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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 STRUCT_MON_NUCL category record details about
* structural properties of a nucleic acid when analyzed at the
* monomer level. Analogous data items for proteins are given in
* the STRUCT_MON_PROT category. For items where the value of the
* property depends on the method employed to calculate it,
* details of the method of calculation are given using data items
* in the STRUCT_MON_DETAILS category.
*/
@Generated("org.rcsb.cif.schema.generator.SchemaGenerator")
public class StructMonNucl extends DelegatingCategory {
public StructMonNucl(Category delegate) {
super(delegate);
}
@Override
protected Column createDelegate(String columnName, Column column) {
switch (columnName) {
case "alpha":
return getAlpha();
case "auth_asym_id":
return getAuthAsymId();
case "auth_comp_id":
return getAuthCompId();
case "auth_seq_id":
return getAuthSeqId();
case "beta":
return getBeta();
case "chi1":
return getChi1();
case "chi2":
return getChi2();
case "delta":
return getDelta();
case "details":
return getDetails();
case "epsilon":
return getEpsilon();
case "gamma":
return getGamma();
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 "mean_B_all":
return getMeanBAll();
case "mean_B_base":
return getMeanBBase();
case "mean_B_phos":
return getMeanBPhos();
case "mean_B_sugar":
return getMeanBSugar();
case "nu0":
return getNu0();
case "nu1":
return getNu1();
case "nu2":
return getNu2();
case "nu3":
return getNu3();
case "nu4":
return getNu4();
case "P":
return getP();
case "RSCC_all":
return getRSCCAll();
case "RSCC_base":
return getRSCCBase();
case "RSCC_phos":
return getRSCCPhos();
case "RSCC_sugar":
return getRSCCSugar();
case "RSR_all":
return getRSRAll();
case "RSR_base":
return getRSRBase();
case "RSR_phos":
return getRSRPhos();
case "RSR_sugar":
return getRSRSugar();
case "tau0":
return getTau0();
case "tau1":
return getTau1();
case "tau2":
return getTau2();
case "tau3":
return getTau3();
case "tau4":
return getTau4();
case "taum":
return getTaum();
case "zeta":
return getZeta();
default:
return new DelegatingColumn(column);
}
}
/**
* The value in degrees of the backbone torsion angle alpha
* (O3'-P-O5'-C5').
* @return FloatColumn
*/
public FloatColumn getAlpha() {
return delegate.getColumn("alpha", DelegatingFloatColumn::new);
}
/**
* A component of the identifier for participants in the site.
*
* 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 participants in the site.
*
* 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 participants in the site.
*
* 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);
}
/**
* The value in degrees of the backbone torsion angle beta
* (P-O5'-C5'-C4').
* @return FloatColumn
*/
public FloatColumn getBeta() {
return delegate.getColumn("beta", DelegatingFloatColumn::new);
}
/**
* The value in degrees of the sugar-base torsion angle chi1
* (O4'-C1'-N1-C2).
* @return FloatColumn
*/
public FloatColumn getChi1() {
return delegate.getColumn("chi1", DelegatingFloatColumn::new);
}
/**
* The value in degrees of the sugar-base torsion angle chi2
* (O4'-C1'-N9-C4).
* @return FloatColumn
*/
public FloatColumn getChi2() {
return delegate.getColumn("chi2", DelegatingFloatColumn::new);
}
/**
* The value in degrees of the backbone torsion angle delta
* (C5'-C4'-C3'-O3').
* @return FloatColumn
*/
public FloatColumn getDelta() {
return delegate.getColumn("delta", DelegatingFloatColumn::new);
}
/**
* A description of special aspects of the residue, its
* conformation, behaviour in refinement, or any other aspect
* that requires annotation.
* @return FloatColumn
*/
public FloatColumn getDetails() {
return delegate.getColumn("details", DelegatingFloatColumn::new);
}
/**
* The value in degrees of the backbone torsion angle epsilon
* (C4'-C3'-O3'-P).
* @return FloatColumn
*/
public FloatColumn getEpsilon() {
return delegate.getColumn("epsilon", DelegatingFloatColumn::new);
}
/**
* The value in degrees of the backbone torsion angle gamma
* (O5'-C5'-C4'-C3').
* @return FloatColumn
*/
public FloatColumn getGamma() {
return delegate.getColumn("gamma", DelegatingFloatColumn::new);
}
/**
* A component of the identifier for participants in the site.
*
* 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 participants in the site.
*
* 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 participants in the site.
*
* 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 participants in the site.
*
* 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);
}
/**
* The mean value of the isotropic displacement parameter
* for all atoms in the monomer.
* @return FloatColumn
*/
public FloatColumn getMeanBAll() {
return delegate.getColumn("mean_B_all", DelegatingFloatColumn::new);
}
/**
* The mean value of the isotropic displacement parameter
* for atoms in the base moiety of the nucleic acid monomer.
* @return FloatColumn
*/
public FloatColumn getMeanBBase() {
return delegate.getColumn("mean_B_base", DelegatingFloatColumn::new);
}
/**
* The mean value of the isotropic displacement parameter
* for atoms in the phosphate moiety of the nucleic acid monomer.
* @return FloatColumn
*/
public FloatColumn getMeanBPhos() {
return delegate.getColumn("mean_B_phos", DelegatingFloatColumn::new);
}
/**
* The mean value of the isotropic displacement parameter
* for atoms in the sugar moiety of the nucleic acid monomer.
* @return FloatColumn
*/
public FloatColumn getMeanBSugar() {
return delegate.getColumn("mean_B_sugar", DelegatingFloatColumn::new);
}
/**
* The value in degrees of the sugar torsion angle nu0
* (C4'-O4'-C1'-C2').
* @return FloatColumn
*/
public FloatColumn getNu0() {
return delegate.getColumn("nu0", DelegatingFloatColumn::new);
}
/**
* The value in degrees of the sugar torsion angle nu1
* (O4'-C1'-C2'-C3').
* @return FloatColumn
*/
public FloatColumn getNu1() {
return delegate.getColumn("nu1", DelegatingFloatColumn::new);
}
/**
* The value in degrees of the sugar torsion angle nu2
* (C1'-C2'-C3'-C4').
* @return FloatColumn
*/
public FloatColumn getNu2() {
return delegate.getColumn("nu2", DelegatingFloatColumn::new);
}
/**
* The value in degrees of the sugar torsion angle nu3
* (C2'-C3'-C4'-O4').
* @return FloatColumn
*/
public FloatColumn getNu3() {
return delegate.getColumn("nu3", DelegatingFloatColumn::new);
}
/**
* The value in degrees of the sugar torsion angle nu4
* (C3'-C4'-O4'-C1').
* @return FloatColumn
*/
public FloatColumn getNu4() {
return delegate.getColumn("nu4", DelegatingFloatColumn::new);
}
/**
* P is the phase angle of pseudorotation for five-membered rings.
* For ribose and deoxyribose sugars in nucleic
* acids
* (tau4 +tau1)-(tau3+tau0)
* P = ATAN (-------------------------)
* 2tau2 (sin 36+sin 72)
*
* If tau2 is <0, then P=P+180 degree (Altona & Sundaralingam,
* 1972).
*
* Ref: Altona, C. & Sundaralingam, M. (1972).
* J. Am. Chem. Soc. 94, 8205-8212.
* @return FloatColumn
*/
public FloatColumn getP() {
return delegate.getColumn("P", DelegatingFloatColumn::new);
}
/**
* The real-space (linear) correlation coefficient RSCC, as
* described by Jones et al. (1991), evaluated over all atoms in the
* nucleic acid monomer.
*
* sum|p~obs~ - <p~obs~>| * sum|p~calc~ - <p~calc~>|
* RSCC = -------------------------------------------------
* [ sum|p~obs~ - <p~obs~> |^2^
* * sum|p~calc~ - <p~calc~>|^2^ ]^1/2^
*
* p~obs~ = the density in an 'experimental' map
* p~calc~ = the density in a 'calculated' map
*
* sum is taken over the specified grid points
*
* Details of how these maps were calculated should be given
* in _struct_mon_details.RSCC. < > indicates an average and the
* sums are taken over all map grid points near the relevant atoms.
* The radius for including grid points in the calculation should
* also be given in _struct_mon_details.RSCC.
*
* Ref: Jones, T. A., Zou, J.-Y., Cowan, S. W. & Kjeldgaard, M.
* (1991). Acta Cryst. A47, 110-119.
* @return FloatColumn
*/
public FloatColumn getRSCCAll() {
return delegate.getColumn("RSCC_all", DelegatingFloatColumn::new);
}
/**
* The real-space (linear) correlation coefficient RSCC, as
* described by Jones et al. (1991), evaluated over all atoms in the
* base moiety of the nucleic acid monomer.
*
* sum|p~obs~ - <p~obs~>| * sum|p~calc~ - <p~calc~>|
* RSCC = -------------------------------------------------
* [ sum|p~obs~ - <p~obs~> |^2^
* * sum|p~calc~ - <p~calc~>|^2^ ]^1/2^
*
* p~obs~ = the density in an 'experimental' map
* p~calc~ = the density in a 'calculated' map
*
* sum is taken over the specified grid points
*
* Details of how these maps were calculated should be given
* in _struct_mon_details.RSCC. < > indicates an average and the
* sums are taken over all map grid points near the relevant atoms.
* The radius for including grid points in the calculation should
* also be given in _struct_mon_details.RSCC.
*
* Ref: Jones, T. A., Zou, J.-Y., Cowan, S. W. & Kjeldgaard, M.
* (1991). Acta Cryst. A47, 110-119.
* @return FloatColumn
*/
public FloatColumn getRSCCBase() {
return delegate.getColumn("RSCC_base", DelegatingFloatColumn::new);
}
/**
* The real-space (linear) correlation coefficient RSCC, as
* described by Jones et al. (1991), evaluated over all atoms in the
* phosphate moiety of the nucleic acid monomer.
*
* sum|p~obs~ - <p~obs~>| * sum|p~calc~ - <p~calc~>|
* RSCC = -------------------------------------------------
* [ sum|p~obs~ - <p~obs~> |^2^
* * sum|p~calc~ - <p~calc~>|^2^ ]^1/2^
*
* p~obs~ = the density in an 'experimental' map
* p~calc~ = the density in a 'calculated' map
*
* sum is taken over the specified grid points
*
* Details of how these maps were calculated should be given
* in _struct_mon_details.RSCC. < > indicates an average and the
* sums are taken over all map grid points near the relevant atoms.
* The radius for including grid points in the calculation should
* also be given in _struct_mon_details.RSCC.
*
* Ref: Jones, T. A., Zou, J.-Y., Cowan, S. W. & Kjeldgaard, M.
* (1991). Acta Cryst. A47, 110-119.
* @return FloatColumn
*/
public FloatColumn getRSCCPhos() {
return delegate.getColumn("RSCC_phos", DelegatingFloatColumn::new);
}
/**
* The real-space (linear) correlation coefficient RSCC, as
* described by Jones et al. (1991), evaluated over all atoms in the
* sugar moiety of the nucleic acid monomer.
*
* sum|p~obs~ - <p~obs~>| * sum|p~calc~ - <p~calc~>|
* RSCC = -------------------------------------------------
* [ sum|p~obs~ - <p~obs~> |^2^
* * sum|p~calc~ - <p~calc~>|^2^ ]^1/2^
*
* p~obs~ = the density in an 'experimental' map
* p~calc~ = the density in a 'calculated' map
*
* sum is taken over the specified grid points
*
* Details of how these maps were calculated should be given
* in _struct_mon_details.RSCC. < > indicates an average and the
* sums are taken over all map grid points near the relevant atoms.
* The radius for including grid points in the calculation should
* also be given in _struct_mon_details.RSCC.
*
* Ref: Jones, T. A., Zou, J.-Y., Cowan, S. W. & Kjeldgaard, M.
* (1991). Acta Cryst. A47, 110-119.
* @return FloatColumn
*/
public FloatColumn getRSCCSugar() {
return delegate.getColumn("RSCC_sugar", DelegatingFloatColumn::new);
}
/**
* The real-space residual RSR, as described by Branden & Jones
* (1990), evaluated over all atoms in the nucleic acid monomer.
*
* sum|p~obs~ - p~calc~|
* RSR = ---------------------
* sum|p~obs~ + p~calc~|
*
* p~obs~ = the density in an 'experimental' map
* p~calc~ = the density in a 'calculated' map
*
* sum is taken over the specified grid points
*
* Details of how these maps were calculated should be given
* in _struct_mon_details.RSR. The sums are taken over all map grid
* points near the relevant atoms. The radius for including grid
* points in the calculation should also be given in
* _struct_mon_details.RSR.
*
* Ref: Branden, C.-I. & Jones, T. A. (1990). Nature (London), 343,
* 687-689.
* @return FloatColumn
*/
public FloatColumn getRSRAll() {
return delegate.getColumn("RSR_all", DelegatingFloatColumn::new);
}
/**
* The real-space residual RSR, as described by Branden & Jones
* (1990), evaluated over all atoms in the base moiety of the
* nucleic acid monomer.
*
* sum|p~obs~ - p~calc~|
* RSR = ---------------------
* sum|p~obs~ + p~calc~|
*
* p~obs~ = the density in an 'experimental' map
* p~calc~ = the density in a 'calculated' map
*
* sum is taken over the specified grid points
*
* Details of how these maps were calculated should be given
* in _struct_mon_details.RSR. The sums are taken over all map grid
* points near the relevant atoms. The radius for including grid
* points in the calculation should also be given in
* _struct_mon_details.RSR.
*
* Ref: Branden, C.-I. & Jones, T. A. (1990). Nature (London), 343,
* 687-689.
* @return FloatColumn
*/
public FloatColumn getRSRBase() {
return delegate.getColumn("RSR_base", DelegatingFloatColumn::new);
}
/**
* The real-space residual RSR, as described by Branden & Jones
* (1990), evaluated over all atoms in the phosphate moiety of the
* nucleic acid monomer.
*
* sum|p~obs~ - p~calc~|
* RSR = ---------------------
* sum|p~obs~ + p~calc~|
*
* p~obs~ = the density in an 'experimental' map
* p~calc~ = the density in a 'calculated' map
*
* sum is taken over the specified grid points
*
* Details of how these maps were calculated should be given
* in _struct_mon_details.RSR. The sums are taken over all map grid
* points near the relevant atoms. The radius for including grid
* points in the calculation should also be given in
* _struct_mon_details.RSR.
*
* Ref: Branden, C.-I. & Jones, T. A. (1990). Nature (London), 343,
* 687-689.
* @return FloatColumn
*/
public FloatColumn getRSRPhos() {
return delegate.getColumn("RSR_phos", DelegatingFloatColumn::new);
}
/**
* The real-space residual RSR, as described by Branden & Jones
* (1990), evaluated over all atoms in the sugar moiety of the
* nucleic acid monomer.
*
* sum|p~obs~ - p~calc~|
* RSR = ---------------------
* sum|p~obs~ + p~calc~|
*
* p~obs~ = the density in an 'experimental' map
* p~calc~ = the density in a 'calculated' map
*
* sum is taken over the specified grid points
*
* Details of how these maps were calculated should be given
* in _struct_mon_details.RSR. The sums are taken over all map grid
* points near the relevant atoms. The radius for including grid
* points in the calculation should also be given in
* _struct_mon_details.RSR.
*
* Ref: Branden, C.-I. & Jones, T. A. (1990). Nature (London), 343,
* 687-689.
* @return FloatColumn
*/
public FloatColumn getRSRSugar() {
return delegate.getColumn("RSR_sugar", DelegatingFloatColumn::new);
}
/**
* The value in degrees of the sugar torsion angle tau0
* (C4'-O4'-C1'-C2').
* @return FloatColumn
*/
public FloatColumn getTau0() {
return delegate.getColumn("tau0", DelegatingFloatColumn::new);
}
/**
* The value in degrees of the sugar torsion angle tau1
* (O4'-C1'-C2'-C3').
* @return FloatColumn
*/
public FloatColumn getTau1() {
return delegate.getColumn("tau1", DelegatingFloatColumn::new);
}
/**
* The value in degrees of the sugar torsion angle tau2
* (C1'-C2'-C3'-C4').
* @return FloatColumn
*/
public FloatColumn getTau2() {
return delegate.getColumn("tau2", DelegatingFloatColumn::new);
}
/**
* The value in degrees of the sugar torsion angle tau3
* (C2'-C3'-C4'-O4').
* @return FloatColumn
*/
public FloatColumn getTau3() {
return delegate.getColumn("tau3", DelegatingFloatColumn::new);
}
/**
* The value in degrees of the sugar torsion angle tau4
* (C3'-C4'-O4'-C1').
* @return FloatColumn
*/
public FloatColumn getTau4() {
return delegate.getColumn("tau4", DelegatingFloatColumn::new);
}
/**
* The maximum amplitude of puckering. This is derived from the
* pseudorotation value P and the torsion angles in the ribose
* ring.
*
* Tau2= Taum cosP
* Tau3= Taum cos(P+144)
* Tau4= Taum cos(P+288)
* Tau0= Taum cos(P+ 72)
* Tau1= Taum cos(P+216)
* @return FloatColumn
*/
public FloatColumn getTaum() {
return delegate.getColumn("taum", DelegatingFloatColumn::new);
}
/**
* The value in degrees of the backbone torsion angle zeta
* (C3'-O3'-P-O5').
* @return FloatColumn
*/
public FloatColumn getZeta() {
return delegate.getColumn("zeta", DelegatingFloatColumn::new);
}
}
