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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 REFINE_LS_SHELL category record details about
* the results of the least-squares refinement broken down into
* shells of resolution.
*/
@Generated("org.rcsb.cif.schema.generator.SchemaGenerator")
public class RefineLsShell extends DelegatingCategory {
public RefineLsShell(Category delegate) {
super(delegate);
}
@Override
protected Column createDelegate(String columnName, Column column) {
switch (columnName) {
case "pdbx_refine_id":
return getPdbxRefineId();
case "d_res_high":
return getDResHigh();
case "d_res_low":
return getDResLow();
case "number_reflns_all":
return getNumberReflnsAll();
case "number_reflns_obs":
return getNumberReflnsObs();
case "number_reflns_R_free":
return getNumberReflnsRFree();
case "number_reflns_R_work":
return getNumberReflnsRWork();
case "percent_reflns_obs":
return getPercentReflnsObs();
case "percent_reflns_R_free":
return getPercentReflnsRFree();
case "R_factor_all":
return getRFactorAll();
case "R_factor_obs":
return getRFactorObs();
case "R_factor_R_free_error":
return getRFactorRFreeError();
case "R_factor_R_work":
return getRFactorRWork();
case "redundancy_reflns_all":
return getRedundancyReflnsAll();
case "redundancy_reflns_obs":
return getRedundancyReflnsObs();
case "wR_factor_all":
return getWRFactorAll();
case "wR_factor_obs":
return getWRFactorObs();
case "wR_factor_R_free":
return getWRFactorRFree();
case "wR_factor_R_work":
return getWRFactorRWork();
case "pdbx_R_complete":
return getPdbxRComplete();
case "pdbx_total_number_of_bins_used":
return getPdbxTotalNumberOfBinsUsed();
case "pdbx_phase_error":
return getPdbxPhaseError();
case "pdbx_fsc_work":
return getPdbxFscWork();
case "pdbx_fsc_free":
return getPdbxFscFree();
case "R_factor_R_free":
return getRFactorRFree();
default:
return new DelegatingColumn(column);
}
}
/**
* This data item uniquely identifies a refinement within an entry.
* _refine_ls_shell.pdbx_refine_id can be used to distinguish the results
* of joint refinements.
* @return StrColumn
*/
public StrColumn getPdbxRefineId() {
return delegate.getColumn("pdbx_refine_id", DelegatingStrColumn::new);
}
/**
* The lowest value for the interplanar spacings for the
* reflection data in this shell. This is called
* the highest resolution.
* @return FloatColumn
*/
public FloatColumn getDResHigh() {
return delegate.getColumn("d_res_high", DelegatingFloatColumn::new);
}
/**
* The highest value for the interplanar spacings for the
* reflection data in this shell. This is called the lowest
* resolution.
* @return FloatColumn
*/
public FloatColumn getDResLow() {
return delegate.getColumn("d_res_low", DelegatingFloatColumn::new);
}
/**
* The number of reflections that satisfy the resolution limits
* established by _refine_ls_shell.d_res_high and
* _refine_ls_shell.d_res_low.
* @return IntColumn
*/
public IntColumn getNumberReflnsAll() {
return delegate.getColumn("number_reflns_all", DelegatingIntColumn::new);
}
/**
* The number of reflections that satisfy the resolution limits
* established by _refine_ls_shell.d_res_high and
* _refine_ls_shell.d_res_low and the observation criterion
* established by _reflns.observed_criterion.
* @return IntColumn
*/
public IntColumn getNumberReflnsObs() {
return delegate.getColumn("number_reflns_obs", DelegatingIntColumn::new);
}
/**
* The number of reflections that satisfy the resolution limits
* established by _refine_ls_shell.d_res_high and
* _refine_ls_shell.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.
* @return IntColumn
*/
public IntColumn getNumberReflnsRFree() {
return delegate.getColumn("number_reflns_R_free", DelegatingIntColumn::new);
}
/**
* The number of reflections that satisfy the resolution limits
* established by _refine_ls_shell.d_res_high and
* _refine_ls_shell.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.
* @return IntColumn
*/
public IntColumn getNumberReflnsRWork() {
return delegate.getColumn("number_reflns_R_work", DelegatingIntColumn::new);
}
/**
* The number of reflections that satisfy the resolution limits
* established by _refine_ls_shell.d_res_high and
* _refine_ls_shell.d_res_low and the observation criterion
* established by _reflns.observed_criterion, expressed as a
* percentage of the number of geometrically observable
* reflections that satisfy the resolution limits.
* @return FloatColumn
*/
public FloatColumn getPercentReflnsObs() {
return delegate.getColumn("percent_reflns_obs", DelegatingFloatColumn::new);
}
/**
* The number of reflections that satisfy the resolution limits
* established by _refine_ls_shell.d_res_high and
* _refine_ls_shell.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, expressed as a percentage of the number of
* geometrically observable reflections that satisfy the
* reflection limits.
* @return FloatColumn
*/
public FloatColumn getPercentReflnsRFree() {
return delegate.getColumn("percent_reflns_R_free", DelegatingFloatColumn::new);
}
/**
* Residual factor R for reflections that satisfy the resolution
* limits established by _refine_ls_shell.d_res_high and
* _refine_ls_shell.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
* @return FloatColumn
*/
public FloatColumn getRFactorAll() {
return delegate.getColumn("R_factor_all", DelegatingFloatColumn::new);
}
/**
* Residual factor R for reflections that satisfy the resolution
* limits established by _refine_ls_shell.d_res_high and
* _refine_ls_shell.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
* @return FloatColumn
*/
public FloatColumn getRFactorObs() {
return delegate.getColumn("R_factor_obs", DelegatingFloatColumn::new);
}
/**
* The estimated error in _refine_ls_shell.R_factor_R_free.
* The method used to estimate the error is described in the
* item _refine.ls_R_factor_R_free_error_details.
* @return FloatColumn
*/
public FloatColumn getRFactorRFreeError() {
return delegate.getColumn("R_factor_R_free_error", DelegatingFloatColumn::new);
}
/**
* Residual factor R for reflections that satisfy the resolution
* limits established by _refine_ls_shell.d_res_high and
* _refine_ls_shell.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
* @return FloatColumn
*/
public FloatColumn getRFactorRWork() {
return delegate.getColumn("R_factor_R_work", DelegatingFloatColumn::new);
}
/**
* The ratio of the total number of observations of the reflections
* that satisfy the resolution limits established by
* _refine_ls_shell.d_res_high and _refine_ls_shell.d_res_low
* to the number of crystallographically unique reflections that
* satisfy the same limits.
* @return FloatColumn
*/
public FloatColumn getRedundancyReflnsAll() {
return delegate.getColumn("redundancy_reflns_all", DelegatingFloatColumn::new);
}
/**
* The ratio of the total number of observations of the
* reflections that satisfy the resolution limits established by
* _refine_ls_shell.d_res_high and _refine_ls_shell.d_res_low and
* the observation criterion established by
* _reflns.observed_criterion to the number of crystallographically
* unique reflections that satisfy the same limits.
* @return FloatColumn
*/
public FloatColumn getRedundancyReflnsObs() {
return delegate.getColumn("redundancy_reflns_obs", DelegatingFloatColumn::new);
}
/**
* Weighted residual factor wR for reflections that satisfy the
* resolution limits established by _refine_ls_shell.d_res_high
* and _refine_ls_shell.d_res_low.
*
* ( sum|w |Y~obs~ - Y~calc~|^2^| )^1/2^
* wR = ( ---------------------------- )
* ( sum|w Y~obs~^2^| )
*
* Y~obs~ = the observed amplitude specified by
* _refine.ls_structure_factor_coef
* Y~calc~ = the calculated amplitude specified by
* _refine.ls_structure_factor_coef
* w = the least-squares weight
*
* sum is taken over the specified reflections
* @return FloatColumn
*/
public FloatColumn getWRFactorAll() {
return delegate.getColumn("wR_factor_all", DelegatingFloatColumn::new);
}
/**
* Weighted residual factor wR for reflections that satisfy the
* resolution limits established by _refine_ls_shell.d_res_high
* and _refine_ls_shell.d_res_low and the observation criterion
* established by _reflns.observed_criterion.
*
* ( sum|w |Y~obs~ - Y~calc~|^2^| )^1/2^
* wR = ( ---------------------------- )
* ( sum|w Y~obs~^2^| )
*
* Y~obs~ = the observed amplitude specified by
* _refine.ls_structure_factor_coef
* Y~calc~ = the calculated amplitude specified by
* _refine.ls_structure_factor_coef
* w = the least-squares weight
*
* sum is taken over the specified reflections
* @return FloatColumn
*/
public FloatColumn getWRFactorObs() {
return delegate.getColumn("wR_factor_obs", DelegatingFloatColumn::new);
}
/**
* Weighted residual factor wR for reflections that satisfy the
* resolution limits established by _refine_ls_shell.d_res_high
* and _refine_ls_shell.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|w |Y~obs~ - Y~calc~|^2^| )^1/2^
* wR = ( ---------------------------- )
* ( sum|w Y~obs~^2^| )
*
* Y~obs~ = the observed amplitude specified by
* _refine.ls_structure_factor_coef
* Y~calc~ = the calculated amplitude specified by
* _refine.ls_structure_factor_coef
* w = the least-squares weight
*
* sum is taken over the specified reflections
* @return FloatColumn
*/
public FloatColumn getWRFactorRFree() {
return delegate.getColumn("wR_factor_R_free", DelegatingFloatColumn::new);
}
/**
* Weighted residual factor wR for reflections that satisfy the
* resolution limits established by _refine_ls_shell.d_res_high
* and _refine_ls_shell.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|w |Y~obs~ - Y~calc~|^2^| )^1/2^
* wR = ( ---------------------------- )
* ( sum|w Y~obs~^2^| )
*
* Y~obs~ = the observed amplitude specified by
* _refine.ls_structure_factor_coef
* Y~calc~ = the calculated amplitude specified by
* _refine.ls_structure_factor_coef
* w = the least-squares weight
*
* sum is taken over the specified reflections
* @return FloatColumn
*/
public FloatColumn getWRFactorRWork() {
return delegate.getColumn("wR_factor_R_work", DelegatingFloatColumn::new);
}
/**
* The crystallographic reliability index Rcomplete for
* reflections that satisfy the resolution limits
* established by _refine_ls_shell.d_res_high and
* _refine_ls_shell.d_res_low and the observation limit
* established by _reflns.observed_criterion
*
* Ref: Luebben, J., Gruene, T., (2015). Proc.Nat.Acad.Sci. 112(29) 8999-9003
* @return FloatColumn
*/
public FloatColumn getPdbxRComplete() {
return delegate.getColumn("pdbx_R_complete", DelegatingFloatColumn::new);
}
/**
* Total number of bins used.
* @return IntColumn
*/
public IntColumn getPdbxTotalNumberOfBinsUsed() {
return delegate.getColumn("pdbx_total_number_of_bins_used", DelegatingIntColumn::new);
}
/**
* The average phase error for all reflections in the resolution shell.
* @return FloatColumn
*/
public FloatColumn getPdbxPhaseError() {
return delegate.getColumn("pdbx_phase_error", DelegatingFloatColumn::new);
}
/**
* Fourier Shell Correlation (FSC) between model and
* observed structure factors for reflections included in refinement.
*
* FSC is a measure of the agreement between observed
* and calculated structure factors as complex numbers.
*
* (sum(|F~o~| |F~c~| fom cos(phi~c~-phi~o~)))
* FSC~work~ = --------------------------------------
* (sum(|F~o~|^2^) (sum(|F~c~|^2^)))^1/2^
*
* |F~o~| = amplitude of observed structure factor
* |F~c~| = amplitude of calculated structure factor
* phi~o~ = phase of observed structure factor
* phi~c~ = phase of calculated structure factor
* fom = figure of merit of the experimental phases.
*
* Summation is carried over all working reflections in the resolution shell.
*
* Ref: Rosenthal P.B., Henderson R.
* "Optimal determination of particle orientation, absolute hand,
* and contrast loss in single-particle electron cryomicroscopy.
* Journal of Molecular Biology. 2003;333(4):721-745, equation (A6).
* @return FloatColumn
*/
public FloatColumn getPdbxFscWork() {
return delegate.getColumn("pdbx_fsc_work", DelegatingFloatColumn::new);
}
/**
* Fourier Shell Correlation (FSC) between model and
* observed structure factors for reflections not included in refinement.
*
* FSC is a measure of the agreement between observed
* and calculated structure factors as complex numbers.
*
* (sum(|F~o~| |F~c~| fom cos(phi~c~-phi~o~)))
* FSC~free~ = --------------------------------------
* (sum(|F~o~|^2^) (sum(|F~c~|^2^)))^1/2^
*
* |F~o~| = amplitude of observed structure factor
* |F~c~| = amplitude of calculated structure factor
* phi~o~ = phase of observed structure factor
* phi~c~ = phase of calculated structure factor
* fom = figure of merit of the experimental phases.
*
* Summation is carried over all free reflections in the resolution shell.
*
* Ref: Rosenthal P.B., Henderson R.
* "Optimal determination of particle orientation, absolute hand,
* and contrast loss in single-particle electron cryomicroscopy.
* Journal of Molecular Biology. 2003;333(4):721-745, equation (A6).
* @return FloatColumn
*/
public FloatColumn getPdbxFscFree() {
return delegate.getColumn("pdbx_fsc_free", DelegatingFloatColumn::new);
}
/**
* Residual factor R for reflections that satisfy the resolution
* limits established by _refine_ls_shell.d_res_high and
* _refine_ls_shell.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
* @return FloatColumn
*/
public FloatColumn getRFactorRFree() {
return delegate.getColumn("R_factor_R_free", DelegatingFloatColumn::new);
}
}
