meshi.molecularElements.extendedAtoms
Class Tyr

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

All Implemented Interfaces:

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

public class Tyr
extends ResidueExtendedAtoms

                O
                |
       N - CA - C...n
       |   |
       H   CB
           |
           CG - CD1 - CE1
           |          |
           CD2- CE2 - CZ-OH









Field Summary




 Atom
CD1



           



 Atom
CD2



           



 Atom
CE1



           



 Atom
CE2



           



 Atom
CG



           



static java.lang.String
COMMENT



           



 Atom
CZ



           



 Atom
OH



           


 
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
Tyr(AtomList atomList,
    ResidueIdentifier id,
    ResidueMode mode)



           
 



Method Summary




 java.lang.String
comment()



           


 
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, 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







CD1
public final Atom CD1







CE1
public final Atom CE1







CZ
public final Atom CZ







CD2
public final Atom CD2







CE2
public final Atom CE2







OH
public final Atom OH







COMMENT
public static final java.lang.String COMMENT


See Also:
Constant Field Values





Constructor Detail



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






Method Detail



comment
public java.lang.String comment()


Overrides:
comment in class Residue