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Removed PDB parsing

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1 parent 6673f0f commit 836d8e5c54f3a5fb01a038adb24e1447aad9e9e4 nisse committed
Showing with 7 additions and 4 deletions.
  1. +7 −4 Bio/PDB/DSSP.py
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11 Bio/PDB/DSSP.py
@@ -68,14 +68,12 @@ class DSSP:
Note that DSSP can only handle one model.
"""
- def __init__(self, pdb_file, dssp="dssp"):
+ def __init__(self, model, pdb_file, dssp="dssp"):
"""
pdb_file --- a PDB file
dssp --- the dssp executable (argument to os.system)
"""
p=PDBParser()
- s=p.get_structure("X", pdb_file)
- model=s[0]
# create DSSP dictionary
self.dssp_dict=dssp_dict_from_pdb_file(pdb_file, dssp)
map={}
@@ -136,7 +134,12 @@ def get_iterator(self):
import sys
- d=DSSP(sys.argv[1])
+ p=PDBParser()
+ s=p.get_structure('X', sys.argv[1])
+
+ model=s[0]
+
+ d=DSSP(model, sys.argv[1])
for r in d.get_iterator():
print r

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