org.wallerlab.yoink.api.model.bootstrap

Enum JobParameter

java.lang.Object

java.lang.Enum<JobParameter>

org.wallerlab.yoink.api.model.bootstrap.JobParameter

All Implemented Interfaces:

java.io.Serializable, java.lang.Comparable<JobParameter>

public enum JobParameter
extends java.lang.Enum<JobParameter>

JobParameter is used to describe the type of parameter in parameters of job Job.

PARTITIONER: the partitioner type DISTANCE/NUMBER/DORI

OUTPUT_FOLDER: the folder for out put files

JOB_NAME: the name of the job, and the prefix of the result file

parameters for distance and number-based partitioning

NUMBER_QM: number of qm molecules in number-based partitioning

NUMBER_BUFFER: number of buffer(transition) molecules in number-based partitioning

DISTANCE_QM: number of qm molecules in distance-based partitioning

DISTANCE_BUFFER: number of buffer(transition) molecules in distance-based partitioning

parameters for density-based partitioning

DORI: DORI threshold in density-based partitioning

SEDD: SEDD threshold in density-based partitioning

DENSITY_SEDD: density threshold in SEDD analysis

DENSITY_DORI: density threshold in DORI analysis

DENSITY_ASR_QMCORE: density threshold of adaptive search region for adaptive qm core (SEDD analysis)

DENSITY_ASR_QM: density threshold of adaptive search region for adaptive qm (DORI analysis)

DENSITY_RATIO_MIN: the minimum of density ratio of two atoms having inter-atomic interaction

DENSITY_RATIO_MAX: the maximum of density ratio of two atoms having inter-atomic interaction

SEDD_STEPSIZE: the step size of the cube in SEDD analysis.

DORI_STEPSIZE: the step size of the cube in DORI analysis.

REGION_CUBE: the region to construct a cube for the DORI/SEDD calculation. The suggested one is ADAPTIVE_SEARCH.

DENSITY_BUFFER: the density threshold for the buffer(transition) region in density-based partitioning

DENSITY_QM: the density threshold for the QM region in density-based partitioning, used in smoothing function.

smoothing

SMOOTHNER: the smoothing type.

smoothing DISTANCE_SCMP

DISTANCE_S_QM_IN: distance threshold for QM molecules into QM region

DISTANCE_T_QM_IN: distance threshold for QM molecules into transition region

DISTANCE_S_QM_OU: distance threshold for QM molecules out of QM region

DISTANCE_T_QM_OUT: distance threshold for QM molecules out of transition

DISTANCE_S_MM_IN: distance threshold for MM molecules into QM region

DISTANCE_T_MM_IN: distance threshold for MM molecules into transition region

DISTANCE_S_MM_OUT: distance threshold for MM molecules out of QM region

DISTANCE_T_MM_OUT: distance threshold for MM molecules out of transition

NUMBER_PARTITION: number of partitioning in DISTANCE_SCMP

DGRID: adopt radial grid for promolecular density

MAX_COMMS: number of max communities of clustering

INTERACTION_WEIGHT: True or False to calculate the strength(weight) of the interaction

WFC_PATH: the database path of radial grid for promolecular density

Enum Constant Summary

Enum Constants

Enum Constant and Description
DENSITY_ASR_QM
DENSITY_ASR_QMCORE
DENSITY_BUFFER
DENSITY_DORI
DENSITY_QM
DENSITY_RATIO_MAX
DENSITY_RATIO_MIN
DENSITY_SEDD
DGRID
DISTANCE_BUFFER
DISTANCE_QM
DISTANCE_S_MM_IN
DISTANCE_S_MM_OUT
DISTANCE_S_QM_IN
DISTANCE_S_QM_OUT
DISTANCE_T_MM_IN
DISTANCE_T_MM_OUT
DISTANCE_T_QM_IN
DISTANCE_T_QM_OUT
DORI
DORI_STEPSIZE
INTERACTION_WEIGHT
JOB_NAME
MAX_COMMS
NUMBER_BUFFER
NUMBER_PARTITION
NUMBER_QM
OUTPUT_FOLDER
PARTITIONER
REGION_CUBE
SEDD
SEDD_STEPSIZE
SMOOTHNER
WFC_PATH

Method Summary

Modifier and Type	Method and Description
static JobParameter	valueOf(java.lang.String name) Returns the enum constant of this type with the specified name.
static JobParameter[]	values() Returns an array containing the constants of this enum type, in the order they are declared.

Methods inherited from class java.lang.Enum

clone, compareTo, equals, finalize, getDeclaringClass, hashCode, name, ordinal, toString, valueOf

Methods inherited from class java.lang.Object

getClass, notify, notifyAll, wait, wait, wait

Enum Constant Detail

PARTITIONER

public static final JobParameter PARTITIONER

OUTPUT_FOLDER

public static final JobParameter OUTPUT_FOLDER

JOB_NAME

public static final JobParameter JOB_NAME

NUMBER_QM

public static final JobParameter NUMBER_QM

NUMBER_BUFFER

public static final JobParameter NUMBER_BUFFER

DISTANCE_QM

public static final JobParameter DISTANCE_QM

DISTANCE_BUFFER

public static final JobParameter DISTANCE_BUFFER

DORI

public static final JobParameter DORI

SEDD

public static final JobParameter SEDD

DENSITY_SEDD

public static final JobParameter DENSITY_SEDD

DENSITY_DORI

public static final JobParameter DENSITY_DORI

DENSITY_ASR_QMCORE

public static final JobParameter DENSITY_ASR_QMCORE

DENSITY_ASR_QM

public static final JobParameter DENSITY_ASR_QM

SEDD_STEPSIZE

public static final JobParameter SEDD_STEPSIZE

DORI_STEPSIZE

public static final JobParameter DORI_STEPSIZE

DENSITY_RATIO_MIN

public static final JobParameter DENSITY_RATIO_MIN

DENSITY_RATIO_MAX

public static final JobParameter DENSITY_RATIO_MAX

REGION_CUBE

public static final JobParameter REGION_CUBE

DENSITY_QM

public static final JobParameter DENSITY_QM

DENSITY_BUFFER

public static final JobParameter DENSITY_BUFFER

SMOOTHNER

public static final JobParameter SMOOTHNER

DISTANCE_S_QM_IN

public static final JobParameter DISTANCE_S_QM_IN

DISTANCE_T_QM_IN

public static final JobParameter DISTANCE_T_QM_IN

DISTANCE_S_QM_OUT

public static final JobParameter DISTANCE_S_QM_OUT

DISTANCE_T_QM_OUT

public static final JobParameter DISTANCE_T_QM_OUT

DISTANCE_S_MM_IN

public static final JobParameter DISTANCE_S_MM_IN

DISTANCE_T_MM_IN

public static final JobParameter DISTANCE_T_MM_IN

DISTANCE_S_MM_OUT

public static final JobParameter DISTANCE_S_MM_OUT

DISTANCE_T_MM_OUT

public static final JobParameter DISTANCE_T_MM_OUT

NUMBER_PARTITION

public static final JobParameter NUMBER_PARTITION

WFC_PATH

public static final JobParameter WFC_PATH

MAX_COMMS

public static final JobParameter MAX_COMMS

INTERACTION_WEIGHT

public static final JobParameter INTERACTION_WEIGHT

DGRID

public static final JobParameter DGRID

Method Detail

values

public static JobParameter[] values()

Returns an array containing the constants of this enum type, in the order they are declared. This method may be used to iterate over the constants as follows:

for (JobParameter c : JobParameter.values())
    System.out.println(c);

Returns:

an array containing the constants of this enum type, in the order they are declared

valueOf

public static JobParameter valueOf(java.lang.String name)

Returns the enum constant of this type with the specified name. The string must match exactly an identifier used to declare an enum constant in this type. (Extraneous whitespace characters are not permitted.)

Parameters:

name - the name of the enum constant to be returned.

Returns:

the enum constant with the specified name

Throws:

java.lang.IllegalArgumentException - if this enum type has no constant with the specified name

java.lang.NullPointerException - if the argument is null