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package org.rcsb.cif.schema.mm;
import org.rcsb.cif.model.*;
import org.rcsb.cif.schema.*;
import javax.annotation.Generated;
/**
* Data items in the PDBX_REFINE_COMPONENT category record
* statistics of the final model relative to the density map.
*/
@Generated("org.rcsb.cif.schema.generator.SchemaGenerator")
public class PdbxRefineComponent extends DelegatingCategory {
public PdbxRefineComponent(Category delegate) {
super(delegate);
}
@Override
protected Column createDelegate(String columnName, Column column) {
switch (columnName) {
case "label_alt_id":
return getLabelAltId();
case "label_asym_id":
return getLabelAsymId();
case "label_comp_id":
return getLabelCompId();
case "label_seq_id":
return getLabelSeqId();
case "auth_asym_id":
return getAuthAsymId();
case "auth_comp_id":
return getAuthCompId();
case "auth_seq_id":
return getAuthSeqId();
case "PDB_ins_code":
return getPDBInsCode();
case "B_iso":
return getBIso();
case "B_iso_main_chain":
return getBIsoMainChain();
case "B_iso_side_chain":
return getBIsoSideChain();
case "shift":
return getShift();
case "shift_side_chain":
return getShiftSideChain();
case "shift_main_chain":
return getShiftMainChain();
case "correlation":
return getCorrelation();
case "correlation_side_chain":
return getCorrelationSideChain();
case "correlation_main_chain":
return getCorrelationMainChain();
case "real_space_R":
return getRealSpaceR();
case "real_space_R_side_chain":
return getRealSpaceRSideChain();
case "real_space_R_main_chain":
return getRealSpaceRMainChain();
case "connect":
return getConnect();
case "density_index":
return getDensityIndex();
case "density_index_main_chain":
return getDensityIndexMainChain();
case "density_index_side_chain":
return getDensityIndexSideChain();
case "density_ratio":
return getDensityRatio();
case "density_ratio_main_chain":
return getDensityRatioMainChain();
case "density_ratio_side_chain":
return getDensityRatioSideChain();
default:
return new DelegatingColumn(column);
}
}
/**
* 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.
* @return StrColumn
*/
public StrColumn getLabelAltId() {
return delegate.getColumn("label_alt_id", DelegatingStrColumn::new);
}
/**
* 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.
* @return StrColumn
*/
public StrColumn getLabelAsymId() {
return delegate.getColumn("label_asym_id", DelegatingStrColumn::new);
}
/**
* 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.
* @return StrColumn
*/
public StrColumn getLabelCompId() {
return delegate.getColumn("label_comp_id", DelegatingStrColumn::new);
}
/**
* 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.
* @return IntColumn
*/
public IntColumn getLabelSeqId() {
return delegate.getColumn("label_seq_id", DelegatingIntColumn::new);
}
/**
* 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.
* @return StrColumn
*/
public StrColumn getAuthAsymId() {
return delegate.getColumn("auth_asym_id", DelegatingStrColumn::new);
}
/**
* 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.
* @return StrColumn
*/
public StrColumn getAuthCompId() {
return delegate.getColumn("auth_comp_id", DelegatingStrColumn::new);
}
/**
* 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.
* @return StrColumn
*/
public StrColumn getAuthSeqId() {
return delegate.getColumn("auth_seq_id", DelegatingStrColumn::new);
}
/**
* A component of the identifier for the component.
*
* This data item is a pointer to _atom_site.pdbx_PDB_ins_code
* ATOM_SITE category.
* @return StrColumn
*/
public StrColumn getPDBInsCode() {
return delegate.getColumn("PDB_ins_code", DelegatingStrColumn::new);
}
/**
* 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
* @return FloatColumn
*/
public FloatColumn getBIso() {
return delegate.getColumn("B_iso", DelegatingFloatColumn::new);
}
/**
* 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
* @return FloatColumn
*/
public FloatColumn getBIsoMainChain() {
return delegate.getColumn("B_iso_main_chain", DelegatingFloatColumn::new);
}
/**
* 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
* @return FloatColumn
*/
public FloatColumn getBIsoSideChain() {
return delegate.getColumn("B_iso_side_chain", DelegatingFloatColumn::new);
}
/**
* 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
* @return FloatColumn
*/
public FloatColumn getShift() {
return delegate.getColumn("shift", DelegatingFloatColumn::new);
}
/**
* 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
* @return FloatColumn
*/
public FloatColumn getShiftSideChain() {
return delegate.getColumn("shift_side_chain", DelegatingFloatColumn::new);
}
/**
* 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
* @return FloatColumn
*/
public FloatColumn getShiftMainChain() {
return delegate.getColumn("shift_main_chain", DelegatingFloatColumn::new);
}
/**
* 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
* @return FloatColumn
*/
public FloatColumn getCorrelation() {
return delegate.getColumn("correlation", DelegatingFloatColumn::new);
}
/**
* 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
* @return FloatColumn
*/
public FloatColumn getCorrelationSideChain() {
return delegate.getColumn("correlation_side_chain", DelegatingFloatColumn::new);
}
/**
* 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
* @return FloatColumn
*/
public FloatColumn getCorrelationMainChain() {
return delegate.getColumn("correlation_main_chain", DelegatingFloatColumn::new);
}
/**
* 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
* @return FloatColumn
*/
public FloatColumn getRealSpaceR() {
return delegate.getColumn("real_space_R", DelegatingFloatColumn::new);
}
/**
* 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
* @return FloatColumn
*/
public FloatColumn getRealSpaceRSideChain() {
return delegate.getColumn("real_space_R_side_chain", DelegatingFloatColumn::new);
}
/**
* 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
* @return FloatColumn
*/
public FloatColumn getRealSpaceRMainChain() {
return delegate.getColumn("real_space_R_main_chain", DelegatingFloatColumn::new);
}
/**
* 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
* @return FloatColumn
*/
public FloatColumn getConnect() {
return delegate.getColumn("connect", DelegatingFloatColumn::new);
}
/**
* 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
* @return FloatColumn
*/
public FloatColumn getDensityIndex() {
return delegate.getColumn("density_index", DelegatingFloatColumn::new);
}
/**
* 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
* @return FloatColumn
*/
public FloatColumn getDensityIndexMainChain() {
return delegate.getColumn("density_index_main_chain", DelegatingFloatColumn::new);
}
/**
* 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
* @return FloatColumn
*/
public FloatColumn getDensityIndexSideChain() {
return delegate.getColumn("density_index_side_chain", DelegatingFloatColumn::new);
}
/**
* 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.
* @return FloatColumn
*/
public FloatColumn getDensityRatio() {
return delegate.getColumn("density_ratio", DelegatingFloatColumn::new);
}
/**
* 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.
* @return FloatColumn
*/
public FloatColumn getDensityRatioMainChain() {
return delegate.getColumn("density_ratio_main_chain", DelegatingFloatColumn::new);
}
/**
* 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.
* @return FloatColumn
*/
public FloatColumn getDensityRatioSideChain() {
return delegate.getColumn("density_ratio_side_chain", DelegatingFloatColumn::new);
}
}
