Package org.rcsb.cif.schema.mm

Class PdbxRefineComponent

java.lang.Object
org.rcsb.cif.schema.DelegatingCategory
org.rcsb.cif.schema.mm.PdbxRefineComponent
All Implemented Interfaces:
Category
@Generated("org.rcsb.cif.schema.generator.SchemaGenerator")
public class PdbxRefineComponent
extends DelegatingCategory
Data items in the PDBX_REFINE_COMPONENT category record statistics of the final model relative to the density map.

  • Constructor Details

  • Method Details

    • createDelegate

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

    • getLabelAltId

      public StrColumn getLabelAltId()
      A component of the identifier for the component. This data item is a pointer to _atom_sites_alt.id in the ATOM_SITES_ALT category.
      Returns:
      StrColumn

    • getLabelAsymId

      public StrColumn getLabelAsymId()
      A component of the identifier for the component. This data item is a pointer to _atom_site.label_asym_id in the ATOM_SITE category.
      Returns:
      StrColumn

    • getLabelCompId

      public StrColumn getLabelCompId()
      A component of the identifier for the component. This data item is a pointer to _atom_site.label_comp_id in the ATOM_SITE category.
      Returns:
      StrColumn

    • getLabelSeqId

      public IntColumn getLabelSeqId()
      A component of the identifier for the component. This data item is a pointer to _atom_site.label_seq_id in the ATOM_SITE category.
      Returns:
      IntColumn

    • getAuthAsymId

      public StrColumn getAuthAsymId()
      A component of the identifier for the component. This data item is a pointer to _atom_site.auth_asym_id in the ATOM_SITE category.
      Returns:
      StrColumn

    • getAuthCompId

      public StrColumn getAuthCompId()
      A component of the identifier for the component. This data item is a pointer to _atom_site.auth_comp_id in the ATOM_SITE category.
      Returns:
      StrColumn

    • getAuthSeqId

      public StrColumn getAuthSeqId()
      A component of the identifier for the component. This data item is a pointer to _atom_site.auth_seq_id in the ATOM_SITE category.
      Returns:
      StrColumn

    • getPDBInsCode

      public StrColumn getPDBInsCode()
      A component of the identifier for the component. This data item is a pointer to _atom_site.pdbx_PDB_ins_code ATOM_SITE category.
      Returns:
      StrColumn

    • getBIso

      public FloatColumn getBIso()
      The average isotropic B factors for the group of atoms (e.g. residue or ligand, side chain, main chain). The B factors for each atom is given by _atom_site.B_iso_or_equiv
      Returns:
      FloatColumn

    • getBIsoMainChain

      public FloatColumn getBIsoMainChain()
      The average isotropic B factors for the group of atoms (e.g. residue or ligand, side chain, main chain). The B factors for each atom is given by _atom_site.B_iso_or_equiv
      Returns:
      FloatColumn

    • getBIsoSideChain

      public FloatColumn getBIsoSideChain()
      The average isotropic B factors for the group of atoms (e.g. residue or ligand, side chain, main chain). The B factors for each atom is given by _atom_site.B_iso_or_equiv
      Returns:
      FloatColumn

    • getShift

      public FloatColumn getShift()
      The tendency of the group of atoms (e.g. residue or ligand, side chain, main chain) to move away from its current position. 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. Ref: Vaguine, A.A., Richelle, J. & Wodak, S.J. (1999). Acta Cryst. D55,199-205
      Returns:
      FloatColumn

    • getShiftSideChain

      public FloatColumn getShiftSideChain()
      The tendency of the group of atoms (e.g. residue or ligand, side chain, main chain) to move away from its current position. 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. Ref: Vaguine, A.A., Richelle, J. & Wodak, S.J. (1999). Acta Cryst. D55,199-205
      Returns:
      FloatColumn

    • getShiftMainChain

      public FloatColumn getShiftMainChain()
      The tendency of the group of atoms (e.g. residue or ligand, side chain, main chain) to move away from its current position. 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. Ref: Vaguine, A.A., Richelle, J. & Wodak, S.J. (1999). Acta Cryst. D55,199-205
      Returns:
      FloatColumn

    • getCorrelation

      public FloatColumn getCorrelation()
      Correlation coefficient of electron density for each residue or ligand, side chain, main chain The density correlation coefficient is calculated for each component from atomic densities of (2Fobs-Fcalc) map - "Robs" and the model map (Fcalc) - "Rcalc" : D_corr = <Robs><Rcalc>/sqrt(<Robs**2><Rcalc**2>) where <Robs> is the mean of "observed" densities of atoms of the component (backbone or side chain). <Rcalc> is the mean of "calculated" densities of component atoms. The value of density for some atom from map R(x) is: sum_i ( R(xi) * Ratom(xi - xa) ) Dens = ---------------------------------- sum_i ( Ratom(xi - xa) ) where Ratom(x) is atomic electron density for the x-th grid point. xa - vector of the centre of atom. xi - vector of the i-th point of grid. Sum is taken over all grid points which have distance from the center of the atom less than the Radius_limit. For all atoms Radius_limit = 2.5 A. Ref: Vaguine, A.A., Richelle, J. & Wodak, S.J. (1999). Acta Cryst. D55,199-205
      Returns:
      FloatColumn

    • getCorrelationSideChain

      public FloatColumn getCorrelationSideChain()
      Correlation coefficient of electron density for each residue or ligand, side chain, main chain The density correlation coefficient is calculated for each component from atomic densities of (2Fobs-Fcalc) map - "Robs" and the model map (Fcalc) - "Rcalc" : D_corr = <Robs><Rcalc>/sqrt(<Robs**2><Rcalc**2>) where <Robs> is the mean of "observed" densities of atoms of the component (backbone or side chain). <Rcalc> is the mean of "calculated" densities of component atoms. The value of density for some atom from map R(x) is: sum_i ( R(xi) * Ratom(xi - xa) ) Dens = ---------------------------------- sum_i ( Ratom(xi - xa) ) where Ratom(x) is atomic electron density for the x-th grid point. xa - vector of the centre of atom. xi - vector of the i-th point of grid. Sum is taken over all grid points which have distance from the center of the atom less than the Radius_limit. For all atoms Radius_limit = 2.5 A. Ref: Vaguine, A.A., Richelle, J. & Wodak, S.J. (1999). Acta Cryst. D55,199-205
      Returns:
      FloatColumn

    • getCorrelationMainChain

      public FloatColumn getCorrelationMainChain()
      Correlation coefficient of electron density for each residue or ligand, side chain, main chain The density correlation coefficient is calculated for each component from atomic densities of (2Fobs-Fcalc) map - "Robs" and the model map (Fcalc) - "Rcalc" : D_corr = <Robs><Rcalc>/sqrt(<Robs**2><Rcalc**2>) where <Robs> is the mean of "observed" densities of atoms of the component (backbone or side chain). <Rcalc> is the mean of "calculated" densities of component atoms. The value of density for some atom from map R(x) is: sum_i ( R(xi) * Ratom(xi - xa) ) Dens = ---------------------------------- sum_i ( Ratom(xi - xa) ) where Ratom(x) is atomic electron density for the x-th grid point. xa - vector of the centre of atom. xi - vector of the i-th point of grid. Sum is taken over all grid points which have distance from the center of the atom less than the Radius_limit. For all atoms Radius_limit = 2.5 A. Ref: Vaguine, A.A., Richelle, J. & Wodak, S.J. (1999). Acta Cryst. D55,199-205
      Returns:
      FloatColumn

    • getRealSpaceR

      public FloatColumn getRealSpaceR()
      Real space R factor of electron density for each component, residue side chain, or main chain. The real space R factor is calculated by the equation R_real = [Sum~i (|Dobs - Dcal|)]/[Sum~i (|Dobs + Dcal|)] Where: Dobs is the observed electron density, Dcal is the calculated electron density, summation is for all the grid points Ref: Branden, C.I. & Jones, T.A. (1990). Nature, 343, 687-689
      Returns:
      FloatColumn

    • getRealSpaceRSideChain

      public FloatColumn getRealSpaceRSideChain()
      Real space R factor of electron density for each component, residue side chain, or main chain. The real space R factor is calculated by the equation R_real = [Sum~i (|Dobs - Dcal|)]/[Sum~i (|Dobs + Dcal|)] Where: Dobs is the observed electron density, Dcal is the calculated electron density, summation is for all the grid points Ref: Branden, C.I. & Jones, T.A. (1990). Nature, 343, 687-689
      Returns:
      FloatColumn

    • getRealSpaceRMainChain

      public FloatColumn getRealSpaceRMainChain()
      Real space R factor of electron density for each component, residue side chain, or main chain. The real space R factor is calculated by the equation R_real = [Sum~i (|Dobs - Dcal|)]/[Sum~i (|Dobs + Dcal|)] Where: Dobs is the observed electron density, Dcal is the calculated electron density, summation is for all the grid points Ref: Branden, C.I. & Jones, T.A. (1990). Nature, 343, 687-689
      Returns:
      FloatColumn

    • getConnect

      public FloatColumn getConnect()
      The index of connectivity is the product of the (2Fobs-Fcal) electron density values for the backbone atoms (N, CA and C) divided by the average value for the structure. Low values (less than 1.0) of this index indicate breaks in the backbone electron density which may be due to flexibility of the chain or incorrect tracing. connect = [(D(xi)...D(xi))^(1/N)] /<D>_all Where: D(xi) = (2*Fobs - Fcal) <D>_all is the averaged value of density for the structure. The product is for N atoms of group. Ref: Vaguine, A.A., Richelle, J. & Wodak, S.J. (1999). Acta Cryst. D55,199-205
      Returns:
      FloatColumn

    • getDensityIndex

      public FloatColumn getDensityIndex()
      The index of density is the product of the (2Fobs-Fcal) electron density values for the group of atoms divided by the average value for the structure. Low values (less than 1.0) may be problematic for model fitting. index = [(D(xi)...D(xi))^(1/N)] /<D>_all Where : D(xi) = (2*Fobs - Fcal) <D>_all is the averaged value of density for the structure. The product is for N atoms of group. Ref: Vaguine, A.A., Richelle, J. & Wodak, S.J. (1999). Acta Cryst. D55,199-205
      Returns:
      FloatColumn

    • getDensityIndexMainChain

      public FloatColumn getDensityIndexMainChain()
      The index of density is the product of the (2Fobs-Fcal) electron density values for the group of atoms divided by the average value for the structure. Low values (less than 1.0) may be problematic for model fitting. index = [(D(xi)...D(xi))^(1/N)] /<D>_all Where : D(xi) = (2*Fobs - Fcal) <D>_all is the averaged value of density for the structure. The product is for N atoms of group. Ref: Vaguine, A.A., Richelle, J. & Wodak, S.J. (1999). Acta Cryst. D55,199-205
      Returns:
      FloatColumn

    • getDensityIndexSideChain

      public FloatColumn getDensityIndexSideChain()
      The index of density is the product of the (2Fobs-Fcal) electron density values for the group of atoms divided by the average value for the structure. Low values (less than 1.0) may be problematic for model fitting. index = [(D(xi)...D(xi))^(1/N)] /<D>_all Where : D(xi) = (2*Fobs - Fcal) <D>_all is the averaged value of density for the structure. The product is for N atoms of group. Ref: Vaguine, A.A., Richelle, J. & Wodak, S.J. (1999). Acta Cryst. D55,199-205
      Returns:
      FloatColumn

    • getDensityRatio

      public FloatColumn getDensityRatio()
      The density ratio is similar to the density index, but summation of the density for the group is used for calculation. The ratio of density is the summation of the (2Fobs-Fcal) electron density values for the group of atoms divided by the average value for the structure. Low values (less than 0.4) of this ratio may be problematic for the group. index = [Sum~i D(xi)]/<D>_all Where: D(xi) = (2*Fobs - Fcal) <D>_all is the average value of density for the structure. The summation is for all the atoms of group.
      Returns:
      FloatColumn

    • getDensityRatioMainChain

      public FloatColumn getDensityRatioMainChain()
      The density ratio is similar to the density index, but summation of the density for the group is used for calculation. The ratio of density is the summation of the (2Fobs-Fcal) electron density values for the group of atoms divided by the average value for the structure. Low values (less than 0.4) of this ratio may be problematic for the group. index = [Sum~i D(xi)]/<D>_all Where: D(xi) = (2*Fobs - Fcal) <D>_all is the average value of density for the structure. The summation is for all the atoms of group.
      Returns:
      FloatColumn

    • getDensityRatioSideChain

      public FloatColumn getDensityRatioSideChain()
      The density ratio is similar to the density index, but summation of the density for the group is used for calculation. The ratio of density is the summation of the (2Fobs-Fcal) electron density values for the group of atoms divided by the average value for the structure. Low values (less than 0.4) of this ratio may be problematic for the group. index = [Sum~i D(xi)]/<D>_all Where: D(xi) = (2*Fobs - Fcal) <D>_all is the average value of density for the structure. The summation is for all the atoms of group.
      Returns:
      FloatColumn