meshi.molecularElements.extendedAtoms
Class ResidueExtendedAtoms

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

All Implemented Interfaces:

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

Direct Known Subclasses:

Ala, Arg, Asn, Asp, BackboneResidue, Cys, Gln, Glu, Gly, His, Ile, Leu, Lys, Met, Phe, Pro, Ser, Thr, Trp, Tyr, Val

public class ResidueExtendedAtoms
extends Residue

Field Summary

Atom	C
Atom	CA
Atom	CB
static ResidueExtendedAtomsCreator	creator
Atom	H
Atom	N
Atom	O
Atom	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

	ResidueExtendedAtoms(ResidueType type, AtomList atomList, ResidueIdentifier id, ResidueMode mode) Do not use this constructor to instantiate a creator object.
protected	ResidueExtendedAtoms(java.lang.String name)

Method Summary

private void	addAtomsAndBonds()
void	addHydrogens(BondParametersList bondParametersList, AngleParametersList angleParametersList)
Atom	amideN()
Atom	c()
Atom	ca()
Atom	cb()
static Atom	getAtom(java.lang.String name, AtomType type, AtomList atomList, Residue residue)
Atom	h()
Atom	head()
Atom	n()
private static java.lang.String	nameConverter(java.lang.String name)
Atom	o()
Atom	tail()
Ala	toAla()
Arg	toArg()
Asn	toAsn()
Asp	toAsp()
Cys	toCys()
Gln	toGln()
Glu	toGlu()
His	toHis()
Ile	toIle()
Leu	toLeu()
Lys	toLys()
Met	toMet()
Pro	toPro()
Ser	toSer()
Thr	toThr()
Trp	toTrp()
Tyr	toTyr()
Val	toVal()

Methods inherited from class meshi.molecularElements.Residue

accessibility, addAttribute, amideH, atoms, bonds, carbonylC, carbonylO, cg, chain, comment, 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

creator

public static final ResidueExtendedAtomsCreator creator

H

public final Atom H

N

public final Atom N

CA

public final Atom CA

CB

public final Atom CB

C

public final Atom C

O

public final Atom O

OXT

public final Atom OXT

Constructor Detail

ResidueExtendedAtoms

protected ResidueExtendedAtoms(java.lang.String name)

ResidueExtendedAtoms

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

Do not use this constructor to instantiate a creator object.

Method Detail

addAtomsAndBonds

private void addAtomsAndBonds()

getAtom

public static Atom getAtom(java.lang.String name,
                           AtomType type,
                           AtomList atomList,
                           Residue residue)

head

public Atom head()

Overrides:

head in class Residue

tail

public Atom tail()

Overrides:

tail in class Residue

nameConverter

private static java.lang.String nameConverter(java.lang.String name)

ca

public final Atom ca()

Overrides:

ca in class Residue

cb

public final Atom cb()

Overrides:

cb in class Residue

c

public final Atom c()

o

public final Atom o()

n

public final Atom n()

h

public final Atom h()

amideN

public final Atom amideN()

Overrides:

amideN in class Residue

toAla

public Ala toAla()

toCys

public Cys toCys()

toAsp

public Asp toAsp()

toGlu

public Glu toGlu()

toHis

public His toHis()

toIle

public Ile toIle()

toLys

public Lys toLys()

toLeu

public Leu toLeu()

toMet

public Met toMet()

toAsn

public Asn toAsn()

toPro

public Pro toPro()

toGln

public Gln toGln()

toArg

public Arg toArg()

toSer

public Ser toSer()

toThr

public Thr toThr()

toVal

public Val toVal()

toTrp

public Trp toTrp()

toTyr

public Tyr toTyr()

addHydrogens

public void addHydrogens(BondParametersList bondParametersList,
                         AngleParametersList angleParametersList)