DeepRank
compute_irmsd_fast() only works on two chains
>>> ref = "ref.pdb"
>>> model = "model.pdb"
>>> sim = StructureSimilarity(model,ref)
>>> irmsd_fast = sim.compute_irmsd_fast()
Traceback (most recent call last):
File "<stdin>", line 1, in <module>
File "/home/lixue/tools/anaconda3/lib/python3.7/site-packages/pdb2sql/StructureSimilarity.py", line 277, in compute_irmsd_fast
resData = self.compute_izone(cutoff, save_file=False)
File "/home/lixue/tools/anaconda3/lib/python3.7/site-packages/pdb2sql/StructureSimilarity.py", line 328, in compute_izone
'exactly two chains are needed for irmsd calculation but we found %d' % len(chains), chains)
ValueError: ('exactly two chains are needed for irmsd calculation but we found 5', ['A', 'B', 'C', 'D', 'E'])
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To solve this issue, I am planning to add an option chain_pairs = ['D:E', 'AB:C'] to compute_izone(). This way, pdb2sql knows which interfaces are of interest when calculating i-RMSD for a multiple-chain complex.
i've suggested to make a few change to Li's work see #80. This basically allows to use get_contact_atoms using multiple chains as :
db.get_contact_atoms(chain1='AB', chain2='C')
This issue is stale because it has been open for 30 days with no activity. Remove stale label or comment or this will be closed in 7 days.