Package org.rcsb.cif.schema.mm

Class PdbxDccMap

java.lang.Object
org.rcsb.cif.schema.DelegatingCategory
org.rcsb.cif.schema.mm.PdbxDccMap
All Implemented Interfaces:
Category
@Generated("org.rcsb.cif.schema.generator.SchemaGenerator")
public class PdbxDccMap
extends DelegatingCategory
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.

  • Constructor Details

  • Method Details

    • createDelegate

      protected Column createDelegate​(String columnName, Column column)
      Overrides:
      createDelegate in class DelegatingCategory

    • 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