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MobleyLab / off-ffcompare

Compare molecular structures after energy minimization in various force fields.
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OPLS input and behavior #46

Closed bannanc closed 7 years ago

bannanc commented 7 years ago

@nthi0625 and @vtlim I'll appologize now for not looking at this more closely sooner. I hadn't used the OPLS script before today, but there are a couple of other things I think it needs/should do

  1. It should raise an error if the schrodinger tool directory doesn't exist, its possible that the "$SCHRODINGER/..." should actually just be an input with $SCHRODINGER as the default; since technically a user can name this directory whatever they want.

  2. I think it would be best if like in min_oe_openMM you could run both OPLS3 and OPLS2005 at the same time, is there a reason why it doesn't just do both?

bannanc commented 7 years ago

It should also raise an error if the input directory doesn't exist

bannanc commented 7 years ago

It should also not perform the minimization if the output file already exists.

vtlim commented 7 years ago

reasonable suggestions, fixed by #47. but about your last comment, if output file already exists, the file could be empty so if do we want to check for this, then we should also add a check that file is not of size 0

bannanc commented 7 years ago

In PR #47 I addressed the follow:

  1. Checks the input directory
  2. Checks that the environment variable $SCHRODINGER exists
  3. It can run 1 or both of 2005 or 3 based on which output directory it was given.
  4. It skips the molecule if the output file exists, but I like your option of checking the size.

I also don't check if the input file is empty, I don't know if that is necessary or not

bannanc commented 7 years ago

We ended up checking if the file was empty in PR #47 so I think this can be closed.