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JMK parser fix to account for xmipp pseudoatom writing changes #134

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JMK parser fix to account for xmipp pseudoatom writing changes #134

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893d5f4
fix pdb parser
jamesmkrieger Nov 2, 2022
87394db
use icode for 5-digit seq
jamesmkrieger Nov 2, 2022
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31 changes: 18 additions & 13 deletions continuousflex/protocols/utilities/pdb_parser.py
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Original file line number Diff line number Diff line change
Expand Up @@ -86,7 +86,7 @@ def m_inout_read_pdb(filename):
pdb_list = []
f = open(filename, 'r')
for line in f:
test_recd = line[0:5]
test_recd = line[:6]

# if test_recd.upper().strip() == "ATOM" or test_recd.upper() == "HETATM":
if ((test_recd.upper().strip() == "ATOM") or (test_recd.upper().strip() == "HETATM")):
Expand All @@ -98,33 +98,38 @@ def m_inout_read_pdb(filename):
except:
pass
try:
new_atom.type = line[12:14]
except:
pass
try:
new_atom.loc = line[14:16]
new_atom.type = line[11:15]
except:
pass
# try:
# new_atom.loc = line[14:16]
# except:
# pass
try:
new_atom.alt = line[16]
except:
pass
try:
new_atom.res = line[17:21]
new_atom.res = line[17:20]
except:
pass
try:
new_atom.chain = line[21]
except:
pass

try:
new_atom.seq = int(line[22:26])
new_atom.seq = int(line[23:27])
except:
pass
try:
new_atom.icode = line[26]
except:
pass
try:
new_atom.seq = int(line[23:26])
except:
pass
try:
new_atom.icode = line[26]
except:
pass

try:
new_atom.x = float(line[30:38])
except:
Expand Down