malformed SDF string causes segfault

[itdaniher]

import chemkit
st = """ 2 1 0 0 0 0 999 V2000
... -0.4125 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
... 0.4125 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0"""
f = chemkit.MoleculeFile()
f.setFormat("sdf")
True
f.readString(st)
Segmentation fault: 11

For your copying and pasting pleasure, the string above is:

' 2 1 0 0 0 0 999 V2000\n -0.4125 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n 0.4125 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n'

[kylelutz]

Strange, I don't get a segfault when I run it. For me, the file is read successfully but only an empty molecule is returned. Could you run it under gdb and post the backtrace?

The main issue is that the file data doesn't start with the three comment lines. Prepending "\n\n\n" to the string resolves the issue and the ethane molecule is read correctly.

[itdaniher]

Interesting, when I run from the string I copied and pasted above, it does not segfault. That said, https://gist.github.com/2923979 does segfault repeatably, and from within gdb.

Program received signal EXC_BAD_ACCESS, Could not access memory.
Reason: KERN_INVALID_ADDRESS at address: 0xfffffffffffffff0
0x0000000102670246 in MdlFileFormat::readSdfFile ()