meshi.molecularElements
Class Residue

java.lang.Object
  meshi.molecularElements.Residue

All Implemented Interfaces:

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

Direct Known Subclasses:

CaResidue, ImageResidue, Pdb2Fasta.MyResidue, ResidueExtendedAtoms

public class Residue
extends java.lang.Object
implements ResidueCreator, java.lang.Comparable, MeshiPotential, MeshiAttribute, Attributable

A generic residue.

Field Summary

private java.lang.String	accessibility
protected AtomList	atoms Atoms of this residue;
private java.util.HashMap	attributes
protected AtomPairList	bonds Co-valiant bonds in the residue.
protected Atom	head First atom of the residue (typicaly N).
private ResidueIdentifier	ID A unique identifier.
ResidueMode	mode
java.lang.String	name Residue name.
private static StringList	names1 A list of Residue names1 (one letter code).
private static StringList	names3 A list of Residue names3 (three letter code).
private static boolean	namesDone The list of residue names is done.
protected Atom	nextAtom
protected Atom	prevAtom
private double	reliability
private SecondaryStructure	secondaryStructure HELIX, SHEET ect.
protected Atom	tail last atom of the residue (typicaly C).
ResidueType	type which of the 20 possible it is.

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

Residue(ResidueIdentifier id)

Residue(ResidueIdentifier id, java.lang.String name)

Residue(java.lang.String name)
Use this constructor to instantiate a creator object..

Residue(java.lang.String name, ResidueType type, ResidueIdentifier id, AtomList atomList, ResidueMode mode)

Method Summary

java.lang.String	accessibility()
void	addAttribute(MeshiAttribute attribute)
Atom	amideH()
Atom	amideN()
AtomList	atoms() Returns a list of the residue atoms.
AtomPairList	bonds() Returns a list of the residue bonds.
Atom	ca()
Atom	carbonylC()
Atom	carbonylO()
Atom	cb()
Atom	cg()
java.lang.String	chain()
java.lang.String	comment()
int	compareTo(java.lang.Object obj) Compares this residue with the given residue according to the order of their ResidueIdentifiers.
Residue	create(AtomList atoms, ResidueIdentifier id, ResidueMode mode) create a residue based on an atoms list.
void	defrost()
boolean	dummy()
boolean	equals(java.lang.Object other)
static Atom	find(AtomList atomList, BBatom bbAtom)
static Atom	find(AtomList atomList, java.lang.String name)
Atom	get(java.lang.String name) Fetches an atom by its name.
Atom	getAtom(java.lang.String atomName)
MeshiAttribute	getAttribute(int key)
ResidueMode	getMode()
Atom	head()
ResidueIdentifier	ID() Returns the ResidueIdentifier of this Residue or throws an exception if (this != ID.RESIDUE).
void	initiateAtoms()
int	key()
Atom	nextAtom()
int	number()
int	position() residue number - 1.
Atom	prevAtom()
double	reliability()
SecondaryStructure	secondaryStructure()
void	setAccessibility(char ac)
void	setAccessibility(java.lang.String accessibility)
void	setNextAtom(Atom atom)
void	setPrevAtom(Atom atom)
void	setPrevNextAtomsToNull()
void	setReliability(double reliability)
void	setResidueInAtoms(AtomList atoms)
void	setSecondaryStructure(char ss)
void	setSecondaryStructure(SecondaryStructure secondaryStructure)
Atom	tail()
java.lang.String	test()
java.lang.String	toString()
ResidueType	type()

Methods inherited from class java.lang.Object

clone, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait

Field Detail

name

public final java.lang.String name

Residue name.

ID

private final ResidueIdentifier ID

A unique identifier. Replaces field number and also includes this residue's chain.

type

public final ResidueType type

which of the 20 possible it is.

atoms

protected AtomList atoms

Atoms of this residue;

bonds

protected AtomPairList bonds

Co-valiant bonds in the residue.

head

protected Atom head

First atom of the residue (typicaly N). The one conncted to the previous residue.

tail

protected Atom tail

last atom of the residue (typicaly C). The one conncted to the next residue.

prevAtom

protected Atom prevAtom

nextAtom

protected Atom nextAtom

names3

private static StringList names3

A list of Residue names3 (three letter code).

names1

private static StringList names1

A list of Residue names1 (one letter code).

namesDone

private static boolean namesDone

The list of residue names is done.

secondaryStructure

private SecondaryStructure secondaryStructure

HELIX, SHEET ect. Acceptable values may be found in meshi/parameters/MeshiPotential.

accessibility

private java.lang.String accessibility

mode

public final ResidueMode mode

reliability

private double reliability

attributes

private java.util.HashMap attributes

Constructor Detail

Residue

public Residue(java.lang.String name)

 Use this constructor to instantiate a creator object..

Residue

public Residue(java.lang.String name,
               ResidueType type,
               ResidueIdentifier id,
               AtomList atomList,
               ResidueMode mode)

Residue

public Residue(ResidueIdentifier id)

Residue

public Residue(ResidueIdentifier id,
               java.lang.String name)

Method Detail

type

public final ResidueType type()

reliability

public double reliability()

setReliability

public void setReliability(double reliability)

atoms

public AtomList atoms()

Returns a list of the residue atoms.

bonds

public AtomPairList bonds()

Returns a list of the residue bonds.

toString

public java.lang.String toString()

Overrides:

toString in class java.lang.Object

getMode

public ResidueMode getMode()

test

public java.lang.String test()

head

public Atom head()

tail

public Atom tail()

prevAtom

public Atom prevAtom()

nextAtom

public Atom nextAtom()

setPrevAtom

public void setPrevAtom(Atom atom)

setNextAtom

public void setNextAtom(Atom atom)

comment

public java.lang.String comment()

position

public int position()

residue number - 1.

create

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

create a residue based on an atoms list. creates a dummyResidue if the list is null or empty.

Specified by:

create in interface ResidueCreator

compareTo

public int compareTo(java.lang.Object obj)

Compares this residue with the given residue according to the order of their ResidueIdentifiers.

Specified by:

compareTo in interface java.lang.Comparable

Throws:

java.lang.ClassCastException - if the given object is not a residue.

See Also:

ResidueIdentifier.compareTo(Object)

get

public Atom get(java.lang.String name)

Fetches an atom by its name.

secondaryStructure

public final SecondaryStructure secondaryStructure()

setSecondaryStructure

public void setSecondaryStructure(SecondaryStructure secondaryStructure)

accessibility

public final java.lang.String accessibility()

setAccessibility

public void setAccessibility(java.lang.String accessibility)

getAtom

public Atom getAtom(java.lang.String atomName)

ca

public Atom ca()

cb

public Atom cb()

cg

public Atom cg()

carbonylC

public Atom carbonylC()

carbonylO

public Atom carbonylO()

amideN

public Atom amideN()

amideH

public Atom amideH()

dummy

public boolean dummy()

find

public static Atom find(AtomList atomList,
                        BBatom bbAtom)

find

public static Atom find(AtomList atomList,
                        java.lang.String name)

setPrevNextAtomsToNull

public void setPrevNextAtomsToNull()

initiateAtoms

public void initiateAtoms()

setSecondaryStructure

public void setSecondaryStructure(char ss)

setAccessibility

public void setAccessibility(char ac)

defrost

public void defrost()

ID

public ResidueIdentifier ID()

Returns the ResidueIdentifier of this Residue or throws an exception if (this != ID.RESIDUE).

chain

public java.lang.String chain()

number

public int number()

setResidueInAtoms

public void setResidueInAtoms(AtomList atoms)

equals

public boolean equals(java.lang.Object other)

Overrides:

equals in class java.lang.Object

key

public int key()

Specified by:

key in interface MeshiAttribute

addAttribute

public final void addAttribute(MeshiAttribute attribute)

Specified by:

addAttribute in interface Attributable

getAttribute

public final MeshiAttribute getAttribute(int key)

Specified by:

getAttribute in interface Attributable