Uses of Class
ffx.potential.cli.TopologyOptions

Packages that use TopologyOptions

Package	Description
ffx.algorithms.cli	The Algorithms CLI package defines options for PicoCLI command line scripts.
ffx.potential.cli	The Potential CLI package defines reusable options for PicoCLI command line scripts.

Uses of TopologyOptions in ffx.algorithms.cli

Methods in ffx.algorithms.cli with parameters of type TopologyOptions

Modifier and Type	Method	Description
MolecularAssembly	MultiDynamicsOptions.openFile(AlgorithmFunctions algorithmFunctions, TopologyOptions topologyOptions, int threadsPer, String toOpen, int topNum, AlchemicalOptions alchemicalOptions, File structureFile, int rank)	Opens a file and processes it.

Uses of TopologyOptions in ffx.potential.cli

Methods in ffx.potential.cli with parameters of type TopologyOptions

Modifier and Type	Method	Description
MolecularAssembly	AlchemicalOptions.openFile(PotentialsFunctions potentialFunctions, TopologyOptions topologyOptions, int threadsPer, String toOpen, int topNum)	Opens a File to a MolecularAssembly for alchemistry.
MolecularAssembly	AlchemicalOptions.processFile(TopologyOptions topologyOptions, MolecularAssembly molecularAssembly, int topNum)	Performs processing on a MolecularAssembly for alchemistry.