org.wallerlab.yoink.api.model.regionizer

Interface Region

All Known Implementing Classes:

SimpleRegion

public interface Region

this interface is for domain model region which contains a certain type of molecules

Nested Class Summary

Nested Classes

Modifier and Type	Interface and Description
static class	Region.Name the names of regions used during adaptive QM/MM partitioning

Method Summary

Modifier and Type	Method and Description
void	addAll(java.util.Map<Molecule,java.lang.Integer> map) add a map into the region
void	addMolecule(Molecule molecule, java.lang.Integer index) add one molecule into molecularMap
void	changeMolecularId() set molecular name as same as region name
void	changeMolecularId(Region.Name name) change molecular name as the given name
boolean	containsAll(java.util.Set<Molecule> molecules) check if the regions contains all molecules
java.util.List<Atom>	getAtoms() Convenient method for getting atoms from a region
Coord	getCenterOfMass() get the center of mass of this region
java.util.Map<Molecule,java.lang.Integer>	getMolecularMap() get the value of molecularMap
java.util.Set<Molecule>	getMolecules() get all molecules in the region
Region.Name	getName() get the name of the region
java.lang.Integer	getSize() get the number of molecules in the region
void	setCenterOfMassComputer(Computer<Coord,java.util.Set<Molecule>> centerOfMassComputer) set the value of CenterOfMassComputer
void	setMolecularMap(java.util.Map<Molecule,java.lang.Integer> molecularMap) set the value of moleculeMap
void	setName(Region.Name name) set the name of the region

Method Detail

getSize

java.lang.Integer getSize()

get the number of molecules in the region

Returns:

the number of molecules-Integer

getMolecules

java.util.Set<Molecule> getMolecules()

get all molecules in the region

Returns:

a Set of Molecules - Molecule

addMolecule

void addMolecule(Molecule molecule,
                 java.lang.Integer index)

add one molecule into molecularMap

Parameters:

molecule - - the key

index - - the value

setMolecularMap

void setMolecularMap(java.util.Map<Molecule,java.lang.Integer> molecularMap)

set the value of moleculeMap

Parameters:

molecularMap - - Molecule as key, Integer as value

getMolecularMap

java.util.Map<Molecule,java.lang.Integer> getMolecularMap()

get the value of molecularMap

Returns:

molecularMap,- Map Molecule as key, Integer as value

getName

Region.Name getName()

get the name of the region

Returns:

Region.Name

setName

void setName(Region.Name name)

set the name of the region

Parameters:

name - Region.Name

addAll

void addAll(java.util.Map<Molecule,java.lang.Integer> map)

add a map into the region

Parameters:

map - - Map Molecule as key, Integer as value

containsAll

boolean containsAll(java.util.Set<Molecule> molecules)

check if the regions contains all molecules

Parameters:

molecules - - a Set of Molecules

Returns:

boolean - if the regions contains all molecules, return true,or return false

getAtoms

java.util.List<Atom> getAtoms()

Convenient method for getting atoms from a region

Returns:

a List of atoms

getCenterOfMass

Coord getCenterOfMass()

get the center of mass of this region

Returns:

Coord - Coord

changeMolecularId

void changeMolecularId()

set molecular name as same as region name

changeMolecularId

void changeMolecularId(Region.Name name)

change molecular name as the given name

Parameters:

name - -Region.Name

setCenterOfMassComputer

void setCenterOfMassComputer(Computer<Coord,java.util.Set<Molecule>> centerOfMassComputer)

set the value of CenterOfMassComputer

Parameters:

centerOfMassComputer - - Computer