[CRITICAL ERROR] If you .write as an inchi, a core dump happens.

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#977 [CRITICAL ERROR] If you .write as an inchi, a core dump happens.

Milestone: 2.4.x

Status: open

Owner: nobody

Labels: inchi (2) pybel (2) pointer (1) error (1)

Priority: 1

Updated: 2016-10-13

Created: 2016-10-13

Creator: annyoinglogin

Private: No

If you try to use pybel to readstring an inchi, then try to write it out as an inchi again, you get a pointer error and a core dump. This is a serious error.

like this:

mol = pybel.readstring("inchi","InChI=1S/C4H10/c1-3-4-2/h3-4H2,1-2H3\n")
mol
<pybel.molecule object="" at="" 0x7fbe5d1611d0="">
mol.write()
'CCCC\t\n'
mol.write("inchi")
*** glibc detected *** python: free(): invalid pointer: 0x00007fbe5c6f14c0 ***
======= Backtrace: =========
/lib64/libc.so.6[0x3e6aa75e66]
/lib64/libc.so.6[0x3e6aa7897a]
/tools/bioinfo/app/openbabel-2.3.1/lib/libinchi.so.0(FreeINCHI+0x11)[0x7fbe5a7d7701]
...
core dump</pybel.molecule>

Please investigate it to see what's going on

Discussion

annyoinglogin - 2016-10-13

Expected output should just be the inchi

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[CRITICAL ERROR] If you .write as an inchi, a core dump happens.

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#977 [CRITICAL ERROR] If you .write as an inchi, a core dump happens.

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