meshi.molecularElements.extendedAtoms
Class Arg

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

All Implemented Interfaces:

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

public class Arg
extends ResidueExtendedAtoms

ARGININ

              O
              |
     N - CA - C...n
     |   |
     H   CB                 
         |                  
         CG - CD - NE - CZ - NH1
                        |
                        NH2









Field Summary




 Atom
CD



           



 Atom
CG



           



static java.lang.String
COMMENT



           



 Atom
CZ



           



 Atom
HE



           



 Atom
NE



           



 Atom
NH1



           



 Atom
NH2



           


 
Fields inherited from class meshi.molecularElements.extendedAtoms.ResidueExtendedAtoms
C, CA, CB, creator, 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
Arg(AtomList atomList,
    ResidueIdentifier id,
    ResidueMode mode)



           
 



Method Summary




 void
addHydrogens(BondParametersList bondParametersList,
             AngleParametersList angleParametersList)



           



 java.lang.String
comment()



           


 
Methods inherited from class meshi.molecularElements.extendedAtoms.ResidueExtendedAtoms
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, create, 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



CG
public final Atom CG







CD
public final Atom CD







NE
public final Atom NE







HE
public final Atom HE







CZ
public final Atom CZ







NH1
public final Atom NH1







NH2
public final Atom NH2







COMMENT
public static final java.lang.String COMMENT


See Also:
Constant Field Values





Constructor Detail



Arg
public Arg(AtomList atomList,
           ResidueIdentifier id,
           ResidueMode mode)






Method Detail



addHydrogens
public void addHydrogens(BondParametersList bondParametersList,
                         AngleParametersList angleParametersList)


Overrides:
addHydrogens in class ResidueExtendedAtoms








comment
public java.lang.String comment()


Overrides:
comment in class Residue