restructure as a package

[Oliver Beckstein]

Conceptually, the code to download pdbs and the code to pull the coordination from a structure are very different. The code will be easier to read if you put them into separate files ("modules"). You could then start making a complete python "package". Come up with a good, short name for the whole thing, let's say "pdbsurvey" and then make a directory of the same name and put the modules under it:

   README.md
   LICENSE
   pdbsurvey/
                    __init__.py              # empty file (just have a single comment in there, needed for python)
                    collection.py            # contains code to get PDB files
                    ioncoordination.py       # contains g(r) code
  doc/
                    report.pdf
  notebooks/
                    Radial_Distribution.ipynb

You can then import the modules as

import pdbsurvey.collection
import pdbsurvey.ioncoordination

You can then also easily add other functionality such as

• running analysis on many files
• other analysis tasks (e.g. finding out how deep ions are inside proteins)
  without ending up with huge files of code that are impossible to read.

[Kacey Aurum]

Should I delete the .gitignore file?

[Oliver Beckstein]

No, leave it. It makes working with git more convenient.

Oliver Beckstein
email: [e-mail]

Am Dec 11, 2015 um 7:43 schrieb "Kathleen Clark (Kacey Reidy)" [e-mail]:

Should I delete the .gitignore file?

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Reply to this email directly or view it on GitHub.

[Kacey Aurum]

Okay, thanks.