astex
Class Molecule

java.lang.Object
  astex.generic.Generic
      astex.Molecule

All Implemented Interfaces:

GenericInterface, Selectable

public class Molecule
extends Generic
implements Selectable

Field Summary

DynamicArray	atoms Dynmamic array of atoms.
DynamicArray	bonds Dynamic array of bonds.
boolean	debug Is debugging on.
static java.lang.String	DisplayBondDetails
static java.lang.String	Displayed
static java.lang.String	DisplayHydrogens
static int	FeatureMolecule
static int	Normal Normal display style.
static int	NormalMolecule Type for a normal molecule.
static int	Off Completely off.
static int	SkeletonMolecule
static int	SymmetryMolecule
static int	Trace Backbone trace.
static int	TraceAlways Backbone trace and atoms.

Fields inherited from class astex.generic.Generic

ClassName

Fields inherited from interface astex.generic.GenericInterface

Name

Constructor Summary

Molecule()
Constructor which prepares a standard molecule.

Method Summary

Atom	addAtom() Add an atom to the molecule and return the reference to it.
Atom	addAtom(Residue res) Add an atom to the chain, residue set.
Bond	addBond(Atom firstAtom, Atom secondAtom) Add a bond between two atoms with default bond order.
Bond	addBond(Atom firstAtom, Atom secondAtom, int bondOrder) Add a bond to the molecule and return a reference to it.
Bond	addBond(Atom firstAtom, Atom secondAtom, int bondOrder, boolean explicit) Add a bond to the molecule and return a reference to it.
Bond	addBond(int firstAtomIndex, int secondAtomIndex) Add a bond to the molecule and return a reference to it.
Bond	addBond(int firstAtomIndex, int secondAtomIndex, int bondOrder) Add a bond to the molecule and return a reference to it.
Bond	addBondFromIds(int firstAtomIndex, int secondAtomIndex, int bondOrder) Add a bond to the molecule and return a reference to it.
Chain	addChain() Add a chain to the molecule.
void	addImproper(Atom a1, Atom a2, Atom a3, Atom a4) Create a improper for the 4 specified atoms.
Residue	addResidue() Add a residue to the current chain.
Ring	addRing() Add a new ring to the molecule.
void	assignAtomNumbers() Assign atom numbers.
boolean	atomNeedsImproper(Atom atom) Does this atom need a improper restraint.
void	clearVisitFlags() Clear the visit flags on all of the atoms.
void	connect() Connect the atoms in a molecule using standard bonding radii.
void	connect2() Connect the atoms using a neighbour grid.
void	connectResidue(Residue residue) Connect all of the atoms in a single residue.
void	connectResidues(Residue firstResidue, Residue secondResidue) Connect all of the atoms in a single residue.
int	countAngles() Count how many bond angles this molecule has.
void	find3Rings() Find 3 membered rings by direct search.
Chain	findChain(java.lang.String name, boolean add) Find or add a particular chain.
void	findRings() Find rings in the structure.
void	findRings(int ringSize) Find rings of a particular size.
void	generateBondImpropers() Generate impropers to keep bonds flat.
void	generateDoubleBondImproper(Bond bond) Generate the improper for this double bond.
void	generatePlanes(DynamicArray planes) Method for CCP4Dictionary that generates list of planes.
void	generateRing(Ring ring) Generate the impropers for one ring.
void	generateRingImpropers() Generate the impropers that are due to rings.
void	generateSingleBondImproper(Bond bond) Generate the improper for this single bond.
void	generateSp2Impropers() Generate impropers for sp2 hybrid atoms.
java.lang.Object	get(java.lang.Object key, java.lang.Object def) Get Object representing key.
Angle	getAngle(int index) Get the specified angle.
java.lang.Object[]	getAngleArray() Get the array of angles.
int	getAngleCount() Get the number of atoms for this molecule.
Atom	getAtom(int index) Return the specified atom.
java.lang.Object[]	getAtomArray() Return the atom array.
int	getAtomCount() Return the number of atoms in the molecule.
Atom	getAtomWithId(int id) Return the atom with the specified id.
Ring	getBestRingContainingBond(Bond bond) Return the best ring containing this bond.
Bond	getBond(int index) Return the specified bond.
java.lang.Object[]	getBondArray() Return the bond array.
int	getBondCount() Return the number of bonds in the molecule.
Point3d	getCenter() Find the center of the molecule.
int	getCentralAtomCount() Get the number of central atoms.
Chain	getChain(int index) Return the specified chain.
int	getChainCount() Return the number of chains.
Chain	getCurrentChain() Get the current chain.
boolean	getDisplayed() Is the molecule displayed?
int	getDisplayStyle() Get the display style.
boolean	getDisplayStyle(int style) Get the display style.
java.lang.String	getFilename() Get the filename.
Improper	getImproper(int index) Get the specified improper.
java.lang.Object[]	getImproperArray() Get the array of impropers.
int	getImproperCount() Get the number of atoms for this molecule.
int	getMaximumId() Get the maximum id for this molecule.
int	getMoleculeType() Return what type of molecule this is.
java.lang.String	getName() Get the molecule name.
java.util.Enumeration	getProperties() Return an enumeration of our properties.
double	getRadius() Get the radius of the molecule.
int	getResidueCount() Get the total number of residues.
Ring	getRing(int index) Return the specified ring.
int	getRingCount() Return the number of rings.
Symmetry	getSymmetry() Get the symmetry object.
java.lang.String	getType() Get the type.
void	initialise() Initialise the molecule.
boolean	isAtomIn3MemberedRing(Atom atom) Is this atom in a 3 membered ring.
boolean	isBondIn6Ring(Bond bond) Is this bond in a 6 membered ring.
boolean	isBondInAromaticRing(Bond bond) Is this bond in an aromatic ring.
boolean	isSpecialAtom(Atom atom) Does this atom need treating specially for bonding.
boolean	isSymmetryMolecule() Is this a symmetry molecule.
void	markRingBonds() Mark the bonds that are part of a ring.
boolean	nitrogenNeedsImproper(Atom atom) Does this nitrogen atom need a improper.
void	possiblyCreateRing(Atom[] atomPath, Bond[] bondPath, int ringSize) Create a ring if the atoms are in the right order.
boolean	propagateCycleSearch(Atom firstAtom, Atom secondAtom, int depth) Propagate the search for cycles.
void	removeAtom(Atom a) Remove an atom from the molecule.
void	removeBond(Bond b) Remove a bond from the molecule.
void	reorderAtoms() Reorder the atoms in a molecule.
int	select(int state) Apply a selection recursively.
java.lang.String	selectStatement()
java.lang.Object	set(java.lang.Object key, java.lang.Object property) Set an object value.
void	setCentralAtomCount(int cac) Set the number of central atoms.
void	setDisplayed(int newState) Set if the molecule is on or off.
void	setDisplayStyle(int style) Set Display style.
void	setFilename(java.lang.String s) Set the filename.
void	setMoleculeType(int t) Set what type of molecule this is.
void	setName(java.lang.String name) Set the molecule name
void	setSpaceGroupName(java.lang.String name) Set the space group name.
void	setSymmetry(Symmetry s) Set the symmetry entry for this molecule.
void	setType(java.lang.String s) Set the type.
void	setUnitCell(double[] newCell) Set the unit cell.
boolean	singleBondRequiresImproper(Bond bond) Does this single bond require a improper.
java.lang.String	toString() Generate a string representation.

Methods inherited from class astex.generic.Generic

addChild, addListener, addParent, getBoolean, getChildren, getClassname, getDouble, getInteger, getParents, getString, main, removeChild, removeListener, removeParent, 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.

bonds

public DynamicArray bonds

Dynamic array of bonds.

Off

public static int Off

Completely off.

Normal

public static int Normal

Normal display style.

Trace

public static int Trace

Backbone trace.

TraceAlways

public static int TraceAlways

Backbone trace and atoms.

NormalMolecule

public static final int NormalMolecule

Type for a normal molecule.

See Also:

Constant Field Values

FeatureMolecule

public static final int FeatureMolecule

See Also:

Constant Field Values

SkeletonMolecule

public static final int SkeletonMolecule

See Also:

Constant Field Values

SymmetryMolecule

public static final int SymmetryMolecule

See Also:

Constant Field Values

debug

public boolean debug

Is debugging on.

Displayed

public static final java.lang.String Displayed

See Also:

Constant Field Values

DisplayHydrogens

public static final java.lang.String DisplayHydrogens

See Also:

Constant Field Values

DisplayBondDetails

public static final java.lang.String DisplayBondDetails

See Also:

Constant Field Values

Constructor Detail

Molecule

public Molecule()

Constructor which prepares a standard molecule.

Method Detail

setCentralAtomCount

public void setCentralAtomCount(int cac)

Set the number of central atoms.

getCentralAtomCount

public int getCentralAtomCount()

Get the number of central atoms.

getMoleculeType

public int getMoleculeType()

Return what type of molecule this is.

setMoleculeType

public void setMoleculeType(int t)

Set what type of molecule this is.

initialise

public void initialise()

Initialise the molecule.

toString

public java.lang.String toString()

Generate a string representation.

Overrides:

toString in class java.lang.Object

setDisplayStyle

public void setDisplayStyle(int style)

Set Display style.

getDisplayStyle

public int getDisplayStyle()

Get the display style.

getDisplayStyle

public boolean getDisplayStyle(int style)

Get the display style.

setDisplayed

public void setDisplayed(int newState)

Set if the molecule is on or off.

getDisplayed

public boolean getDisplayed()

Is the molecule displayed?

getAtomCount

public int getAtomCount()

Return the number of atoms in the molecule.

getAtom

public Atom getAtom(int index)

Return the specified atom.

getAtomWithId

public Atom getAtomWithId(int id)

Return the atom with the specified id.

assignAtomNumbers

public void assignAtomNumbers()

Assign atom numbers.

isSymmetryMolecule

public boolean isSymmetryMolecule()

Is this a symmetry molecule.

getBondCount

public int getBondCount()

Return the number of bonds in the molecule.

getBond

public Bond getBond(int index)

Return the specified bond.

getAngleCount

public int getAngleCount()

Get the number of atoms for this molecule.

getAngle

public Angle getAngle(int index)

Get the specified angle.

getAngleArray

public java.lang.Object[] getAngleArray()

Get the array of angles.

getImproperCount

public int getImproperCount()

Get the number of atoms for this molecule.

getImproper

public Improper getImproper(int index)

Get the specified improper.

getImproperArray

public java.lang.Object[] getImproperArray()

Get the array of impropers.

getAtomArray

public java.lang.Object[] getAtomArray()

Return the atom array.

getBondArray

public java.lang.Object[] getBondArray()

Return the bond array.

getRing

public Ring getRing(int index)

Return the specified ring.

getRingCount

public int getRingCount()

Return the number of rings.

getChainCount

public int getChainCount()

Return the number of chains.

getChain

public Chain getChain(int index)

Return the specified chain.

getCurrentChain

public Chain getCurrentChain()

Get the current chain.

getResidueCount

public int getResidueCount()

Get the total number of residues.

addChain

public Chain addChain()

Add a chain to the molecule.

findChain

public Chain findChain(java.lang.String name,
                       boolean add)

Find or add a particular chain.

addResidue

public Residue addResidue()

Add a residue to the current chain.

getMaximumId

public int getMaximumId()

Get the maximum id for this molecule.

addAtom

public Atom addAtom()

Add an atom to the molecule and return the reference to it.

addAtom

public Atom addAtom(Residue res)

Add an atom to the chain, residue set.

reorderAtoms

public void reorderAtoms()

Reorder the atoms in a molecule. This needs doing to make the molecule master atom list reflect the order of atoms in chains/residues.

addRing

public Ring addRing()

Add a new ring to the molecule.

addBond

public Bond addBond(Atom firstAtom,
                    Atom secondAtom,
                    int bondOrder)

Add a bond to the molecule and return a reference to it.

addBond

public Bond addBond(Atom firstAtom,
                    Atom secondAtom,
                    int bondOrder,
                    boolean explicit)

Add a bond to the molecule and return a reference to it.

addBond

public Bond addBond(Atom firstAtom,
                    Atom secondAtom)

Add a bond between two atoms with default bond order.

addBond

public Bond addBond(int firstAtomIndex,
                    int secondAtomIndex,
                    int bondOrder)

Add a bond to the molecule and return a reference to it.

addBond

public Bond addBond(int firstAtomIndex,
                    int secondAtomIndex)

Add a bond to the molecule and return a reference to it.

addBondFromIds

public Bond addBondFromIds(int firstAtomIndex,
                           int secondAtomIndex,
                           int bondOrder)

Add a bond to the molecule and return a reference to it.

removeAtom

public void removeAtom(Atom a)

Remove an atom from the molecule.

removeBond

public void removeBond(Bond b)

Remove a bond from the molecule.

isSpecialAtom

public boolean isSpecialAtom(Atom atom)

Does this atom need treating specially for bonding.

connect2

public void connect2()

Connect the atoms using a neighbour grid.

connect

public void connect()

Connect the atoms in a molecule using standard bonding radii.

connectResidue

public void connectResidue(Residue residue)

Connect all of the atoms in a single residue.

connectResidues

public void connectResidues(Residue firstResidue,
                            Residue secondResidue)

Connect all of the atoms in a single residue.

countAngles

public int countAngles()

Count how many bond angles this molecule has.

findRings

public void findRings()

Find rings in the structure.

findRings

public void findRings(int ringSize)

Find rings of a particular size.

find3Rings

public void find3Rings()

Find 3 membered rings by direct search.

possiblyCreateRing

public void possiblyCreateRing(Atom[] atomPath,
                               Bond[] bondPath,
                               int ringSize)

Create a ring if the atoms are in the right order. The ring is only created if 1. the first atom has the lowest index. 2. the second atom has a lower index than the last atom.

isBondInAromaticRing

public boolean isBondInAromaticRing(Bond bond)

Is this bond in an aromatic ring.

getBestRingContainingBond

public Ring getBestRingContainingBond(Bond bond)

Return the best ring containing this bond.

isBondIn6Ring

public boolean isBondIn6Ring(Bond bond)

Is this bond in a 6 membered ring.

isAtomIn3MemberedRing

public boolean isAtomIn3MemberedRing(Atom atom)

Is this atom in a 3 membered ring.

setName

public void setName(java.lang.String name)

Set the molecule name

getName

public java.lang.String getName()

Get the molecule name.

setFilename

public void setFilename(java.lang.String s)

Set the filename.

getFilename

public java.lang.String getFilename()

Get the filename.

setType

public void setType(java.lang.String s)

Set the type.

getType

public java.lang.String getType()

Get the type.

generateRingImpropers

public void generateRingImpropers()

Generate the impropers that are due to rings.

generateRing

public void generateRing(Ring ring)

Generate the impropers for one ring.

generateBondImpropers

public void generateBondImpropers()

Generate impropers to keep bonds flat.

singleBondRequiresImproper

public boolean singleBondRequiresImproper(Bond bond)

Does this single bond require a improper.

generateDoubleBondImproper

public void generateDoubleBondImproper(Bond bond)

Generate the improper for this double bond.

generateSingleBondImproper

public void generateSingleBondImproper(Bond bond)

Generate the improper for this single bond.

generateSp2Impropers

public void generateSp2Impropers()

Generate impropers for sp2 hybrid atoms.

addImproper

public void addImproper(Atom a1,
                        Atom a2,
                        Atom a3,
                        Atom a4)

Create a improper for the 4 specified atoms.

atomNeedsImproper

public boolean atomNeedsImproper(Atom atom)

Does this atom need a improper restraint.

nitrogenNeedsImproper

public boolean nitrogenNeedsImproper(Atom atom)

Does this nitrogen atom need a improper.

generatePlanes

public void generatePlanes(DynamicArray planes)

Method for CCP4Dictionary that generates list of planes.

getCenter

public Point3d getCenter()

Find the center of the molecule.

getRadius

public double getRadius()

Get the radius of the molecule.

setUnitCell

public void setUnitCell(double[] newCell)

Set the unit cell.

getSymmetry

public Symmetry getSymmetry()

Get the symmetry object.

setSymmetry

public void setSymmetry(Symmetry s)

Set the symmetry entry for this molecule.

setSpaceGroupName

public void setSpaceGroupName(java.lang.String name)

Set the space group name.

clearVisitFlags

public void clearVisitFlags()

Clear the visit flags on all of the atoms.

markRingBonds

public void markRingBonds()

Mark the bonds that are part of a ring. This method is extremely inefficient (O(N^2)), but I can't figure out how to implement the linear time method without allocating extra storage for each atom (which I don't want to do).

propagateCycleSearch

public boolean propagateCycleSearch(Atom firstAtom,
                                    Atom secondAtom,
                                    int depth)

Propagate the search for cycles.

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

set

public java.lang.Object set(java.lang.Object key,
                            java.lang.Object property)

Description copied from interface: GenericInterface

Set an object value.

Specified by:

set in interface GenericInterface

Overrides:

set in class Generic

get

public java.lang.Object get(java.lang.Object key,
                            java.lang.Object def)

Description copied from interface: GenericInterface

Get Object representing key.

Specified by:

get in interface GenericInterface

Overrides:

get in class Generic

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