org.wallerlab.yoink.regionizer.service

Class SizeConsistentRegionizer

java.lang.Object

org.wallerlab.yoink.regionizer.service.ParameterRegionizer

org.wallerlab.yoink.regionizer.service.SizeConsistentRegionizer

All Implemented Interfaces:

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

@Service
public class SizeConsistentRegionizer
extends ParameterRegionizer

this class is the calculation of size consistent qm/mm partitioning. for details please see, "Size-Consistent Multipartitioning QM/MM: A Stable and Efficient Adaptive QM/MM Method"

Field Summary

Fields inherited from class org.wallerlab.yoink.regionizer.service.ParameterRegionizer

simpleRegionFactory

Constructor Summary

Constructors

Constructor and Description
SizeConsistentRegionizer()

Method Summary

Modifier and Type	Method and Description
protected void	checkEveryNonQMCoreMolecule(Region qmAdaptiveRegion, java.util.Map<JobParameter,java.lang.Object> parameters, Region bufferRegion, Coord centerCoord, java.util.Set<Molecule> nonQMCoreMolecules) moleculeSequence is ordered by the ascending distance between molecule and the center of mass of QM core, and take first 2/3 qmNumber of molecules from the moleculeSequence as adaptive QM molecules.
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 org.wallerlab.yoink.regionizer.service.ParameterRegionizer

calculateQMAdaptiveAndBufferRegionRegion, calculateQMRegion, loopOverMoleculesInNonQmRegion

Methods inherited from class java.lang.Object

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

Constructor Detail

SizeConsistentRegionizer

public SizeConsistentRegionizer()

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>>

Overrides:

regionize in class ParameterRegionizer

Parameters:

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

parameters - -specified argument

Returns:

return type is specified T

checkEveryNonQMCoreMolecule

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

moleculeSequence is ordered by the ascending distance between molecule and the center of mass of QM core, and take first 2/3 qmNumber of molecules from the moleculeSequence as adaptive QM molecules. those molecules between distance_s_qm_in and distance_t_qm_out are in buffer region.

Overrides:

checkEveryNonQMCoreMolecule in class ParameterRegionizer