Bugs item #3165083, was opened at 2011-01-25 06:24
Message generated for change (Tracker Item Submitted) made by dalke
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Category: File Translation
Group: 2.3.x
Status: Open
Resolution: None
Priority: 5
Private: No
Submitted By: Andrew Dalke (dalke)
Assigned to: Nobody/Anonymous (nobody)
Summary: minor buffer overflow in SMILES parser
Initial Comment:
atomic weight information leaks over into the atomic symbol in
OBSmilesParser::ParseComplex .
Here are two reproducibles
>>> mol = pybel.readstring("smi", "[987U]")
>>> mol.atoms[0].OBAtom.GetType()
'U87'
>>> pybel.readstring("smi", "[1234z]").write("smi")
==============================
*** Open Babel Warning in ParseComplex
Illegal aromatic element z]34
This is because the 'char symbol[7]' is used for isotope parsing then reused
for symbol parsing but without properly clearing the field.
The solution is to put a memset(symbol, '\0', 7*sizeof(char)) after
isotope = atoi(symbol);
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