Regarding installing module MDAnalysis.lib.distances

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Deepshikha Ghosh 19310001

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Aug 12, 2022, 2:24:47 AMAug 12
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Dear Users

I am trying to calculate the distance between two residues (only for CA atoms) and this is the script which I am using:


import numpy as np
import MDAnalysis as mda
import pandas as pd
from MDAnalysis.lib.distance import distance_array

u= mda.Universe("protein_2000ns_autopsf.psf" , "protein_2000ns.dcd")
residues1 = u.select_atoms('protein and resid 1:85').residues
residues2 = u.select_atoms('protein and resid 1:85').residues

But I am getting the following error: No module named 'MDAnalysis.lib.distance'

I tried to install the above stated module but I am not able to do so (Note: I already have MDAnalysis installed). Any kind of help will be appreciated.

Thanks & Regards
Deepshikha Ghosh
IIT Gandhinagar

Hugo Macdermott-Opeskin

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Aug 12, 2022, 2:59:27 AMAug 12
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Hi Deepshikha and welcome! 

Just a simple bit of misspelling as far as I can see. You need  

MDAnalysis.lib.distances

Not 

MDAnalysis.lib.distance

Cheers

Hugo 

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Hugo MacDermott-Opeskin

Deepshikha Ghosh 19310001

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Aug 12, 2022, 3:30:14 AMAug 12
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Thankyou for your response.

I tried correcting it but still it is not working. I tried installing in the following manner:

conda config --add channels conda-forge
conda install MDAnalysis.lib.distances

Am I doing it the wrong way?

Thanks & Regards
Deepshikha Ghosh
IIT Gandhinagar 

Hugo Macdermott-Opeskin

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Aug 12, 2022, 3:33:47 AMAug 12
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You do not need to (/it’s I not possible to) conda install individual sub modules of MDAnalysis. The distances module should already be a part of your existing MDAnalysis installation. Can you import MDAnalysis currently ?


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Hugo MacDermott-Opeskin

Deepshikha Ghosh 19310001

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Aug 12, 2022, 4:25:27 AMAug 12
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Thankyou for your response. Yes I can import MDAnalysis currently, but when I try to use this particular module named " MDAnalysis.lib.distances", it is showing an error.

Thanks & Regards

Deepshikha Ghosh
IIT Gandhinagar


Hugo Macdermott-Opeskin

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Aug 12, 2022, 5:09:58 AMAug 12
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Would you be able to post the full error trace so I can see what it might be ?

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Hugo MacDermott-Opeskin

Deepshikha Ghosh 19310001

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Aug 12, 2022, 11:51:26 AMAug 12
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Kindly find the attachment.

Thanks & Regards
Deepshikha Ghosh
IIT Gandhinagar
check1.jpg

Oliver Beckstein

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Aug 12, 2022, 11:55:51 AMAug 12
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Hello Deepshikha Ghosh,

According to your error message, you are trying to `import MDAnalysis.lib.distance` but this is the WRONG name. Instead, use

import MDAnalysis.lib.distances

(the name of the module is ‘distances’ https://docs.mdanalysis.org/stable/documentation_pages/lib/distances.html#low-level-modules-for-mdanalysis-lib-distances ) — Hugo had already pointed out this problem in an earlier message.

Given that you’re using a notebook, I suggest you try “TAB-completion” when writing your code. This approach will automatically give you the correct names when you write your import statement.

Best,
Oliver


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Oliver Beckstein (he/his/him)

GitHub: @orbeckst

MDAnalysis – a NumFOCUS fiscally sponsored project





Deepshikha Ghosh 19310001

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Aug 14, 2022, 11:01:00 AMAug 14
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Thankyou for your response.

Regards
Deepshikha Ghosh
IIT Gandhinagar

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