Package org.rcsb.cif.model.generated

Class PdbxRefineComponent

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

    • Constructor Detail

      • PdbxRefineComponent

        public PdbxRefineComponent​(String name,
                           int rowCount,
                           Object[] encodedColumns)

      • PdbxRefineComponent

        public PdbxRefineComponent​(String name)

    • Method Detail

      • 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