org.wallerlab.yoink.regionizer.service

Class ParameterRegionizer

java.lang.Object

org.wallerlab.yoink.regionizer.service.ParameterRegionizer

All Implemented Interfaces:

Regionizer<java.util.Map<Region.Name,Region>,java.util.Map<JobParameter,java.lang.Object>>

Direct Known Subclasses:

DistanceRegionizer, NumberRegionizer, SizeConsistentRegionizer

public class ParameterRegionizer
extends java.lang.Object
implements Regionizer<java.util.Map<Region.Name,Region>,java.util.Map<JobParameter,java.lang.Object>>

this class is for parameter based adaptive qm/mm partitioning (distance and number). it is to get QM region, QM_ADAPTIVE region and buffer region

Field Summary

Fields

Modifier and Type	Field and Description
protected Factory<Region,Region.Name>	simpleRegionFactory

Constructor Summary

Constructors

Constructor and Description
ParameterRegionizer()

Method Summary

Modifier and Type	Method and Description
protected void	calculateQMAdaptiveAndBufferRegionRegion(Region qmAdaptiveRegion, java.util.Map<Region.Name,Region> regions, java.util.Map<JobParameter,java.lang.Object> parameters)
protected void	calculateQMRegion(java.util.Map<Region.Name,Region> regions, Region qmAdaptiveRegion)
protected void	checkEveryNonQMCoreMolecule(Region qmAdaptiveRegion, java.util.Map<JobParameter,java.lang.Object> parameters, Region bufferRegion, Coord centerCoord, java.util.Set<Molecule> nonQMCoreMolecules)
protected void	loopOverMoleculesInNonQmRegion(Region qmAdaptiveRegion, java.util.Map<Region.Name,Region> regions, java.util.Map<JobParameter,java.lang.Object> parameters, Region bufferRegion)
java.util.Map<Region.Name,Region>	regionize(java.util.Map<Region.Name,Region> regions, java.util.Map<JobParameter,java.lang.Object> parameters)

Methods inherited from class java.lang.Object

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

Field Detail

simpleRegionFactory

protected Factory<Region,Region.Name> simpleRegionFactory

Constructor Detail

ParameterRegionizer

public ParameterRegionizer()

Method Detail

regionize

public java.util.Map<Region.Name,Region> regionize(java.util.Map<Region.Name,Region> regions,
                                                   java.util.Map<JobParameter,java.lang.Object> parameters)

Specified by:

regionize in interface Regionizer<java.util.Map<Region.Name,Region>,java.util.Map<JobParameter,java.lang.Object>>

Parameters:

regions - , a Map, Region.Name as Key, Region as Value

parameters - -specified argument

Returns:

return type is specified T

calculateQMAdaptiveAndBufferRegionRegion

protected void calculateQMAdaptiveAndBufferRegionRegion(Region qmAdaptiveRegion,
                                                        java.util.Map<Region.Name,Region> regions,
                                                        java.util.Map<JobParameter,java.lang.Object> parameters)

loopOverMoleculesInNonQmRegion

protected void loopOverMoleculesInNonQmRegion(Region qmAdaptiveRegion,
                                              java.util.Map<Region.Name,Region> regions,
                                              java.util.Map<JobParameter,java.lang.Object> parameters,
                                              Region bufferRegion)

checkEveryNonQMCoreMolecule

protected void checkEveryNonQMCoreMolecule(Region qmAdaptiveRegion,
                                           java.util.Map<JobParameter,java.lang.Object> parameters,
                                           Region bufferRegion,
                                           Coord centerCoord,
                                           java.util.Set<Molecule> nonQMCoreMolecules)

calculateQMRegion

protected void calculateQMRegion(java.util.Map<Region.Name,Region> regions,
                                 Region qmAdaptiveRegion)