astex
Class Residue

java.lang.Object
  astex.generic.Generic
      astex.Residue

All Implemented Interfaces:

GenericInterface, Selectable

public class Residue
extends Generic
implements Selectable

A class for storing a group of atoms that form part of a protein residue.

Field Summary

DynamicArray	atoms Dynmamic array of atoms.
static int	Coil Sheet secondary structure type.
static int	Helix Helix secondary structure type.
static int	Helix310 Helix secondary structure type.
static java.lang.String	ResidueColor
static int	Sheet Sheet secondary structure type.
static java.lang.String	TorsionFormat
static java.lang.String	TorsionGreek
static java.lang.String	TorsionRadius
static java.lang.String	Torsions
static int	Turn Sheet secondary structure type.
static int	Undefined Sheet secondary structure type.
static java.lang.String	undefinedResidueName Undefined resiude name.
static int	undefinedResidueNumber Undefined residue number.

Fields inherited from class astex.generic.Generic

ClassName

Fields inherited from interface astex.generic.GenericInterface

Name

Method Summary

void	addAtom(Atom atom) Add an atom to the list.
static Residue	create() Public interface for creating residues.
void	delete() Remove this residue.
Atom	findAtom(java.lang.String name) Default to alternate location 'A'.
Atom	findAtom(java.lang.String name, char code) Similar to getAtom(String name) but will search in the previous residue if the name ends with '-' or the next residue if the name ends with '+'.
Atom	getAtom(int index) Return the specified atom.
Atom	getAtom(java.lang.String nm) Return the atom with the given name.
Atom	getAtom(java.lang.String nm, char code) Return the atom with the given name.
int	getAtomCount() Return the number of atoms in the molecule.
DynamicArray	getAtoms() Return the DynamicArray of atoms.
char	getInsertionCode() Get the insertion code.
java.lang.String	getName() Get the residue name.
int	getNumber() Get the residue number.
Chain	getParent() Get the parent.
java.util.Enumeration	getProperties() Return an enumeration of our properties.
int	getSecondaryStructure() Get the value of secondaryStructure.
int	getSequentialNumber() Get the sequential residue number.
boolean	hasSelectedAtoms()
boolean	isIon() Is this residue an ion.
boolean	isIsolated() Does this residue contain bonds to atoms in any other residues.
boolean	isNucleicAcid() Is this a solvent residue.
boolean	isSolvent() Is this a solvent residue.
boolean	isStandardAminoAcid() Is this residue a standard amino acid.
void	removeAtom(Atom atom) Remove an atom from the residue.
int	select(int state) Apply a selection recursively.
java.lang.String	selectStatement()
void	setInsertionCode(char code) Set the insertion code.
void	setName(java.lang.String newName) Set the residue name.
void	setNumber(int newNumber) Set the residue number.
void	setParent(Chain chain) Set the parent chain.
void	setSecondaryStructure(int v) Set the value of secondaryStructure.
void	setSequentialNumber(int sNumber)
java.lang.String	toString() Print out a residue.

Methods inherited from class astex.generic.Generic

addChild, addListener, addParent, get, getBoolean, getChildren, getClassname, getDouble, getInteger, getParents, getString, main, removeChild, removeListener, removeParent, set, setBoolean, setClassname, setDouble, setInteger, setString

Methods inherited from class java.lang.Object

equals, getClass, hashCode, notify, notifyAll, wait, wait, wait

Field Detail

atoms

public DynamicArray atoms

Dynmamic array of atoms.

undefinedResidueNumber

public static int undefinedResidueNumber

Undefined residue number.

undefinedResidueName

public static java.lang.String undefinedResidueName

Undefined resiude name.

Undefined

public static final int Undefined

Sheet secondary structure type.

See Also:

Constant Field Values

Sheet

public static final int Sheet

Sheet secondary structure type.

See Also:

Constant Field Values

Helix

public static final int Helix

Helix secondary structure type.

See Also:

Constant Field Values

Helix310

public static final int Helix310

Helix secondary structure type.

See Also:

Constant Field Values

Turn

public static final int Turn

Sheet secondary structure type.

See Also:

Constant Field Values

Coil

public static final int Coil

Sheet secondary structure type.

See Also:

Constant Field Values

ResidueColor

public static final java.lang.String ResidueColor

See Also:

Constant Field Values

Torsions

public static final java.lang.String Torsions

See Also:

Constant Field Values

TorsionRadius

public static final java.lang.String TorsionRadius

See Also:

Constant Field Values

TorsionGreek

public static final java.lang.String TorsionGreek

See Also:

Constant Field Values

TorsionFormat

public static final java.lang.String TorsionFormat

See Also:

Constant Field Values

Method Detail

create

public static Residue create()

Public interface for creating residues.

setParent

public void setParent(Chain chain)

Set the parent chain.

getParent

public Chain getParent()

Get the parent.

setInsertionCode

public void setInsertionCode(char code)

Set the insertion code.

getInsertionCode

public char getInsertionCode()

Get the insertion code.

setName

public void setName(java.lang.String newName)

Set the residue name.

hasSelectedAtoms

public boolean hasSelectedAtoms()

getName

public java.lang.String getName()

Get the residue name.

getSecondaryStructure

public int getSecondaryStructure()

Get the value of secondaryStructure.

Returns:

value of secondaryStructure.

setSecondaryStructure

public void setSecondaryStructure(int v)

Set the value of secondaryStructure.

Parameters:

v - Value to assign to secondaryStructure.

setSequentialNumber

public void setSequentialNumber(int sNumber)

setNumber

public void setNumber(int newNumber)

Set the residue number.

getSequentialNumber

public int getSequentialNumber()

Get the sequential residue number.

getNumber

public int getNumber()

Get the residue number.

addAtom

public void addAtom(Atom atom)

Add an atom to the list.

removeAtom

public void removeAtom(Atom atom)

Remove an atom from the residue.

delete

public void delete()

Remove this residue.

getAtomCount

public int getAtomCount()

Return the number of atoms in the molecule.

getAtom

public Atom getAtom(int index)

Return the specified atom.

getAtom

public Atom getAtom(java.lang.String nm)

Return the atom with the given name.

getAtom

public Atom getAtom(java.lang.String nm,
                    char code)

Return the atom with the given name.

findAtom

public Atom findAtom(java.lang.String name)

Default to alternate location 'A'.

findAtom

public Atom findAtom(java.lang.String name,
                     char code)

Similar to getAtom(String name) but will search in the previous residue if the name ends with '-' or the next residue if the name ends with '+'. Maybe this should be rolled into one function but prefer this way in case names genuinely end with + or -. This method is only used by torsion angle search functions.

getAtoms

public DynamicArray getAtoms()

Return the DynamicArray of atoms.

isStandardAminoAcid

public boolean isStandardAminoAcid()

Is this residue a standard amino acid.

isIon

public boolean isIon()

Is this residue an ion.

isSolvent

public boolean isSolvent()

Is this a solvent residue.

isNucleicAcid

public boolean isNucleicAcid()

Is this a solvent residue.

isIsolated

public boolean isIsolated()

Does this residue contain bonds to atoms in any other residues.

selectStatement

public java.lang.String selectStatement()

Specified by:

selectStatement in interface Selectable

select

public int select(int state)

Apply a selection recursively.

Specified by:

select in interface Selectable

toString

public java.lang.String toString()

Print out a residue.

Overrides:

toString in class java.lang.Object

getProperties

public java.util.Enumeration getProperties()

Description copied from interface: GenericInterface

Return an enumeration of our properties.

Specified by:

getProperties in interface GenericInterface

Overrides:

getProperties in class Generic