phosphate atoms.
    
    Returns:
    
    FloatColumn
  - getWRSRZPhosphateGroup
```
public FloatColumn getWRSRZPhosphateGroup()
```
    Zscore of weighted Real Space Rfactor (RSR/RSCC) for the phosphate atoms.
    
    Returns:
    
    FloatColumn
  - getBisoMeanPhosphateGroup
```
public FloatColumn getBisoMeanPhosphateGroup()
```
    The occupancy weighted average isotropic B factors for the phosphate atoms.
    
    Returns:
    
    FloatColumn
  - getOccupancyMeanPhosphateGroup
```
public FloatColumn getOccupancyMeanPhosphateGroup()
```
    The averaged occupancy forthe phosphate atoms.
    
    Returns:
    
    FloatColumn
  - getShift
```
public FloatColumn getShift()
```
    Defined in sfcheck (displacement/sigma_of_displacement). Displacement of atoms from electron density is estimated from the difference (Fobs - Fcal) map. The displacement vector is the ratio of the gradient of difference density to the curvature. The amplitude of the displacement vector is an indicator of the positional error.
    
    Returns:
    
    FloatColumn
  - getShiftMainChain
```
public FloatColumn getShiftMainChain()
```
    The same as _pdbx_dcc_map.density_shift, but it is for main chain.
    
    Returns:
    
    FloatColumn
  - getShiftSideChain
```
public FloatColumn getShiftSideChain()
```
    The same as _pdbx_dcc_map.density_shift, but it is for side chain.
    
    Returns:
    
    FloatColumn
  - getDensityConnectivity
```
public FloatColumn getDensityConnectivity()
```
    Defined in sfcheck. It is the product of the (2Fobs-Fcal) electron density values for the backbone atoms N, CA and C, and in the case of RNA/DNA, for P, O5', C5', C3', O3'. Low values of this index indicate breaks in the backbone electron density which may be due to flexibility of the chain or incorrect tracing.
    
    Returns:
    
    FloatColumn
  - getDensityIndexMainChain
```
public FloatColumn getDensityIndexMainChain()
```
    Defined in sfcheck. It is the mean density of the main chain atoms divided by the mean density of the map.
    
    Returns:
    
    FloatColumn
  - getDensityIndexSideChain
```
public FloatColumn getDensityIndexSideChain()
```
    Defined in sfcheck. It is the mean density of the side chain atoms divided by the mean density of the map.
    
    Returns:
    
    FloatColumn
  - getRSZD
```
public FloatColumn getRSZD()
```
    The real space difference density Z score (defined as Delta_rho/sigma(Delta_rho)) from Tickle (2012). It is related to the model accuracy. RSZD>3, significant extra positive density around the residue; RSZD<-3, significant extra negative density around the residue.
    
    Returns:
    
    FloatColumn
  - getRSZO
```
public FloatColumn getRSZO()
```
    The real space observed density Z score (defined as <rho_obs>/sigma(Delta_rho)) from Tickle (2012). It is related to the model precision (B factors). Small or large value means weak or strong density for the residue.
    
    Returns:
    
    FloatColumn
  - getRSZOZscore
```
public FloatColumn getRSZOZscore()
```
    The Zscore of RSZO (or the Zscore of <rho_obs>/sigma(Delta_rho)).
    
    Returns:
    
    FloatColumn
  - getLLDF
```
public FloatColumn getLLDF()
```
    It is the Ligand Local Density Function defined as the (<RsR>_local - RsR_Ligand)/sigma_RsR, where <RsR>_local is the mean RSR of polymer residues in 5 Angstrom (including the crystallographic symmetry) surrounding the ligand, and sigma_RsR is sigma value calculated from the surrounding residues.
    
    Returns:
    
    FloatColumn
  - getRSZDMainChain
```
public FloatColumn getRSZDMainChain()
```
    The same as _pdbx_dcc_map.RSZD, use for the main chain atoms.
    
    Returns:
    
    FloatColumn
  - getRSZOMainChain
```
public FloatColumn getRSZOMainChain()
```
    The same as _pdbx_dcc_map.RSZO, use for the main chain atoms.
    
    Returns:
    
    FloatColumn
  - getRSZDSideChain
```
public FloatColumn getRSZDSideChain()
```
    The same as _pdbx_dcc_map.RSZD, use for the side chain atoms.
    
    Returns:
    
    FloatColumn
  - getRSZOSideChain
```
public FloatColumn getRSZOSideChain()
```
    The same as _pdbx_dcc_map.RSZO, use for the side chain atoms.
    
    Returns:
    
    FloatColumn
  - getRSZDPhosphateGroup
```
public FloatColumn getRSZDPhosphateGroup()
```
    The same as _pdbx_dcc_map.RSZD, use for the phosphate atoms of nucleic acids.
    
    Returns:
    
    FloatColumn
  - getRSZOPhosphateGroup
```
public FloatColumn getRSZOPhosphateGroup()
```
    The same as _pdbx_dcc_map.RSZO, use for the phosphate atoms of nucleic acids.
    
    Returns:
    
    FloatColumn
  - getQualityIndicator
```
public StrColumn getQualityIndicator()
```
    The value indicates any problems with this group of atoms. If given as 'd', it means there is problem of local model accuracy. If given as 'w', it means weak density (there is problem of local model precision). If given as 'dw', both then problems exist.
    
    Returns:
    
    StrColumn

Class PdbxDccMap

Field Summary

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

Constructor Summary

Method Summary

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

Methods inherited from class java.lang.Object

Methods inherited from interface org.rcsb.cif.model.Category

Constructor Detail

PdbxDccMap

PdbxDccMap

PdbxDccMap

Method Detail

getId

getModelId

getPdbId

getAuthAsymId

getAuthCompId

getAuthSeqId

getLabelAltId

getLabelInsCode

getRSCC

getRSR

getWeightedRSR

getRSRZ

getWeightedRSRZ

getBisoMean

getOccupancyMean

getRSCCMainChain

getRSRMainChain

getWRSRMainChain

getRSRZMainChain

getWRSRZMainChain

getBisoMeanMainChain

getOccupancyMeanMainChain

getRSCCSideChain

getRSRSideChain

getWRSRSideChain

getRSRZSideChain

getWRSRZSideChain

getBisoMeanSideChain

getOccupancyMeanSideChain

getRSCCPhosphateGroup

getRSRPhosphateGroup

getWRSRPhosphateGroup

getRSRZPhosphateGroup

getWRSRZPhosphateGroup

getBisoMeanPhosphateGroup

getOccupancyMeanPhosphateGroup

getShift

getShiftMainChain

getShiftSideChain

getDensityConnectivity

getDensityIndexMainChain

getDensityIndexSideChain

getRSZD

getRSZO

getRSZOZscore

getLLDF

getRSZDMainChain

getRSZOMainChain

getRSZDSideChain

getRSZOSideChain

getRSZDPhosphateGroup

getRSZOPhosphateGroup

getQualityIndicator