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OpenBioSim / biosimspace_tutorials

A tutorials suite for BioSimSpace.
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Added missing help(process) cell in tutorial #9

Closed akalpokas closed 1 year ago

akalpokas commented 1 year ago

In the introductory tutorial notebook, specifically in https://github.com/OpenBioSim/biosimspace_tutorials/blob/main/01_introduction/03_molecular_dynamics.ipynb there is a cell missing that should show user how to get more information on the BioSimSpace.Process._amber object after equilibration calculation was ran with Amber. Currently that cell reads:

It's possible to query many other thermodynamic records. What's available depends on type of protocol and the MD package that is used to run the protocol. To get more information, run:

N.B. Certain functionality is specific to the process in question, i.e. BSS.Process.Amber will have different options to BSS.Process.Gromacs, but, for the purposes of interoperability, there is a core set of functionality that is consistent across all Process classes, e.g. all classes implement a getSystem method.)

This PR adds the missing help(process) code cell so that section now reads:

It's possible to query many other thermodynamic records. What's available depends on type of protocol and the MD package that is used to run the protocol. To get more information, run:

help(process)

N.B. Certain functionality is specific to the process in question, i.e. BSS.Process.Amber will have different options to BSS.Process.Gromacs, but, for the purposes of interoperability, there is a core set of functionality that is consistent across all Process classes, e.g. all classes implement a getSystem method.)

This addition is based on tutorial in the https://github.com/CCPBioSim/biosimspace-workshop/blob/master/01_introduction.ipynb notebook, where that help(process) cell is present but missing in https://github.com/michellab/BioSimSpaceTutorials/blob/main/01_introduction/03_molecular_dynamics.ipynb, which I assume is why it got carried over during the migration.