Package etomica.species

Class SpeciesGeneral

java.lang.Object

etomica.species.SpeciesGeneral

All Implemented Interfaces:

ISpecies

public class SpeciesGeneral
extends java.lang.Object
implements ISpecies

Nested Class Summary

Nested Classes

Modifier and Type	Class	Description
static interface	SpeciesGeneral.AtomFactory

Constructor Summary

Constructors

Constructor	Description
SpeciesGeneral(AtomType[] atomTypes, IConformation conformation, java.lang.String[] atomNames, int[][] orientation, boolean isDynamic, boolean isMoleculeOriented, Vector momentOfInertia, Space space, SpeciesGeneral.AtomFactory atomFactory)

Method Summary

Modifier and Type	Method	Description
static SpeciesGeneral.AtomFactory	defaultAtomFactory(Space space, boolean isDynamic)
int	getAtomByTypeName(java.lang.String name)	Get the index within the molecule of the first atom of a given AtomType name.
int	getAtomByTypeName(java.lang.String name, int number)	Get the index within the molecule of the nth atom of given AtomType name.
AtomType	getAtomType(int index)	Returns the child type of this Species for the specified index.
int	getAtomTypeCount()	Returns the number of unique AtomTypes that make up this Species.
java.util.List<AtomType>	getAtomTypes()	Get the list of AtomTypes that make up this Species.
int	getByName(java.lang.String atomName)	Get the index within a molecule instance of a named atom for this Species.
IConformation	getConformation()
int	getIndex()	Returns the index for this ISpecies, within the context of an Simulation.
int	getLeafAtomCount()
AtomType	getLeafType()
double	getMass()
Vector	getMomentOfInertia()
Space	getSpace()
AtomType	getTypeByName(java.lang.String typeName)	Get the AtomType with a given name used in this Species.
void	initializeConformation(IMolecule molecule)	Initializes the molecule's IAtoms in their standard arrangement.
boolean	isDynamic()	Returns whether the Species is dynamic.
IMolecule	makeMolecule()	Builds and returns the IMolecule of this ISpecies.
static SpeciesGeneral	monatomic(Space space, AtomType atomType)
static SpeciesGeneral	monatomic(Space space, AtomType atomType, boolean isDynamic)
void	setIndex(int newIndex)	Informs the ISpecies what its index should be.
java.lang.String	toString()

Methods inherited from class java.lang.Object

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

Constructor Detail

SpeciesGeneral

public SpeciesGeneral(AtomType[] atomTypes,
                      IConformation conformation,
                      java.lang.String[] atomNames,
                      int[][] orientation,
                      boolean isDynamic,
                      boolean isMoleculeOriented,
                      Vector momentOfInertia,
                      Space space,
                      SpeciesGeneral.AtomFactory atomFactory)

Method Detail

monatomic

public static SpeciesGeneral monatomic(Space space,
                                       AtomType atomType)

monatomic

public static SpeciesGeneral monatomic(Space space,
                                       AtomType atomType,
                                       boolean isDynamic)

getIndex

public int getIndex()

Description copied from interface: ISpecies

Returns the index for this ISpecies, within the context of an Simulation. The index is the ISpecies' position in the array returned by SpeciesManager.getSpecies().

Specified by:

getIndex in interface ISpecies

setIndex

public void setIndex(int newIndex)

Description copied from interface: ISpecies

Informs the ISpecies what its index should be. This should only be called by the SpeciesManager.

Specified by:

setIndex in interface ISpecies

makeMolecule

public IMolecule makeMolecule()

Description copied from interface: ISpecies

Builds and returns the IMolecule of this ISpecies.

Specified by:

makeMolecule in interface ISpecies

isDynamic

public boolean isDynamic()

Description copied from interface: ISpecies

Returns whether the Species is dynamic. If a Species is dynamic and has oriented molecules, then the molecules will have a velocity component. If a Species is dynamic and is not oriented, its atoms will have a velocity component.

Specified by:

isDynamic in interface ISpecies

Returns:

whether the Species is dynamic

getSpace

public Space getSpace()

Specified by:

getSpace in interface ISpecies

Returns:

the Space of the Species. This is the Space that molecules and atoms are constructed with.

getAtomTypeCount

public int getAtomTypeCount()

Description copied from interface: ISpecies

Returns the number of unique AtomTypes that make up this Species.

Specified by:

getAtomTypeCount in interface ISpecies

getLeafAtomCount

public int getLeafAtomCount()

Specified by:

getLeafAtomCount in interface ISpecies

Returns:

the total number of atoms in this Species.

getAtomType

public AtomType getAtomType(int index)

Description copied from interface: ISpecies

Returns the child type of this Species for the specified index.

Specified by:

getAtomType in interface ISpecies

getLeafType

public AtomType getLeafType()

Specified by:

getLeafType in interface ISpecies

Returns:

the singular AtomType that makes up this Species.

getAtomTypes

public java.util.List<AtomType> getAtomTypes()

Description copied from interface: ISpecies

Get the list of AtomTypes that make up this Species.

The returned list should not be modified.

Specified by:

getAtomTypes in interface ISpecies

initializeConformation

public void initializeConformation(IMolecule molecule)

Description copied from interface: ISpecies

Initializes the molecule's IAtoms in their standard arrangement. The overall position of the molecule may be changed by this method.

Specified by:

initializeConformation in interface ISpecies

getConformation

public IConformation getConformation()

Specified by:

getConformation in interface ISpecies

Returns:

the Conformation used by this Species to initialize positions of atoms within a molecule.

getByName

public int getByName(java.lang.String atomName)

Description copied from interface: ISpecies

Get the index within a molecule instance of a named atom for this Species.

Specified by:

getByName in interface ISpecies

Parameters:

atomName - the name for a specific Atom in this Species.

Returns:

an index for use in IMolecule.getChildList()

getAtomByTypeName

public int getAtomByTypeName(java.lang.String name,
                             int number)

Description copied from interface: ISpecies

Get the index within the molecule of the nth atom of given AtomType name.

Specified by:

getAtomByTypeName in interface ISpecies

Parameters:

name - String matching the name for the AtomType.

number - The nth atom with that type to get, starting at 1.

Returns:

the index of that atom within a molecule of this species.

getAtomByTypeName

public int getAtomByTypeName(java.lang.String name)

Description copied from interface: ISpecies

Get the index within the molecule of the first atom of a given AtomType name.

Specified by:

getAtomByTypeName in interface ISpecies

Parameters:

name - String matching the name for the AtomType.

Returns:

the index of that atom within a molecule of this species.

getTypeByName

public AtomType getTypeByName(java.lang.String typeName)

Description copied from interface: ISpecies

Get the AtomType with a given name used in this Species.

Specified by:

getTypeByName in interface ISpecies

Parameters:

typeName - String matching the name for the AtomType.

Returns:

AtomType with the given name.

getMomentOfInertia

public Vector getMomentOfInertia()

Specified by:

getMomentOfInertia in interface ISpecies

Returns:

the moment of inertia for a molecule of this Species.

getMass

public double getMass()

Specified by:

getMass in interface ISpecies

Returns:

the total mass of all the atoms in a molecule of this Species.

toString

public java.lang.String toString()

Overrides:

toString in class java.lang.Object

defaultAtomFactory

public static SpeciesGeneral.AtomFactory defaultAtomFactory(Space space,
                                                            boolean isDynamic)