Many resources are needed to download a project. Please understand that we have to compensate our server costs. Thank you in advance. Project price only 1 $
You can buy this project and download/modify it how often you want.
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_ANALYZE category record details
* about the refined structure that are often used to analyze the
* refinement and assess its quality. A given computer program
* may or may not produce values corresponding to these data
* names.
*/
@Generated("org.rcsb.cif.schema.generator.SchemaGenerator")
public class RefineAnalyze extends DelegatingCategory {
public RefineAnalyze(Category delegate) {
super(delegate);
}
@Override
protected Column createDelegate(String columnName, Column column) {
switch (columnName) {
case "entry_id":
return getEntryId();
case "pdbx_refine_id":
return getPdbxRefineId();
case "Luzzati_coordinate_error_free":
return getLuzzatiCoordinateErrorFree();
case "Luzzati_coordinate_error_obs":
return getLuzzatiCoordinateErrorObs();
case "Luzzati_d_res_low_free":
return getLuzzatiDResLowFree();
case "Luzzati_d_res_low_obs":
return getLuzzatiDResLowObs();
case "Luzzati_sigma_a_free":
return getLuzzatiSigmaAFree();
case "Luzzati_sigma_a_free_details":
return getLuzzatiSigmaAFreeDetails();
case "Luzzati_sigma_a_obs":
return getLuzzatiSigmaAObs();
case "Luzzati_sigma_a_obs_details":
return getLuzzatiSigmaAObsDetails();
case "number_disordered_residues":
return getNumberDisorderedResidues();
case "occupancy_sum_hydrogen":
return getOccupancySumHydrogen();
case "occupancy_sum_non_hydrogen":
return getOccupancySumNonHydrogen();
case "RG_d_res_high":
return getRGDResHigh();
case "RG_d_res_low":
return getRGDResLow();
case "RG_free":
return getRGFree();
case "RG_work":
return getRGWork();
case "RG_free_work_ratio":
return getRGFreeWorkRatio();
case "pdbx_Luzzati_d_res_high_obs":
return getPdbxLuzzatiDResHighObs();
default:
return new DelegatingColumn(column);
}
}
/**
* This data item is a pointer to _entry.id in the ENTRY category.
* @return StrColumn
*/
public StrColumn getEntryId() {
return delegate.getColumn("entry_id", DelegatingStrColumn::new);
}
/**
* This data item uniquely identifies a refinement within an entry.
* _refine_analyze.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 estimated coordinate error obtained from the plot of
* the R value versus sin(theta)/lambda for the reflections
* treated as a test set during refinement.
*
* Ref: Luzzati, V. (1952). Traitement statistique des erreurs
* dans la determination des structures cristallines. Acta
* Cryst. 5, 802-810.
* @return FloatColumn
*/
public FloatColumn getLuzzatiCoordinateErrorFree() {
return delegate.getColumn("Luzzati_coordinate_error_free", DelegatingFloatColumn::new);
}
/**
* The estimated coordinate error obtained from the plot of
* the R value versus sin(theta)/lambda for reflections classified
* as observed.
*
* Ref: Luzzati, V. (1952). Traitement statistique des erreurs
* dans la determination des structures cristallines. Acta
* Cryst. 5, 802-810.
* @return FloatColumn
*/
public FloatColumn getLuzzatiCoordinateErrorObs() {
return delegate.getColumn("Luzzati_coordinate_error_obs", DelegatingFloatColumn::new);
}
/**
* The value of the low-resolution cutoff used in constructing the
* Luzzati plot for reflections treated as a test set during
* refinement.
*
* Ref: Luzzati, V. (1952). Traitement statistique des erreurs
* dans la determination des structures cristallines. Acta
* Cryst. 5, 802-810.
* @return FloatColumn
*/
public FloatColumn getLuzzatiDResLowFree() {
return delegate.getColumn("Luzzati_d_res_low_free", DelegatingFloatColumn::new);
}
/**
* The value of the low-resolution cutoff used in
* constructing the Luzzati plot for reflections classified as
* observed.
*
* Ref: Luzzati, V. (1952). Traitement statistique des erreurs
* dans la determination des structures cristallines. Acta
* Cryst. 5, 802-810.
* @return FloatColumn
*/
public FloatColumn getLuzzatiDResLowObs() {
return delegate.getColumn("Luzzati_d_res_low_obs", DelegatingFloatColumn::new);
}
/**
* The value of sigma~a~ used in constructing the Luzzati plot for
* the reflections treated as a test set during refinement.
* Details of the estimation of sigma~a~ can be specified
* in _refine_analyze.Luzzati_sigma_a_free_details.
*
* Ref: Luzzati, V. (1952). Traitement statistique des erreurs
* dans la determination des structures cristallines. Acta
* Cryst. 5, 802-810.
* @return FloatColumn
*/
public FloatColumn getLuzzatiSigmaAFree() {
return delegate.getColumn("Luzzati_sigma_a_free", DelegatingFloatColumn::new);
}
/**
* Details of the estimation of sigma~a~ for the reflections
* treated as a test set during refinement.
*
* Ref: Luzzati, V. (1952). Traitement statistique des erreurs
* dans la determination des structures cristallines. Acta
* Cryst. 5, 802-810.
* @return StrColumn
*/
public StrColumn getLuzzatiSigmaAFreeDetails() {
return delegate.getColumn("Luzzati_sigma_a_free_details", DelegatingStrColumn::new);
}
/**
* The value of sigma~a~ used in constructing the Luzzati plot for
* reflections classified as observed. Details of the
* estimation of sigma~a~ can be specified in
* _refine_analyze.Luzzati_sigma_a_obs_details.
*
* Ref: Luzzati, V. (1952). Traitement statistique des erreurs
* dans la determination des structures cristallines. Acta
* Cryst. 5, 802-810.
* @return FloatColumn
*/
public FloatColumn getLuzzatiSigmaAObs() {
return delegate.getColumn("Luzzati_sigma_a_obs", DelegatingFloatColumn::new);
}
/**
* Special aspects of the estimation of sigma~a~ for the
* reflections classified as observed.
*
* Ref: Luzzati, V. (1952). Traitement statistique des erreurs
* dans la determination des structures cristallines. Acta
* Cryst. 5, 802-810.
* @return StrColumn
*/
public StrColumn getLuzzatiSigmaAObsDetails() {
return delegate.getColumn("Luzzati_sigma_a_obs_details", DelegatingStrColumn::new);
}
/**
* The number of discretely disordered residues in the refined
* model.
* @return FloatColumn
*/
public FloatColumn getNumberDisorderedResidues() {
return delegate.getColumn("number_disordered_residues", DelegatingFloatColumn::new);
}
/**
* The sum of the occupancies of the hydrogen atoms in the refined
* model.
* @return FloatColumn
*/
public FloatColumn getOccupancySumHydrogen() {
return delegate.getColumn("occupancy_sum_hydrogen", DelegatingFloatColumn::new);
}
/**
* The sum of the occupancies of the non-hydrogen atoms in the
* refined model.
* @return FloatColumn
*/
public FloatColumn getOccupancySumNonHydrogen() {
return delegate.getColumn("occupancy_sum_non_hydrogen", DelegatingFloatColumn::new);
}
/**
* The value of the high-resolution cutoff in angstroms
* used in the calculation of the Hamilton generalized
* R factor (RG) stored in _refine_analyze.RG_work and
* _refine_analyze.RG_free.
*
* Ref: Hamilton, W. C. (1965). Acta Cryst. 18, 502-510.
* @return FloatColumn
*/
public FloatColumn getRGDResHigh() {
return delegate.getColumn("RG_d_res_high", DelegatingFloatColumn::new);
}
/**
* The value of the low-resolution cutoff in angstroms
* used in the calculation of the Hamilton generalized
* R factor (RG) stored in _refine_analyze.RG_work and
* _refine_analyze.RG_free.
*
* Ref: Hamilton, W. C. (1965). Acta Cryst. 18, 502-510.
* @return FloatColumn
*/
public FloatColumn getRGDResLow() {
return delegate.getColumn("RG_d_res_low", DelegatingFloatColumn::new);
}
/**
* The Hamilton generalized R factor for all reflections that
* satisfy the resolution limits established by
* _refine_analyze.RG_d_res_high and
* _refine_analyze.RG_d_res_low for the free R set of
* reflections that were excluded from the refinement.
*
* sum_i sum_j w_{i,j}(|Fobs|_i - G|Fcalc|_i)(|Fobs|_j - G|Fcalc|_j)
* RG = Sqrt( ----------------------------------------------------------------- )
* sum_i sum_j w_{i,j} |Fobs|_i |Fobs|_j
*
* where
*
* |Fobs| = the observed structure-factor amplitudes
* |Fcalc| = the calculated structure-factor amplitudes
* G = the scale factor which puts |Fcalc| on the
* same scale as |Fobs|
* w_{i,j} = the weight for the combination of the reflections
* i and j.
*
* sum_i and sum_j are taken over the specified reflections
*
* When the covariance of the amplitudes of reflection i and
* reflection j is zero (i.e. the reflections are independent)
* w{i,i} can be redefined as w_i and the nested sums collapsed
* into one sum.
*
* sum_i w_i(|Fobs|_i - G|Fcalc|_i)^2
* RG = Sqrt( ----------------------------------- )
* sum_i w_i |Fobs|_i^2
*
* Ref: Hamilton, W. C. (1965). Acta Cryst. 18, 502-510.
* @return FloatColumn
*/
public FloatColumn getRGFree() {
return delegate.getColumn("RG_free", DelegatingFloatColumn::new);
}
/**
* The Hamilton generalized R factor for all reflections
* that satisfy the resolution limits established by
* _refine_analyze.RG_d_res_high and
* _refine_analyze.RG_d_res_low and for those
* reflections included in the working set when a free R set
* of reflections is omitted from the refinement.
*
* sum_i sum_j w_{i,j}(|Fobs|_i - G|Fcalc|_i)(|Fobs|_j - G|Fcalc|_j)
* RG = Sqrt( ----------------------------------------------------------------- )
* sum_i sum_j w_{i,j} |Fobs|_i |Fobs|_j
*
* where
*
* |Fobs| = the observed structure-factor amplitudes
* |Fcalc| = the calculated structure-factor amplitudes
* G = the scale factor which puts |Fcalc| on the
* same scale as |Fobs|
* w_{i,j} = the weight for the combination of the reflections
* i and j.
*
* sum_i and sum_j are taken over the specified reflections
*
* When the covariance of the amplitudes of reflection i and
* reflection j is zero (i.e. the reflections are independent)
* w{i,i} can be redefined as w_i and the nested sums collapsed
* into one sum.
*
* sum_i w_i(|Fobs|_i - G|Fcalc|_i)^2
* RG = Sqrt( ----------------------------------- )
* sum_i w_i |Fobs|_i^2
*
* Ref: Hamilton, W. C. (1965). Acta Cryst. 18, 502-510.
* @return FloatColumn
*/
public FloatColumn getRGWork() {
return delegate.getColumn("RG_work", DelegatingFloatColumn::new);
}
/**
* The observed ratio of RGfree to RGwork. The expected RG ratio
* is the value that should be achievable at the end of a structure
* refinement when only random uncorrelated errors exist in the data
* and the model provided that the observations are properly
* weighted. When compared with the observed RG ratio it may
* indicate that a structure has not reached convergence or a
* model has been over-refined with no corresponding improvement
* in the model.
*
* In an unrestrained refinement, the ratio of RGfree to RGwork with
* only random uncorrelated errors at convergence depends only
* on the number of reflections and the number of parameters
* according to
*
* sqrt[(f + m) / (f - m) ]
*
* where f = the number of included structure amplitudes and
* target distances, and
* m = the number of parameters being refined.
*
* In the restrained case, RGfree is calculated from a random
* selection of residuals including both structure amplitudes
* and restraints. When restraints are included in the refinement,
* the RG ratio requires a term for the contribution to the
* minimized residual at convergence, D~restr~, due to those
* restraints:
*
* D~restr~ = r - sum [w_i . (a_i)^t . (H)^-1 a_i]
*
* where
*
* r is the number of geometrical, displacement-parameter and
* other restraints
* H is the (m,m) normal matrix given by A^t.W.A
* W is the (n,n) symmetric weight matrix of the included
* observations
* A is the least-squares design matrix of derivatives of
* order (n,m)
* a_i is the ith row of A
*
* Then the expected RGratio becomes
*
* sqrt [ (f + (m - r + D~restr~))/ (f - (m - r + D~restr~)) ]
*
* There is no data name for the expected value of RGfree/RGwork yet.
*
* Ref: Tickle, I. J., Laskowski, R. A. & Moss, D. S. (1998).
* Acta Cryst. D54, 547-557.
* @return FloatColumn
*/
public FloatColumn getRGFreeWorkRatio() {
return delegate.getColumn("RG_free_work_ratio", DelegatingFloatColumn::new);
}
/**
* record the high resolution for calculating Luzzati statistics.
* @return FloatColumn
*/
public FloatColumn getPdbxLuzzatiDResHighObs() {
return delegate.getColumn("pdbx_Luzzati_d_res_high_obs", DelegatingFloatColumn::new);
}
}
