Package ffx.xray.cli

Class XrayOptions

java.lang.Object

ffx.xray.cli.DataRefinementOptions

ffx.xray.cli.XrayOptions

public class XrayOptions
extends DataRefinementOptions

Represents command line options for scripts that utilize X-ray data with a maximum likelihood target.

Since:

1.0

Author:

Michael J. Schnieders

Field Summary

Fields

Modifier and Type	Field	Description
RefinementMinimize.RefinementMode	refinementMode	The refinement mode to use.
CrystalReciprocalSpace.SolventModel	solventModel	The SolventModel to use.

Fields inherited from class ffx.xray.cli.DataRefinementOptions

wA

Constructor Summary

Constructors

Constructor	Description
XrayOptions()

Method Summary

Modifier and Type	Method	Description
DiffractionData	getDiffractionData(List<String> filenames, MolecularAssembly[] assemblies, org.apache.commons.configuration2.CompositeConfiguration properties)	Process input from opened molecular assemblies to a DiffractionData.
void	init()	Parse options.
List<DiffractionFile>	processData(List<String> filenames, MolecularAssembly[] systems)	Process input to collect Diffraction Files.
void	setProperties(picocli.CommandLine.ParseResult parseResult, org.apache.commons.configuration2.CompositeConfiguration properties)	setProperties.
RefinementEnergy	toXrayEnergy(DiffractionData diffractionData)	Process input from opened molecular assemblies and diffraction data to a RefinementEnergy.

Methods inherited from class ffx.xray.cli.DataRefinementOptions

getwA

Methods inherited from class java.lang.Object

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

Field Details

refinementMode

public RefinementMinimize.RefinementMode refinementMode

The refinement mode to use.

solventModel

public CrystalReciprocalSpace.SolventModel solventModel

The SolventModel to use.

Constructor Details

XrayOptions

public XrayOptions()

Method Details

init

public void init()

Parse options.

processData

public List<DiffractionFile> processData(List<String> filenames,
 MolecularAssembly[] systems)

Process input to collect Diffraction Files.

Parameters:

filenames - Input filenames (first filename is ignored).

systems - Currently open systems.

Returns:

a list of DiffractionFile instances.

setProperties

public void setProperties(picocli.CommandLine.ParseResult parseResult,
 org.apache.commons.configuration2.CompositeConfiguration properties)

setProperties.

Parameters:

parseResult - a CommandLine.ParseResult object.

properties - a CompositeConfiguration object.

getDiffractionData

public DiffractionData getDiffractionData(List<String> filenames,
 MolecularAssembly[] assemblies,
 org.apache.commons.configuration2.CompositeConfiguration properties)

Process input from opened molecular assemblies to a DiffractionData.

Parameters:

filenames - All filenames included in the diffraction data.

assemblies - All molecular assemblies included in the diffraction data.

properties - The properties to apply.

Returns:

An assembled DiffractionData

toXrayEnergy

public RefinementEnergy toXrayEnergy(DiffractionData diffractionData)

Process input from opened molecular assemblies and diffraction data to a RefinementEnergy.

Parameters:

diffractionData - Diffraction data.

Returns:

An assembled RefinementEnergy with X-ray energy.