java.lang.Object
- org.rcsb.cif.model.BaseCategory
- - org.rcsb.cif.model.generated.StructMonNucl

All Implemented Interfaces:

Category
```
@Generated("org.rcsb.cif.generator.SchemaGenerator")
public class StructMonNucl
extends BaseCategory
```
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.

Field Summary
- Fields inherited from class org.rcsb.cif.model.BaseCategory
  isText, textFields

Constructor Summary

Constructors
Constructor	Description
`StructMonNucl(String name)`
`StructMonNucl(String name, int rowCount, Object[] encodedColumns)`
`StructMonNucl(String name, Map<String,Column> columns)`

Method Summary

All Methods Instance Methods Concrete Methods
Modifier and Type	Method	Description
`FloatColumn`	`getAlpha()`	The value in degrees of the backbone torsion angle alpha (O3'-P-O5'-C5').
`StrColumn`	`getAuthAsymId()`	A component of the identifier for participants in the site.
`StrColumn`	`getAuthCompId()`	A component of the identifier for participants in the site.
`StrColumn`	`getAuthSeqId()`	A component of the identifier for participants in the site.
`FloatColumn`	`getBeta()`	The value in degrees of the backbone torsion angle beta (P-O5'-C5'-C4').
`FloatColumn`	`getChi1()`	The value in degrees of the sugar-base torsion angle chi1 (O4'-C1'-N1-C2).
`FloatColumn`	`getChi2()`	The value in degrees of the sugar-base torsion angle chi2 (O4'-C1'-N9-C4).
`FloatColumn`	`getDelta()`	The value in degrees of the backbone torsion angle delta (C5'-C4'-C3'-O3').
`FloatColumn`	`getDetails()`	A description of special aspects of the residue, its conformation, behaviour in refinement, or any other aspect that requires annotation.
`FloatColumn`	`getEpsilon()`	The value in degrees of the backbone torsion angle epsilon (C4'-C3'-O3'-P).
`FloatColumn`	`getGamma()`	The value in degrees of the backbone torsion angle gamma (O5'-C5'-C4'-C3').
`StrColumn`	`getLabelAltId()`	A component of the identifier for participants in the site.
`StrColumn`	`getLabelAsymId()`	A component of the identifier for participants in the site.
`StrColumn`	`getLabelCompId()`	A component of the identifier for participants in the site.
`IntColumn`	`getLabelSeqId()`	A component of the identifier for participants in the site.
`FloatColumn`	`getMeanBAll()`	The mean value of the isotropic displacement parameter for all atoms in the monomer.
`FloatColumn`	`getMeanBBase()`	The mean value of the isotropic displacement parameter for atoms in the base moiety of the nucleic acid monomer.
`FloatColumn`	`getMeanBPhos()`	The mean value of the isotropic displacement parameter for atoms in the phosphate moiety of the nucleic acid monomer.
`FloatColumn`	`getMeanBSugar()`	The mean value of the isotropic displacement parameter for atoms in the sugar moiety of the nucleic acid monomer.
`FloatColumn`	`getNu0()`	The value in degrees of the sugar torsion angle nu0 (C4'-O4'-C1'-C2').
`FloatColumn`	`getNu1()`	The value in degrees of the sugar torsion angle nu1 (O4'-C1'-C2'-C3').
`FloatColumn`	`getNu2()`	The value in degrees of the sugar torsion angle nu2 (C1'-C2'-C3'-C4').
`FloatColumn`	`getNu3()`	The value in degrees of the sugar torsion angle nu3 (C2'-C3'-C4'-O4').
`FloatColumn`	`getNu4()`	The value in degrees of the sugar torsion angle nu4 (C3'-C4'-O4'-C1').
`FloatColumn`	`getP()`	P is the phase angle of pseudorotation for five-membered rings.
`FloatColumn`	`getRSCCAll()`	The real-space (linear) correlation coefficient RSCC, as described by Jones et al.
`FloatColumn`	`getRSCCBase()`	The real-space (linear) correlation coefficient RSCC, as described by Jones et al.
`FloatColumn`	`getRSCCPhos()`	The real-space (linear) correlation coefficient RSCC, as described by Jones et al.
`FloatColumn`	`getRSCCSugar()`	The real-space (linear) correlation coefficient RSCC, as described by Jones et al.
`FloatColumn`	`getRSRAll()`	The real-space residual RSR, as described by Branden & Jones (1990), evaluated over all atoms in the nucleic acid monomer.
`FloatColumn`	`getRSRBase()`	The real-space residual RSR, as described by Branden & Jones (1990), evaluated over all atoms in the base moiety of the nucleic acid monomer.
`FloatColumn`	`getRSRPhos()`	The real-space residual RSR, as described by Branden & Jones (1990), evaluated over all atoms in the phosphate moiety of the nucleic acid monomer.
`FloatColumn`	`getRSRSugar()`	The real-space residual RSR, as described by Branden & Jones (1990), evaluated over all atoms in the sugar moiety of the nucleic acid monomer.
`FloatColumn`	`getTau0()`	The value in degrees of the sugar torsion angle tau0 (C4'-O4'-C1'-C2').
`FloatColumn`	`getTau1()`	The value in degrees of the sugar torsion angle tau1 (O4'-C1'-C2'-C3').
`FloatColumn`	`getTau2()`	The value in degrees of the sugar torsion angle tau2 (C1'-C2'-C3'-C4').
`FloatColumn`	`getTau3()`	The value in degrees of the sugar torsion angle tau3 (C2'-C3'-C4'-O4').
`FloatColumn`	`getTau4()`	The value in degrees of the sugar torsion angle tau4 (C3'-C4'-O4'-C1').
`FloatColumn`	`getTaum()`	The maximum amplitude of puckering.
`FloatColumn`	`getZeta()`	The value in degrees of the backbone torsion angle zeta (C3'-O3'-P-O5').

Methods inherited from class org.rcsb.cif.model.BaseCategory
getBinaryColumn, getCategoryName, getColumn, getColumnNames, getRowCount, isDefined

Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Methods inherited from interface org.rcsb.cif.model.Category
columnNames, columns, get

- Constructor Detail
  - StructMonNucl
```
public StructMonNucl(String name,
                     Map<String,Column> columns)
```
  - StructMonNucl
```
public StructMonNucl(String name,
                     int rowCount,
                     Object[] encodedColumns)
```
  - StructMonNucl
```
public StructMonNucl(String name)
```
- Method Detail
  - getAlpha
```
public FloatColumn getAlpha()
```
    The value in degrees of the backbone torsion angle alpha (O3'-P-O5'-C5').
    
    Returns:
    
    FloatColumn
  - getAuthAsymId
```
public StrColumn getAuthAsymId()
```
    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.
    
    Returns:
    
    StrColumn
  - getAuthCompId
```
public StrColumn getAuthCompId()
```
    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.
    
    Returns:
    
    StrColumn
  - getAuthSeqId
```
public StrColumn getAuthSeqId()
```
    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.
    
    Returns:
    
    StrColumn
  - getBeta
```
public FloatColumn getBeta()
```
    The value in degrees of the backbone torsion angle beta (P-O5'-C5'-C4').
    
    Returns:
    
    FloatColumn
  - getChi1
```
public FloatColumn getChi1()
```
    The value in degrees of the sugar-base torsion angle chi1 (O4'-C1'-N1-C2).
    
    Returns:
    
    FloatColumn
  - getChi2
```
public FloatColumn getChi2()
```
    The value in degrees of the sugar-base torsion angle chi2 (O4'-C1'-N9-C4).
    
    Returns:
    
    FloatColumn
  - getDelta
```
public FloatColumn getDelta()
```
    The value in degrees of the backbone torsion angle delta (C5'-C4'-C3'-O3').
    
    Returns:
    
    FloatColumn
  - getDetails
```
public FloatColumn getDetails()
```
    A description of special aspects of the residue, its conformation, behaviour in refinement, or any other aspect that requires annotation.
    
    Returns:
    
    FloatColumn
  - getEpsilon
```
public FloatColumn getEpsilon()
```
    The value in degrees of the backbone torsion angle epsilon (C4'-C3'-O3'-P).
    
    Returns:
    
    FloatColumn
  - getGamma
```
public FloatColumn getGamma()
```
    The value in degrees of the backbone torsion angle gamma (O5'-C5'-C4'-C3').
    
    Returns:
    
    FloatColumn
  - getLabelAltId
```
public StrColumn getLabelAltId()
```
    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.
    
    Returns:
    
    StrColumn
  - getLabelAsymId
```
public StrColumn getLabelAsymId()
```
    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.
    
    Returns:
    
    StrColumn
  - getLabelCompId
```
public StrColumn getLabelCompId()
```
    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.
    
    Returns:
    
    StrColumn
  - getLabelSeqId
```
public IntColumn getLabelSeqId()
```
    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.
    
    Returns:
    
    IntColumn
  - getMeanBAll
```
public FloatColumn getMeanBAll()
```
    The mean value of the isotropic displacement parameter for all atoms in the monomer.
    
    Returns:
    
    FloatColumn
  - getMeanBBase
```
public FloatColumn getMeanBBase()
```
    The mean value of the isotropic displacement parameter for atoms in the base moiety of the nucleic acid monomer.
    
    Returns:
    
    FloatColumn
  - getMeanBPhos
```
public FloatColumn getMeanBPhos()
```
    The mean value of the isotropic displacement parameter for atoms in the phosphate moiety of the nucleic acid monomer.
    
    Returns:
    
    FloatColumn
  - getMeanBSugar
```
public FloatColumn getMeanBSugar()
```
    The mean value of the isotropic displacement parameter for atoms in the sugar moiety of the nucleic acid monomer.
    
    Returns:
    
    FloatColumn
  - getNu0
```
public FloatColumn getNu0()
```
    The value in degrees of the sugar torsion angle nu0 (C4'-O4'-C1'-C2').
    
    Returns:
    
    FloatColumn
  - getNu1
```
public FloatColumn getNu1()
```
    The value in degrees of the sugar torsion angle nu1 (O4'-C1'-C2'-C3').
    
    Returns:
    
    FloatColumn
  - getNu2
```
public FloatColumn getNu2()
```
    The value in degrees of the sugar torsion angle nu2 (C1'-C2'-C3'-C4').
    
    Returns:
    
    FloatColumn
  - getNu3
```
public FloatColumn getNu3()
```
    The value in degrees of the sugar torsion angle nu3 (C2'-C3'-C4'-O4').
    
    Returns:
    
    FloatColumn
  - getNu4
```
public FloatColumn getNu4()
```
    The value in degrees of the sugar torsion angle nu4 (C3'-C4'-O4'-C1').
    
    Returns:
    
    FloatColumn
  - getP
```
public FloatColumn getP()
```
    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.
    
    Returns:
    
    FloatColumn
  - getRSCCAll
```
public FloatColumn getRSCCAll()
```
    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.
    
    Returns:
    
    FloatColumn
  - getRSCCBase
```
public FloatColumn getRSCCBase()
```
    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.
    
    Returns:
    
    FloatColumn
  - getRSCCPhos
```
public FloatColumn getRSCCPhos()
```
    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.
    
    Returns:
    
    FloatColumn
  - getRSCCSugar
```
public FloatColumn getRSCCSugar()
```
    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.
    
    Returns:
    
    FloatColumn
  - getRSRAll
```
public FloatColumn getRSRAll()
```
    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.
    
    Returns:
    
    FloatColumn
  - getRSRBase
```
public FloatColumn getRSRBase()
```
    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.
    
    Returns:
    
    FloatColumn
  - getRSRPhos
```
public FloatColumn getRSRPhos()
```
    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.
    
    Returns:
    
    FloatColumn
  - getRSRSugar
```
public FloatColumn getRSRSugar()
```
    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.
    
    Returns:
    
    FloatColumn
  - getTau0
```
public FloatColumn getTau0()
```
    The value in degrees of the sugar torsion angle tau0 (C4'-O4'-C1'-C2').
    
    Returns:
    
    FloatColumn
  - getTau1
```
public FloatColumn getTau1()
```
    The value in degrees of the sugar torsion angle tau1 (O4'-C1'-C2'-C3').
    
    Returns:
    
    FloatColumn
  - getTau2
```
public FloatColumn getTau2()
```
    The value in degrees of the sugar torsion angle tau2 (C1'-C2'-C3'-C4').
    
    Returns:
    
    FloatColumn
  - getTau3
```
public FloatColumn getTau3()
```
    The value in degrees of the sugar torsion angle tau3 (C2'-C3'-C4'-O4').
    
    Returns:
    
    FloatColumn
  - getTau4
```
public FloatColumn getTau4()
```
    The value in degrees of the sugar torsion angle tau4 (C3'-C4'-O4'-C1').
    
    Returns:
    
    FloatColumn
  - getTaum
```
public FloatColumn getTaum()
```
    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)
    
    Returns:
    
    FloatColumn
  - getZeta
```
public FloatColumn getZeta()
```
    The value in degrees of the backbone torsion angle zeta (C3'-O3'-P-O5').
    
    Returns:
    
    FloatColumn

Class StructMonNucl

Field Summary

Fields inherited from class org.rcsb.cif.model.BaseCategory

Constructor Summary

Method Summary

Methods inherited from class org.rcsb.cif.model.BaseCategory

Methods inherited from class java.lang.Object

Methods inherited from interface org.rcsb.cif.model.Category

Constructor Detail

StructMonNucl

StructMonNucl

StructMonNucl

Method Detail

getAlpha

getAuthAsymId

getAuthCompId

getAuthSeqId

getBeta

getChi1

getChi2

getDelta

getDetails

getEpsilon

getGamma

getLabelAltId

getLabelAsymId

getLabelCompId

getLabelSeqId

getMeanBAll

getMeanBBase

getMeanBPhos

getMeanBSugar

getNu0

getNu1

getNu2

getNu3

getNu4

getP

getRSCCAll

getRSCCBase

getRSCCPhos

getRSCCSugar

getRSRAll

getRSRBase

getRSRPhos

getRSRSugar

getTau0

getTau1

getTau2

getTau3

getTau4

getTaum

getZeta