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 |
RSoft Attributes¶
The following provides a list of attributes that can be used on RSoft objects.
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 |