RSoftPython

RSoftPython is a set of python code meant to easily facilitate some of the less computationally intensive proceedures of the RSoft project. Eventually, we would like to wrap all of the C++ code in the RSoft project and make it pythonic. In the meantime, the following sets of code primarily allow a user to do four things:

  • Design your own structure functions: In RSoftTools.RSoft, see OutputRSoftSF and the README on the RSoft github page.
  • Train and test hyperplanes: In RSoftTools.RSoft, see OpenDynamicsI, OpenSFI, OpenPlaneO, SelectTrainingSet, Train, WritePlane, CloseDynamicsI, CloseSFI, ClosePlaneO, and the tutorial in the README on the RSoft github page.
  • Interact with structure functions directly: In RSoftTools.RSoft, see OpenSFI, OpenSFO, CloseSFI, CloseSFO, GetAngular, GetRadial, SetAngular, and SetRadial.
  • Find distances between particles and construct neighbor lists (slow): In RSoftTools.MDTools, see DeltaR and GetNList. These are particularly helpful when one has periodic boundary conditions.

RSoftTools Classes

The following are classes within RSoftTools. They may be used by invoking the commands ‘from RSoftTools import RSoft’ and ‘from RSoftTools import MDTools’.

RSoftTools.RSoft() RSoft package for python.
RSoftTools.MDTools() Molecular Dynamics Tools for python

RSoft Methods

The following provides a list of functions that can be used on RSoft objects.

RSoftTools.RSoft.OpenDynamicsI(nc_file_name, …) Opens dynamic file in AMBER (netCDF) file format
RSoftTools.RSoft.OpenPlaneO(nc_file_name) Opens RSoftPlane file
RSoftTools.RSoft.OpenSFI(nc_file_name) Opens RSoftSF file
RSoftTools.RSoft.OpenSFO(nc_file_name) Opens RSoftSF file
RSoftTools.RSoft.CloseDynamicsI() CLoses input of AMBER NetCDF dynamics file
RSoftTools.RSoft.ClosePlaneO() Closes output of RSoftPlane file
RSoftTools.RSoft.CloseSFI() Closes input of RSoftSF file
RSoftTools.RSoft.CloseSFO() Closes output of RSoftSF
RSoftTools.RSoft.GetAngular(f) Gets angular structure functions
RSoftTools.RSoft.GetRadial(f) Gets radial structure functions
RSoftTools.RSoft.SetAngular(f, SF) Sets angular structure functions
RSoftTools.RSoft.SetRadial(f, SF) Sets radial structure functions
RSoftTools.RSoft.SelectTrainingSet(…[, …]) Selects training set
RSoftTools.RSoft.Train([n_eg, K, …]) Trains a softness hyperplane
RSoftTools.RSoft.WritePlane() Writes plane to RSoftPlane file

MDTools Methods

The following provides a list of functions that can be used on MDTool objects.

RSoftTools.MDTools.DeltaR(rf, ri, bb, bc) Difference between two vectors or sets of vectors
RSoftTools.MDTools.GetNList(pos_t, bb_t, bc, R_c) Obtains a neighbor list for a set of particles