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Instability in fetching database #3

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flautodipan opened this issue Aug 19, 2021 · 1 comment
Open

Instability in fetching database #3

flautodipan opened this issue Aug 19, 2021 · 1 comment

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@flautodipan
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flautodipan commented Aug 19, 2021

Hi

CONTEXT

I am fetching the pdb database using rcsbsearch in order to find out if a certain ligand is covalently bound in a certain pdb of interest.

CODE
from rscbserach import Attr

results = Attr('rcsb_nonpolymer_instance_feature_summary.comp_id').exact_match(ligands[ii_lig]).and_('rcsb_nonpolymer_instance_feature_summary.type').exact_match('HAS_COVALENT_LINKAGE').and_('rcsb_nonpolymer_instance_feature_summary.count').equals(0).exec('assembly')

pdbs_not_cov = [r for r in results]

as an example, take
now_pdb = '6ymj'
ligands[ii_lig] = 'ADN'

PROBLEM
out.txt

With different runs of the same code, with exactly the same settings, I get different results. From PDB website ligand ADN result NOT covalently bound and so I should find it in the pdbs_not_cov list, but I don't, at least not always.

Attached you find a file with the results of two different runs in which the pdb in question 6ymj is found in the first run and not found in the second run, where you can find 6ymj in the first and not in the second.
The code to print is simply

for r in results:
print(r)

I tried almost everything. In the code I pasted I use the "fluent syntax" but I tried also the other one. Initially I thought the problem was using a set() when defining pdbs_not_cov, but then I realized that I had the same problem also without. I can't guess to which kind of problem this should be linked, can you please help me?

Thank you

@flautodipan
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p.s.
I am using the newest version of rcsbsearch 0.2.3

@flautodipan flautodipan changed the title Results of rcsbsearch are not stable Instability in fetching database Aug 20, 2021
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