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Improved handling of insertion codes #184

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Aug 9, 2019
Merged

Improved handling of insertion codes #184

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17 changes: 11 additions & 6 deletions pdbfixer/pdbfixer.py
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Original file line number Diff line number Diff line change
Expand Up @@ -599,12 +599,17 @@ def findMissingResidues(self):
# Find the sequence of each chain, with gaps for missing residues.

for chain in chains:
minResidue = min(int(r.id) for r in chain.residues())
maxResidue = max(int(r.id) for r in chain.residues())
residues = [None]*(maxResidue-minResidue+1)
for r in chain.residues():
residues[int(r.id)-minResidue] = r.name
chainWithGaps[chain] = residues
residues = list(chain.residues())
ids = [int(r.id) for r in residues]
for i, res in enumerate(residues):
if res.insertionCode not in ('', ' '):
for j in range(i, len(residues)):
ids[j] += 1
minResidue = min(ids)
maxResidue = max(ids)
chainWithGaps[chain] = [None]*(maxResidue-minResidue+1)
for r, id in zip(residues, ids):
chainWithGaps[chain][id-minResidue] = r.name

# Try to find the chain that matches each sequence.

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