MpiMolecule

java.lang.Object
- etomica.molecule.iterator.MpiMolecule

All Implemented Interfaces:

AtomsetIterator, AtomsetIteratorDirectable, MoleculesetIterator, MoleculesetIteratorBoxDependent, MoleculesetIteratorPDT, MoleculesetIteratorTargetable, java.io.Serializable
```
public class MpiMolecule
extends java.lang.Object
implements MoleculesetIteratorPDT, java.io.Serializable
```
Adapater class that wraps three atomPair iterators, one suitable for iterating over all molecule pairs in a box (AA), another suitable for iterating over all molecule pairs formed with a target molecule (1A), and the third suitable for iterating over a single molecule pair (11). Appropriate iterator is selected based on argument given to setTarget method. If setTarget method is never called, or has count == 0, the all-pair iterator is used by default.
This class may be set up to do inter- or intra-species iteration, depending on choice of inner iterators given at construction. Wrapped iterators are final and cannot be changed after construction.

See Also:

Serialized Form

Constructor Summary

Constructors
Constructor Description

MpiMolecule(MoleculesetIteratorPDT api1A, MoleculesetIteratorBoxDependent apiAA)
Constructs iterator by wrapping three others.

Constructors
Constructor	Description
`MpiMolecule(MoleculesetIteratorPDT api1A, MoleculesetIteratorBoxDependent apiAA)`	Constructs iterator by wrapping three others.

Method Summary

All Methods Instance Methods Concrete Methods
Modifier and Type	Method	Description
`MoleculesetIteratorPDT`	`getApi1A()`	Returns the 1A iterator set at construction.
`MoleculesetIteratorBoxDependent`	`getApiAA()`	Returns the AA iterator set at construction.
`int`	`nBody()`	Returns 2, indicating that this is a pair iterator.
`IMoleculeList`	`next()`	Same as nextPair.
`void`	`reset()`	Readies iterator for iteration.
`void`	`setBox(Box box)`	Specifies the box from which iterates are taken.
`void`	`setDirection(IteratorDirective.Direction direction)`	Specifies the direction from which partners of a target atoms are taken to form iterates.
`void`	`setTarget(IMolecule targetAtom)`	Sets target atoms and determines the pair iterator according to the value of targetAtom.
`int`	`size()`	Returns the number of iterates that would be given when iterating after reset.
`void`	`unset()`	Sets iterator to state in which hasNext is false.

Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

- Constructor Detail
  - MpiMolecule
```
public MpiMolecule(MoleculesetIteratorPDT api1A,
                   MoleculesetIteratorBoxDependent apiAA)
```
    Constructs iterator by wrapping three others.
    
    Parameters:
    
    api1A - iterator for all pairs formed with a target molecule
    
    apiAA - iterator for all pairs in the box
- Method Detail
  - setTarget
```
public void setTarget(IMolecule targetAtom)
```
    Sets target atoms and determines the pair iterator according to the value of targetAtom. Thus, for targetAtom equal to
    - null, AA iterator is indicated
    - not-null, 1A iterator is indicated
    Target is passed on to setTarget method of corresponding iterator, which ultimately determines the behavior of this iterator.
    Specified by:
    
    setTarget in interface MoleculesetIteratorTargetable
  - setBox
```
public void setBox(Box box)
```
    Specifies the box from which iterates are taken.
    
    Specified by:
    
    setBox in interface MoleculesetIteratorBoxDependent
  - setDirection
```
public void setDirection(IteratorDirective.Direction direction)
```
    Specifies the direction from which partners of a target atoms are taken to form iterates. Has no effect if performing AA or 11 iteration (that is, if set target has count not equal to 1).
    
    Specified by:
    
    setDirection in interface AtomsetIteratorDirectable
  - reset
```
public void reset()
```
    Readies iterator for iteration.
    
    Specified by:
    
    reset in interface AtomsetIterator
  - unset
```
public void unset()
```
    Sets iterator to state in which hasNext is false.
    
    Specified by:
    
    unset in interface AtomsetIterator
  - next
```
public IMoleculeList next()
```
    Same as nextPair.
    
    Specified by:
    
    next in interface MoleculesetIterator
  - size
```
public int size()
```
    Returns the number of iterates that would be given when iterating after reset. Does not require reset; clobbers iteration state.
    
    Specified by:
    
    size in interface AtomsetIterator
  - nBody
```
public final int nBody()
```
    Returns 2, indicating that this is a pair iterator.
    
    Specified by:
    
    nBody in interface AtomsetIterator
    
    Returns:
  - getApi1A
```
public MoleculesetIteratorPDT getApi1A()
```
    Returns the 1A iterator set at construction.
  - getApiAA
```
public MoleculesetIteratorBoxDependent getApiAA()
```
    Returns the AA iterator set at construction.

Class MpiMolecule

Constructor Summary

Method Summary

Methods inherited from class java.lang.Object

Constructor Detail

MpiMolecule

Method Detail

setTarget

setBox

setDirection

reset

unset

next

size

nBody

getApi1A

getApiAA