Package ffx.realspace.cli

Class RealSpaceOptions

java.lang.Object

ffx.xray.cli.DataRefinementOptions

ffx.realspace.cli.RealSpaceOptions

public class RealSpaceOptions
extends DataRefinementOptions

Represents command line options for scripts that utilize a real-space density map.

Since:

1.0

Author:

Michael J. Schnieders, Soham Ali

Field Summary

Fields

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

Fields inherited from class ffx.xray.cli.DataRefinementOptions

wA

Constructor Summary

Constructors

Constructor	Description
RealSpaceOptions()

Method Summary

Modifier and Type	Method	Description
List<RealSpaceFile>	processData(List<String> filenames, MolecularAssembly molecularAssembly)	Process input to collect Real Space Files.
RefinementEnergy	toRealSpaceEnergy(List<String> filenames, MolecularAssembly[] molecularAssemblies)	Process input from opened molecular assemblies 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.

Constructor Details

RealSpaceOptions

public RealSpaceOptions()

Method Details

processData

public List<RealSpaceFile> processData(List<String> filenames,
 MolecularAssembly molecularAssembly)

Process input to collect Real Space Files.

Parameters:

filenames - Input filenames (first filename is ignored).

molecularAssembly - Currently open molecularAssembly.

Returns:

a list of Real Space File instances.

toRealSpaceEnergy

public RefinementEnergy toRealSpaceEnergy(List<String> filenames,
 MolecularAssembly[] molecularAssemblies)

Process input from opened molecular assemblies to a RefinementEnergy

Parameters:

filenames - All filenames included in the real-space data.

molecularAssemblies - Array of MolecularAssembly instances.

Returns:

An assembled RefinementEnergy with real-space energy.