Package org.rcsb.cif.schema.mm

Class StructMonProt

java.lang.Object
org.rcsb.cif.schema.DelegatingCategory
org.rcsb.cif.schema.mm.StructMonProt
All Implemented Interfaces:
Category
@Generated("org.rcsb.cif.schema.generator.SchemaGenerator")
public class StructMonProt
extends DelegatingCategory
Data items in the STRUCT_MON_PROT category record details about structural properties of a protein when analyzed at the monomer level. Analogous data items for nucleic acids are given in the STRUCT_MON_NUCL 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

    • getChi1

      public FloatColumn getChi1()
      The value in degrees of the side-chain torsion angle chi1, for those residues containing such an angle.
      Returns:
      FloatColumn

    • getChi2

      public FloatColumn getChi2()
      The value in degrees of the side-chain torsion angle chi2, for those residues containing such an angle.
      Returns:
      FloatColumn

    • getChi3

      public FloatColumn getChi3()
      The value in degrees of the side-chain torsion angle chi3, for those residues containing such an angle.
      Returns:
      FloatColumn

    • getChi4

      public FloatColumn getChi4()
      The value in degrees of the side-chain torsion angle chi4, for those residues containing such an angle.
      Returns:
      FloatColumn

    • getChi5

      public FloatColumn getChi5()
      The value in degrees of the side-chain torsion angle chi5, for those residues containing such an angle.
      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

    • getLabelAltId

      public StrColumn getLabelAltId()
      A component of the identifier for the monomer. 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 the monomer. 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 the monomer. 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 the monomer. This data item is a pointer to _atom_site.label_seq_id in the ATOM_SITE category.
      Returns:
      IntColumn

    • getAuthAsymId

      public StrColumn getAuthAsymId()
      A component of the identifier for the monomer. 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 the monomer. 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 the monomer. This data item is a pointer to _atom_site.auth_seq_id in the ATOM_SITE category.
      Returns:
      StrColumn

    • getRSCCAll

      public FloatColumn getRSCCAll()
      The real-space (linear) correlation coefficient RSCC, as described by Jones et al. (1991), evaluated over all atoms in the 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

    • getRSCCMain

      public FloatColumn getRSCCMain()
      The real-space (linear) correlation coefficient RSCC, as described by Jones et al. (1991), evaluated over all atoms in the main chain of the 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

    • getRSCCSide

      public FloatColumn getRSCCSide()
      The real-space (linear) correlation coefficient RSCC, as described by Jones et al. (1991), evaluated over all atoms in the side chain of the 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 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

    • getRSRMain

      public FloatColumn getRSRMain()
      The real-space residual RSR, as described by Branden & Jones (1990), evaluated over all atoms in the main chain of the 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

    • getRSRSide

      public FloatColumn getRSRSide()
      The real-space residual RSR, as described by Branden & Jones (1990), evaluated over all atoms in the side chain of the 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

    • getMeanBAll

      public FloatColumn getMeanBAll()
      The mean value of the isotropic displacement parameter for all atoms in the monomer.
      Returns:
      FloatColumn

    • getMeanBMain

      public FloatColumn getMeanBMain()
      The mean value of the isotropic displacement parameter for atoms in the main chain of the monomer.
      Returns:
      FloatColumn

    • getMeanBSide

      public FloatColumn getMeanBSide()
      The mean value of the isotropic displacement parameter for atoms in the side chain of the monomer.
      Returns:
      FloatColumn

    • getOmega

      public FloatColumn getOmega()
      The value in degrees of the main-chain torsion angle omega.
      Returns:
      FloatColumn

    • getPhi

      public FloatColumn getPhi()
      The value in degrees of the main-chain torsion angle phi.
      Returns:
      FloatColumn

    • getPsi

      public FloatColumn getPsi()
      The value in degrees of the main-chain torsion angle psi.
      Returns:
      FloatColumn