meshi.molecularElements.extendedAtoms
Class BackboneResidue

java.lang.Object
  meshi.molecularElements.Residue
      meshi.molecularElements.extendedAtoms.ResidueExtendedAtoms
          meshi.molecularElements.extendedAtoms.BackboneResidue

All Implemented Interfaces:

java.lang.Comparable, ResidueCreator, MeshiPotential, Attributable, MeshiAttribute

public class BackboneResidue
extends ResidueExtendedAtoms
implements ResidueCreator

 Alanin from Levitt, JMB 168:592 (1983) table 2.
           CB  O
           |   |
      N - CA - C...n
      |
      H









Field Summary




static java.lang.String
COMMENT



           



static BackboneResidue
creator



           


 
Fields inherited from class meshi.molecularElements.extendedAtoms.ResidueExtendedAtoms
C, CA, CB, H, N, O, OXT
 
Fields inherited from class meshi.molecularElements.Residue
atoms, bonds, head, mode, name, nextAtom, prevAtom, tail, type
 
Fields inherited from interface meshi.parameters.MeshiPotential
ACCESSIBLE, ALPHA_ANGLE_PARAMETERS, ALPHA_TORSION_PARAMETERS, ANGLE_PARAMETERS, ATOMIC_PAIRWISE_PMF_SUMMA_PARAMETERS, BOND_PARAMETERS, BURIED, COIL, COMPOSITE_PROPENSITY_2D_PARAMETERS, COMPOSITE_PROPENSITY_2D_WITH_PP_PARAMETERS, COMPOSITE_PROPENSITY_PARAMETERS, COMPOSITE_TORSIONS_PARAMETERS, CONTACTS_ENVIRONMENT_PARAMETERS, CONTACTS_PARAMETERS, COOPERATIVE_ATOMIC_PAIRWISE_PMF_SUMMA_PARAMETERS, COOPERATIVE_PROPENSITY_PARAMETERS, COOPERATIVE_RAMACHANDRAN_PARAMETERS, ELECTROSTATICS_PARAMETERS, EXCLUDED_VOL_PARAMETERS, FLAT_RAMACH_PARAMETERS, HELIX, HELIX_OR_COIL, HYDROGEN_BONDS_PAIRS_BETA_PARAMETERS, HYDROGEN_BONDS_PAIRS_HELIX_PARAMETERS, HYDROGEN_BONDS_PAIRS_PARAMETERS_SURFACE, LENNARD_JONES_PARAMETERS, LENNARD_JONES_PARAMETERS_BACKBONE, LENNARD_JONES_PARAMETERS_CA, LJ_ENVIRONMENT_PARAMETERS, LJ_ENVIRONMENT_PARAMETERS_BACKBONE, LJ_ENVIRONMENT_PARAMETERS_CA, ONE_ANGLE_PARAMETERS, OUT_OF_PLANE_PARAMETERS, PLANE_PARAMETERS, PROPENSITY_ANGLE_PARAMETERS, PROPENSITY_TORSION_PARAMETERS, SHEET, SHEET_OR_COIL, SOLVATE_LONG_HB_PARAMETERS, SOLVATE_MINIMIZE_HB_PARAMETERS, SOLVATE_NOHB_PARAMETERS, SOLVATE_PARAMETERS, SOLVATE_SC_PARAMETERS, TWO_ANGLES_PARAMETERS, TWO_TORSIONS_PARAMETERS
 
Fields inherited from interface meshi.util.MeshiAttribute
BEAUTIFY_ATTRIBUTE, CN_ATTRIBUTE, DISTANCE_FROM_CATALYTIC_ATTRIBUTE, EXCLUDED_VOLUME_ELEMENT_ATTRIBUTE, GAUSSIAN_ALPHA, GAUSSIAN_ATTRIBUTE, HYDROGEN_BONDS_ATTRIBUTE, LENNARD_JONES_ELEMENT_ATTRIBUTE, LOOP_RESIDUE, ORIGINAL_ATOM, RESIDUE_ATTRIBUTE, RESIDUE_TORSIONS_ATTRIBUTE, SECONDARY_STRUCTURE_ATTRIBUTE, SEQUENCE_ALIGNMENT_COLUMN_ATTRIBUTE, SIDE_CHAIN_SOLVATE_ALL_ATOM_ATTRIBUTE, SOLVATE_ALL_ATOM_ATTRIBUTE, SOLVATE_CA_ATTRIBUTE, SOLVATE_ROT1_ATTRIBUTE, SUMMA_ATTRIBUTE
 



Constructor Summary
BackboneResidue(ResidueType type,
                AtomList atomList,
                ResidueIdentifier id,
                ResidueMode mode)



           
BackboneResidue(java.lang.String name)



           
 



Method Summary




 java.lang.String
comment()



           



 Residue
create(AtomList atoms,
       ResidueIdentifier id,
       ResidueMode mode)



          create a residue based on an atoms list.


 
Methods inherited from class meshi.molecularElements.extendedAtoms.ResidueExtendedAtoms
addHydrogens, amideN, c, ca, cb, getAtom, h, head, n, o, tail, toAla, toArg, toAsn, toAsp, toCys, toGln, toGlu, toHis, toIle, toLeu, toLys, toMet, toPro, toSer, toThr, toTrp, toTyr, toVal
 
Methods inherited from class meshi.molecularElements.Residue
accessibility, addAttribute, amideH, atoms, bonds, carbonylC, carbonylO, cg, chain, compareTo, defrost, dummy, equals, find, find, get, getAtom, getAttribute, getMode, ID, initiateAtoms, key, nextAtom, number, position, prevAtom, reliability, secondaryStructure, setAccessibility, setAccessibility, setNextAtom, setPrevAtom, setPrevNextAtomsToNull, setReliability, setResidueInAtoms, setSecondaryStructure, setSecondaryStructure, test, toString, type
 
Methods inherited from class java.lang.Object
clone, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait
 





Field Detail



COMMENT
public static final java.lang.String COMMENT


See Also:
Constant Field Values




creator
public static final BackboneResidue creator








Constructor Detail



BackboneResidue
public BackboneResidue(java.lang.String name)





BackboneResidue
public BackboneResidue(ResidueType type,
                       AtomList atomList,
                       ResidueIdentifier id,
                       ResidueMode mode)






Method Detail



comment
public java.lang.String comment()


Overrides:
comment in class Residue








create
public Residue create(AtomList atoms,
                      ResidueIdentifier id,
                      ResidueMode mode)

Description copied from class: Residue
create a residue based on an atoms list.
 creates a dummyResidue if the list is null or empty.


Specified by:
create in interface ResidueCreator
Overrides:
create in class Residue