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LokeyLab / Peptide-Library-Utility

Create linear and cyclic peptide libraries in silico and evaluate some basic cheminformatic values.
MIT License
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Invalid VCS root mappings #11

Closed engstromyo closed 2 years ago

engstromyo commented 2 years ago

When I run setup, I get this error... pls hel

Screen Shot 2022-08-23 at 10 00 22 AM

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brodohfasho commented 2 years ago

Hi Adam,

Not sure what happened, it was working last week but both Alex and I are now getting this invalid VCS root mapping error. I went into the .ideas folder and removed VCS.html which seems to clear up the error, but it still isn't working properly. It seems to be enumerating the library properly but no excel or sdf files are being saved to my computer (a folder isn't even being made).

Any ideas?

~Grant

brodohfasho commented 2 years ago

Error2 Error3 Error

brodohfasho commented 2 years ago

Get these errors when I debug the code

brodohfasho commented 2 years ago

Those errors are only when the VCS.html is removed. No reported errors other than the other Alex posted when that file is in the .ideas folder. Still no files being saved when we run the peptide library utility though.

brodohfasho commented 2 years ago

Sorry, I think I also get those same errors even if VCS.html is in the folder. It only spits those errors if you try to debug after\while running a library generation

Adiaslow commented 2 years ago

@engstromyo @brodohfasho Taking a look at the issue now, will let y'all know what I find!

Adiaslow commented 2 years ago

Update: Trying to use pathlib2 to fix the path issues that might come up. This may or may not fix the issue.

Adiaslow commented 2 years ago

@engstromyo @brodohfasho Can you send me the input spreadsheet you are using?

brodohfasho commented 2 years ago

Yep, i’ll send it to you around 1pm today!

On Thu, Aug 25, 2022 at 11:18 AM Adam Murray @.***> wrote:

@engstromyo https://github.com/engstromyo @brodohfasho https://github.com/brodohfasho Can you send me the input spreadsheet you are using?

— Reply to this email directly, view it on GitHub https://github.com/LokeyLab/Peptide-Library-Utility/issues/11#issuecomment-1227611294, or unsubscribe https://github.com/notifications/unsubscribe-auth/A2MAKNGLZTQUB3U63XHPIZTV262ITANCNFSM57MH4S3A . You are receiving this because you were mentioned.Message ID: @.***>

-- Grant Koch Graduate Student Lokey Research Group Department of Chemistry and Biochemistry University of California, Santa Cruz

brodohfasho commented 2 years ago

Hey adam,

Your UCSC email seems to be dead. Here's my spreadsheet!

~Grant LDEL_LESpreadsheet.csv

engstromyo commented 2 years ago

PROTALs - input (6).csv

Adiaslow commented 2 years ago

@engstromyo @brodohfasho Brother's, in the mean time, perhaps give this a try.

You many need this.

This may be a problem with the way I'd showed you how to get the script. I'd had you download the ZIP instead of clone it directly. Cloning it would allow you to more easily keep it up to date by just "pulling" the repository from PyCharm instead of having to go and delete a folder and stuff.

A reminder when doing this, keep your subunit spread sheets somewhere so they don't get overwritten. Unless you're into that kind of thing 😏. No judgement.

I'll keep working on getting this issue fixed so it works either way though and keep y'all updates.

brodohfasho commented 2 years ago

Hey Adam,

I have Git version 2.33.0 installed already!

I managed to clone the project and it seems to work properly now... I'll update once I've tested some custom subunits and such.

Thanks Adam!!

Adiaslow commented 2 years ago

@brodohfasho SWEEEETTT!!!! I'm working on a big revamp of the program.. It'll be a sec, but I'm hoping to have all the amino acids and their variants down perfectly with the next update.

Good luck!

brodohfasho commented 2 years ago

Sick. I managed to get the beta homo amino acids to work well, I've attached my misc subunit file if you wanna copy that.

A few things I've noticed when using it that could be fixed\improved -When you're in the peptide library generator, the program will default to presenting the main screen after you select an input excel file, which is mildly annoying but not a big deal. -The program tends to crash when generating the excel and sdf files. It'll gray screen and say "waiting for program to respond" but will still work and finish the job. Not sure if there's anything you can do about that. It's particularly bad when making bigger libraries. -Implementing that AlogP_86 calculator Jaru found would be extremely useful for our lab so we wouldn't have to mess around in discovery studio (sdf file is massive and takes a long time to load and manipulate)

Thanks so much Adam. We miss you dawg. Lab aint the same without you!

~Grant

On Wed, Sep 7, 2022 at 9:25 AM Adam Murray @.***> wrote:

@brodohfasho https://github.com/brodohfasho SWEEEETTT!!!! I'm working on a big revamp of the program.. It'll be a sec, but I'm hoping to have all the amino acids and their variants down perfectly with the next update.

Good luck!

— Reply to this email directly, view it on GitHub https://github.com/LokeyLab/Peptide-Library-Utility/issues/11#issuecomment-1239616078, or unsubscribe https://github.com/notifications/unsubscribe-auth/A2MAKNEQZVF3H3MYFI7257DV5C6WPANCNFSM57MH4S3A . You are receiving this because you were mentioned.Message ID: @.***>

-- Grant Koch Graduate Student Lokey Research Group Department of Chemistry and Biochemistry University of California, Santa Cruz

Adiaslow commented 2 years ago

@brodohfasho

Glad you are able to work around some of the issues that pop up for you! This is a good place to put them as you find 'em and I'll get to them at some point.

The switching to the main window, I think, is a simple fix. Hope to have that done soon. I may fix it when I release the new version of the GUI.

Hoping also the crashing may be an easy fix.

The AlogP_86 is not so simple, but seems possible. It is in Java and this is in Python. Options I am exploring is writing some code to be able to call Java methods in Python or, if possible, just implementing the AlogP_86 by hand in Python. We'll see which one is more feasible / functional.

You are very welcome. I miss y'all too. I am really looking forward to at least being in the same building if not working together again soon.

Bunch of love and gratitude, Adam