Group Meeting 11.4.19 - TechnionYP5779/SimuMole GitHub Wiki

Participants: Eyal, Idan, Ilanit, Michael, Nitzan.

Meeting duration: 45 minutes.

Meeting summary

We reviewed our progress since the previous meeting:

  • Fetch PDB files with PyMOL using the script pymol_test.py:

    • The input is the PDB files: each of the parameters can be a path to a local PDB file or a PDB ID (in case that the molecule has ID that can be retrieved from an Internet database such as RCSB).
    • The script loads the two molecules into PyMOL (without any movement of them - it uses the original coordinates of the molecules).
    • The output is a single PDB file that describes the two molecules as now displayed by PyMOL (i.e., the two PDB files are merged into a single PDB file, without any change of coordinates).

  • Move a molecule along the axes (x,y,z) using the script transformations.py:

    • The input is the name of the original PDB file, the name of the new PDB file that will be written by the script, and delta(x,y,z) - the distance each atom will move along each axis.
    • The output is a new PDB file, which is identical to the original PDB file, except that the coordinates of each atom were shifted by delta(x,y,z).

  • Generate OpenMM code using the script OpenMM_scriptBuilder.py:

    • The input is a list of parameters that OpenMM requires for the creation of a simulation (for example, the input PDB file). Each parameter has a default value.
    • The output is a python file with the generated code (another option is to run the generated code directly).

  • Create the web app and upload PDB files into it using Django:

    • The base folders of the application were uploaded to GitHub (for example, SimuMole/SimuMole describes the backend and SimuMole/SimuMoleWeb describes the frontend).
    • Upload files to the web app: this can be done via Django, but we are still investigating exactly how it can be done.

Tasks for the next meeting:

  • Follow Django web-app tutorial, as shown in this wiki.
  • Follow Django tutorials and understand Django web-app's structure. In addition, we need to understand how to upload PDB files into the web app, and how to run our python scripts through it.