Package org.rcsb.cif.schema.mm

Class RefineHist

java.lang.Object
org.rcsb.cif.schema.DelegatingCategory
org.rcsb.cif.schema.mm.RefineHist
All Implemented Interfaces:
Category
@Generated("org.rcsb.cif.schema.generator.SchemaGenerator")
public class RefineHist
extends DelegatingCategory
Data items in the REFINE_HIST category record details about the steps during the refinement of the structure. These data items are not meant to be as thorough a description of the refinement as is provided for the final model in other categories; rather, these data items provide a mechanism for sketching out the progress of the refinement, supported by a small set of representative statistics.

  • Constructor Details

  • Method Details

    • createDelegate

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

    • getPdbxRefineId

      public StrColumn getPdbxRefineId()
      This data item uniquely identifies a refinement within an entry. _refine_hist.pdbx_refine_id can be used to distinguish the results of joint refinements.
      Returns:
      StrColumn

    • getCycleId

      public StrColumn getCycleId()
      The value of _refine_hist.cycle_id must uniquely identify a record in the REFINE_HIST list. Note that this item need not be a number; it can be any unique identifier.
      Returns:
      StrColumn

    • getDetails

      public StrColumn getDetails()
      A description of special aspects of this cycle of the refinement process.
      Returns:
      StrColumn

    • getDResHigh

      public FloatColumn getDResHigh()
      The lowest value for the interplanar spacings for the reflection data for this cycle of refinement. This is called the highest resolution.
      Returns:
      FloatColumn

    • getDResLow

      public FloatColumn getDResLow()
      The highest value for the interplanar spacings for the reflection data for this cycle of refinement. This is called the lowest resolution.
      Returns:
      FloatColumn

    • getNumberAtomsSolvent

      public IntColumn getNumberAtomsSolvent()
      The number of solvent atoms that were included in the model at this cycle of the refinement.
      Returns:
      IntColumn

    • getNumberAtomsTotal

      public IntColumn getNumberAtomsTotal()
      The total number of atoms that were included in the model at this cycle of the refinement.
      Returns:
      IntColumn

    • getNumberReflnsAll

      public IntColumn getNumberReflnsAll()
      The number of reflections that satisfy the resolution limits established by _refine_hist.d_res_high and _refine_hist.d_res_low.
      Returns:
      IntColumn

    • getNumberReflnsObs

      public IntColumn getNumberReflnsObs()
      The number of reflections that satisfy the resolution limits established by _refine_hist.d_res_high and _refine_hist.d_res_low and the observation criterion established by _reflns.observed_criterion.
      Returns:
      IntColumn

    • getNumberReflnsRFree

      public IntColumn getNumberReflnsRFree()
      The number of reflections that satisfy the resolution limits established by _refine_hist.d_res_high and _refine_hist.d_res_low and the observation limit established by _reflns.observed_criterion, and that were used as the test reflections (i.e. were excluded from the refinement) when the refinement included the calculation of a 'free' R factor. Details of how reflections were assigned to the working and test sets are given in _reflns.R_free_details.
      Returns:
      IntColumn

    • getNumberReflnsRWork

      public IntColumn getNumberReflnsRWork()
      The number of reflections that satisfy the resolution limits established by _refine_hist.d_res_high and _refine_hist.d_res_low and the observation limit established by _reflns.observed_criterion, and that were used as the working reflections (i.e. were included in the refinement) when the refinement included the calculation of a 'free' R factor. Details of how reflections were assigned to the working and test sets are given in _reflns.R_free_details.
      Returns:
      IntColumn

    • getRFactorAll

      public FloatColumn getRFactorAll()
      Residual factor R for reflections that satisfy the resolution limits established by _refine_hist.d_res_high and _refine_hist.d_res_low. sum|F~obs~ - F~calc~| R = --------------------- sum|F~obs~| F~obs~ = the observed structure-factor amplitudes F~calc~ = the calculated structure-factor amplitudes sum is taken over the specified reflections
      Returns:
      FloatColumn

    • getRFactorObs

      public FloatColumn getRFactorObs()
      Residual factor R for reflections that satisfy the resolution limits established by _refine_hist.d_res_high and _refine_hist.d_res_low and the observation criterion established by _reflns.observed_criterion. sum|F~obs~ - F~calc~| R = --------------------- sum|F~obs~| F~obs~ = the observed structure-factor amplitudes F~calc~ = the calculated structure-factor amplitudes sum is taken over the specified reflections
      Returns:
      FloatColumn

    • getRFactorRFree

      public FloatColumn getRFactorRFree()
      Residual factor R for reflections that satisfy the resolution limits established by _refine_hist.d_res_high and _refine_hist.d_res_low and the observation limit established by _reflns.observed_criterion, and that were used as the test reflections (i.e. were excluded from the refinement) when the refinement included the calculation of a 'free' R factor. Details of how reflections were assigned to the working and test sets are given in _reflns.R_free_details. sum|F~obs~ - F~calc~| R = --------------------- sum|F~obs~| F~obs~ = the observed structure-factor amplitudes F~calc~ = the calculated structure-factor amplitudes sum is taken over the specified reflections
      Returns:
      FloatColumn

    • getRFactorRWork

      public FloatColumn getRFactorRWork()
      Residual factor R for reflections that satisfy the resolution limits established by _refine_hist.d_res_high and _refine_hist.d_res_low and the observation limit established by _reflns.observed_criterion, and that were used as the working reflections (i.e. were included in the refinement) when the refinement included the calculation of a 'free' R factor. Details of how reflections were assigned to the working and test sets are given in _reflns.R_free_details. sum|F~obs~ - F~calc~| R = --------------------- sum|F~obs~| F~obs~ = the observed structure-factor amplitudes F~calc~ = the calculated structure-factor amplitudes sum is taken over the specified reflections
      Returns:
      FloatColumn

    • getPdbxNumberResiduesTotal

      public IntColumn getPdbxNumberResiduesTotal()
      Total number of polymer residues included in refinement.
      Returns:
      IntColumn

    • getPdbxBIsoMeanLigand

      public FloatColumn getPdbxBIsoMeanLigand()
      Mean isotropic B-value for ligand molecules included in refinement.
      Returns:
      FloatColumn

    • getPdbxBIsoMeanSolvent

      public FloatColumn getPdbxBIsoMeanSolvent()
      Mean isotropic B-value for solvent molecules included in refinement.
      Returns:
      FloatColumn

    • getPdbxNumberAtomsProtein

      public IntColumn getPdbxNumberAtomsProtein()
      Number of protein atoms included in refinement
      Returns:
      IntColumn

    • getPdbxNumberAtomsNucleicAcid

      public IntColumn getPdbxNumberAtomsNucleicAcid()
      Number of nucleic atoms included in refinement
      Returns:
      IntColumn

    • getPdbxNumberAtomsLigand

      public IntColumn getPdbxNumberAtomsLigand()
      Number of ligand atoms included in refinement
      Returns:
      IntColumn

    • getPdbxNumberAtomsLipid

      public IntColumn getPdbxNumberAtomsLipid()
      Number of lipid atoms included in refinement
      Returns:
      IntColumn

    • getPdbxNumberAtomsCarb

      public IntColumn getPdbxNumberAtomsCarb()
      Number of carbohydrate atoms included in refinement
      Returns:
      IntColumn

    • getPdbxPseudoAtomDetails

      public StrColumn getPdbxPseudoAtomDetails()
      Details of pseduo atoms used to model unexplained density
      Returns:
      StrColumn

    • getPdbxNumberAtomsSolvent

      public IntColumn getPdbxNumberAtomsSolvent()
      Number of solvent atoms used in refinement
      Returns:
      IntColumn

    • getPdbxNumberAtomsTotal

      public IntColumn getPdbxNumberAtomsTotal()
      Number of atoms used in refinement
      Returns:
      IntColumn