meshi.molecularElements.extendedAtoms
Class Trp

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

All Implemented Interfaces:

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

public class Trp
extends ResidueExtendedAtoms

                O
                |
       N - CA - C...n
       |   |
       H   CB   CE3 - CZ3 - CH2
           |    |           |
           CG - CD2 - CE2 - CZ2
           |           |
           CD1 ------ NE1 - HE1









Field Summary




 Atom
CD1



           



 Atom
CD2



           



 Atom
CE2



           



 Atom
CE3



           



 Atom
CG



           



 Atom
CH2



           



static java.lang.String
COMMENT



           



 Atom
CZ2



           



 Atom
CZ3



           



 Atom
HE1



           



 Atom
NE1



           


 
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
Trp(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







CD1
public final Atom CD1







NE1
public final Atom NE1







HE1
public final Atom HE1







CE2
public final Atom CE2







CZ2
public final Atom CZ2







CH2
public final Atom CH2







CZ3
public final Atom CZ3







CE3
public final Atom CE3







CD2
public final Atom CD2







COMMENT
public static final java.lang.String COMMENT


See Also:
Constant Field Values





Constructor Detail



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






Method Detail



comment
public java.lang.String comment()


Overrides:
comment in class Residue








addHydrogens
public void addHydrogens(BondParametersList bondParametersList,
                         AngleParametersList angleParametersList)


Overrides:
addHydrogens in class ResidueExtendedAtoms