Instability in fetching database

[flautodipan]

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]

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