missing import file - Githubissues

cerabinowitz commented 1 year ago

In des3pi_one_run.py there seems to be a missing file for import clustering, can the file be added to the repo?

maxence92 commented 1 year ago

Dear cerabinowitz,

Thank you for your interest in our method.

There were probably an upload issue. The module clustering.py have just been added to the repo. We also updated the file des3pi_one_run.py, so please update the whole repository before trying again.

Please let us know if you need any help in the use of Des3PI.

Regards.

cerabinowitz commented 1 year ago

Thank you!

There also seems to be a missing directory called "aa_library", would you be able to upload that as well?

maxence92 commented 1 year ago

Sure, it has been done.

Sorry for these upload problems.

I keep this discussion open until you are able to run the software.

Regards.

cerabinowitz commented 1 year ago

I am running into another error now.

Traceback (most recent call last):
  File "/home/Public_Des3PI/des3pi_one_run.py", line 65, in <module>
    compute_ca.compute_ca(start_dir,nb_dock)
  File "/home/Public_Des3PI/compute_ca.py", line 17, in compute_ca
    os.chdir(fragment_name)
FileNotFoundError: [Errno 2] No such file or directory: 'ile'

Is there just supposed to be a line above this that creates a directory fragment_name?

maxence92 commented 1 year ago

The line that was suppose to create the fragment directory and run the docking of all the amino acids was muted to test part of the code.

I just fixed the muted line to make it work.

You just need to update the repository on your local machine

Tell me if everything is ok after this.

cerabinowitz commented 1 year ago

I am having some trouble installing vina - how did you install it to use it in run_simulation.py?

maxence92 commented 1 year ago

As the installation of VINA was done a long time before my PhD position in the team, I just know that we are using AutoDock Vina 1.1.2 that you can download here https://vina.scripps.edu/downloads/. The program has to be installed on your Linux system. Des3PI calls VINA function using a bash command line. Make sure you are able to call "vina" on a linux terminal.

If you don't find a way to install VINA, I will check the way it is done on my computer in the beginning of next week (Tomorrow is a day-off in France, I don't have the access to the lab).

Regards

thaduong commented 1 year ago

Dear Cerabinowitz,

To install Vina, please visit the web site https://vina.scripps.edu/downloads/ and follow the installation instruction. If you are on a Debian-based Linux, I think that you can also open a terminal and simply type the command : "sudo apt install vina"

Best regards,

Pr Tâp HA-DUONG BioCIS - UMR CNRS 8076 - Équipe FLUOPEPIT 17 avenue des Sciences, 91400 ORSAY Bâtiment HM1 - 1er étage - Bureau 1804 Tel : 01 80 00 63 76

De: "cerabinowitz" @.> À: "des3pi/Public_Des3PI" @.> Cc: "Subscribed" @.***> Envoyé: Jeudi 13 Juillet 2023 21:48:02 Objet: Re: [des3pi/Public_Des3PI] missing import file (Issue #1)

I am having some trouble installing vina - how did you install it to use it in run_simulation.py?

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cerabinowitz commented 1 year ago

Thank you, I think I got it working.

I had to change the vina command to the path of the vina binary file.

des3pi / Public_Des3PI

missing import file #1