Hi again Bakary, Another very naive question: How can I modify the "get_spectrophore" script in order to specify the various options for "obspectrophore"? The options are -i : molecular input file; -n: type of normalization; -a accuracy; -s: type of cage; -r: resolution. Can I add these in the "cmd" line?
Thanks. -- Rudy On Tue, Mar 17, 2020 at 9:28 AM Rudy Richardson <rjr...@umich.edu> wrote: > 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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