Package org.rcsb.cif.schema.mm

Class StructMonNucl

java.lang.Object
org.rcsb.cif.schema.DelegatingCategory
org.rcsb.cif.schema.mm.StructMonNucl
All Implemented Interfaces:
Category
@Generated("org.rcsb.cif.schema.generator.SchemaGenerator")
public class StructMonNucl
extends DelegatingCategory
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.

  • Constructor Details

  • Method Details

    • createDelegate

      protected Column createDelegate​(String columnName, Column column)
      Overrides:
      createDelegate in class DelegatingCategory

    • 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