Uses of Class
ffx.potential.cli.PotentialCommand

Packages that use PotentialCommand

Package	Description
ffx.potential.commands
ffx.potential.commands.test
ffx.potential.utils	The Utils package implements core functionality needed for using the Potential package, such as opening and closing structure files, basic force field energy evaluations, etc.

Uses of PotentialCommand in ffx.potential.commands

Subclasses of PotentialCommand in ffx.potential.commands

Modifier and Type	Class	Description
class	Biotype	Print out Biotype records for the atoms in an XYZ file.
class	Cart2Frac	Convert from Cartesian to fractional coordinates.
class	ChainBreaks	Fix chain breaks in a PDB file.
class	Density	Calculate the mean system density for single topology systems.
class	Energy	Compute the force field potential energy.
class	ExportQE	Generate Quantum Espresso (QE) input from an XYZ file.
class	Fasta	Fasta outputs a sub-sequence from a FASTA file.
class	FeatureMap	Create a Feature Map for a given protein structure.
class	FFtoXML	The FFtoXML command saves a force field as an XML file usable by OpenMM.
class	Frac2Cart	Convert from fractional to Cartesian coordinates.
class	ImportCIF	Convert a CIF file to PDB/XYZ format.
class	MoveIntoUnitCell	Move the center of mass of each molecule into the unit cell.
class	NucleicAcidAnalysis	Calculates nucleic acid torsions as well as information regarding the sugar pucker.
class	PhEnergy	The Energy script evaluates the energy of a system.
class	PrepareSpaceGroups	Create sub-directories for selected space groups.
class	SaveAsP1	Expand the system to P1 and then save it.
class	SaveAsPDB	Save the system as a PDB file.
class	SaveAsXYZ	Save the system as an XYZ (or ARC) file.
class	Solvator	The Solvator script puts a box of solvent around a solute.
class	Timer	The Timer command evaluates the wall clock time for energy and forces.
class	Volume	Calculate the surface area and volume using the GaussVol (default) or Connolly algorithm.
class	VolumeArc	Calculate the surface area and volume using the GaussVol (default) or Connolly algorithm for each snapshot in an ARC file.
class	WriteRestraints	WriteRestraints logs "restrain-position" properties for a PDB/XYZ file.

Uses of PotentialCommand in ffx.potential.commands.test

Subclasses of PotentialCommand in ffx.potential.commands.test

Modifier and Type	Class	Description
class	Gradient	The Gradient script evaluates the consistency of the energy and gradient.
class	LambdaGradient	The LambdaGradient script tests numeric gradients w.r.t. lambda against numeric, finite-difference gradients Usage: ffxc test.LambdaGradient [options] <filename> [file2...]
class	PhGradient	The Gradient script evaluates the consistency of the energy and gradient for CpHMD.
class	PrmToProperty	The PrmToProperty script converts a TINKER *.prm file to Java properties.
class	ReorderAtoms	The ReorderAtoms script sorts the atoms within an XYZ file based on atomic weight.
class	SaveAsConstantPhPDB	Save a PDB file that includes all titrating tautomer hydrogen atoms.

Uses of PotentialCommand in ffx.potential.utils

Fields in ffx.potential.utils declared as PotentialCommand

Modifier and Type	Field	Description
PotentialCommand	PotentialTest.potentialScript