Tleap InterMol support #146
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| @@ -2,6 +2,7 @@ name: paprika-dev | |||
| channels: | |||
| - conda-forge | |||
| - omnia | |||
| - mwt | |||
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Any thought about getting intermol onto conda-forge? I can't even find this channel after spending five minutes of Googling.
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Yeah, that's just my "personal" channel where I dump stuff from time to time. It's not really intended to be used by others, although I didn't put anything in place to prevent that. I don't believe I advertised this build, but again there's nothing hidden about it.
Putting it on conda-forge is something that probably should be done at some point. It should be feasible - the deps are really light - but some of the package structure might need a refresh. I can take it on.
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Ah! I didn't even connect mwt with @mattwthompson. Ha.
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Yeah, I found the package by searching Intermol on the anaconda website. It's not urgent, but if you can get it to conda-forge then 😍
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@j-wags do you want to take a look at this one, too, based on your experience getting multi-package support with OpenFF? |
paprika/tleap.py
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| class ConversionToolkit(Enum): | ||
| """ | ||
| An enumeration of the different toolkits for converting AMBER files to other MD formats. | ||
| """ | ||
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| ParmEd = "parmed" | ||
| InterMol = "intermol" |
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Not a strong opinion, but unless there's a compelling reason that each System should own a copy of this enum, it may be better to define it at the module level.
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No specific comments, but this is super cool. Thanks for tagging me! If you like, it should be possible to make a plugin registry for conversion packages like ParmEd and InterMol, so that it's easier to add more. I'm not sure it'd be worth the work (how many other conversion packages are there?), but it might allow some neat System format gymnastics. |
I'm not very familiar with this project, but if the goal is to convert AMBER files into other formats, the utility drops off quickly after these two packages. |
| assert is_file_and_not_empty(top_file) is True | ||
| assert is_file_and_not_empty(gro_file) is True |
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Totally out of scope here, but if for any reason you find yourself needing to also compare the energies before and after conversion, InterMol does that pretty well. I'll be working on doing this independently elsewhere in the next month or two, so it could possibly be something you can get for free in the future.
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Yeah, that would be a better way for testing, but you would need the MD executables to evaluate the energies?
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Yes, but they're mostly/all conda installable (save Desmond, I think) so it's possible to do that in a separate CI build
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I will (most) probably need help in configuring the CI build (sometime in the future). This will be useful to test the simulation wrappers as well.
For now, yes, the goal is just to convert AMBER files to other formats. I do plan on creating a class analogous to the |
A PR that enables the
tleapmodule to convert AMBER files to GROMACS, CHARMM, LAMMPS, and DESMOND format usingInterMol. For GROMACS and CHARMM, users have the option to convert the files usingParmEd.