Bakary, I am very new to using python, but I think I have addressed the problem by adding the following line to "obspectrophores_euclidean" after "import numpy as np" (without the ==== or the quote marks):
===== "from get_spectrophore import get_spectrophore" ===== Is this a valid thing to do? In any event, the script now runs and appears to be giving correct results. BTW, I forgot to mention that previously I also got an error about indentation and I fixed that. Thanks again for so kindly furnishing the scripts! Best regards, Rudy On Tue, Mar 17, 2020 at 8:56 AM Rudy Richardson <rjr...@umich.edu> wrote: > Hi Bakary, > > The get_spectrophore.py script works for me, but the > obspectrophores_euclidean.py script does not. I get the following message: > ===== > Traceback (most recent call last): > File "obspectrophores_euclidean.py", line 21, in <module> > print(obspectrophores_euclidean(test_ligand, test_ligand)) #should > return zero > File "obspectrophores_euclidean.py", line 9, in obspectrophores_euclidean > ligand1_spectrophore = get_spectrophore(ligand1) > NameError: name 'get_spectrophore' is not defined > ===== > > Suggestions welcome! Thanks. > > -- Rudy > > > > > On Mon, Mar 16, 2020 at 3:11 PM Bakary N'tji Diallo < > diallobaka...@gmail.com> wrote: > >> Sure! >> That what the obspectrophores_euclidean.py does. It supports sdf with >> multiple compounds. >> >> >> On Mon, 16 Mar 2020 at 20:06, Rudy Richardson <rjr...@umich.edu> wrote: >> >>> Hi Bakary, >>> >>> Thanks for the scripts! >>> >>> Is there a way to expand upon the Euclidean script to calculate the >>> distance from a reference ligand spectrophore and N spectrophores from N >>> different ligands? >>> >>> -- Rudy >>> >>> >>> On Mon, Mar 16, 2020 at 1:46 PM Bakary N'tji Diallo < >>> diallobaka...@gmail.com> wrote: >>> >>>> >>>> If you working in python this should help you. >>>> I wrote these scripts when using obspectrophores. "get_spectrophore.py" >>>> will get you a compound spectrophore (tested with sdf but should work with >>>> other obabel supported format).The second one will compute their euclidean >>>> distances. >>>> >>>> >> >> -- >> >> Bakary N’tji DIALLO >> >> PhD Student (Bioinformatics) <http://linkedin.com/in/bakarydiallo>, Research >> Unit in Bioinformatics (RUBi) <https://rubi.ru.ac.za/> >> >> Mail: diallobaka...@gmail.com | Skype: diallobakary4 >> >> Tel: +27798233845 | +223 74 56 57 22 | +223 97 39 77 14 >> >>
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