"--gen3D" option generates a segmentation fault when converting hydrogen isotopomers in InChI to MOL/SDF format.

[hunter-moseley]

• I believe this to be a bug with Open Babel
  This bug may be related to other "--gen3D" bugs reported, but it is not obvious from the description of those issues.

Environment Information

Open Babel version: 2.4.1
Operating system and version: Fedora 27

Expected Behavior

The "--gen3D" would create a stereospecific MOL/SDF file for a stereospecific InChI.
The following command should work without generating a segmentation fault:
% obabel -iinchi alpha-d-glucopyranose_modified_H13-2H.inchi -omol -Oalpha-d-glucopyranose_modified_H13-2H.inchi.mol --gen3D

Actual Behavior

Conversion of the following InChI strings into MOL/SDF format with the "--gen3D" option generates a Segmentation Fault.

InChI=1S/C6H12O6/c7-1-2-3(8)4(9)5(10)6(11)12-2/h2-11H,1H2/t2-,3-,4+,5-,6+/m1/s1/i1D/t1-,2-,3-,4+,5-,6+
InChI=1S/C6H12O6/c7-1-2-3(8)4(9)5(10)6(11)12-2/h2-11H,1H2/t2-,3-,4+,5-,6+/m1/s1/i1D/t1-,2+,3+,4-,5+,6-/m0

Even the non-stereospecific InChI causes a seg fault with the --gen3D option:

InChI=1S/C6H12O6/c7-1-2-3(8)4(9)5(10)6(11)12-2/h2-11H,1H2/t2-,3-,4+,5-,6+/m1/s1/i1D

Steps to Reproduce

Just use the InChI provided to reproduce.

[serval2412]

On pc Debian x86-64 with master sources updated today, I could reproduce this.
Here's the bt:
bt.txt

[hunter-moseley]

FYI. The following is the correct non-stereospecific InChI string:
InChI=1S/C6H12O6/c7-1-2-3(8)4(9)5(10)6(11)12-2/h2-11H,1H2/t2-,3-,4+,5-,6+/m1/s1/i1D/t1?,2-,3-,4+,5-,6+

[timvdm]

The issue is that OBAtom::GetType() always returns "D" for deuterium.

  char *OBAtom::GetType()
  {
    ...
    if (_ele == 1 && _isotope == 2)
      snprintf(_type, 6, "%s", "D");

    return(_type);
  }

Adding an entry for D in UFF.prm fixes the issue.

Fix can be found here: https://github.com/timvdm/openbabel/tree/issue1794

[hunter-moseley]

Thanks for the fix!

…

On Tue, Jan 7, 2020 at 6:09 PM Tim Vandermeersch ***@***.***> wrote: The issue is that OBAtom::GetType() always returns "D" for deuterium. char *OBAtom::GetType() { ... if (_ele == 1 && _isotope == 2) snprintf(_type, 6, "%s", "D"); return(_type); } Adding an entry for D in UFF.prm fixes the issue. Fix can be found here: https://github.com/timvdm/openbabel/tree/issue1794 — You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub <#1794?email_source=notifications&email_token=ADEP7B2DPP5RCMDFURZLUTLQ4UDSRA5CNFSM4EV3O3AKYY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOEIKTO3Q#issuecomment-571815790>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ADEP7B7ZQWEH7LDEAIHACGTQ4UDSRANCNFSM4EV3O3AA> .

-- Hunter Moseley, Ph.D. -- Univ. of Kentucky Associate Professor, Dept. of Molec. & Cell. Biochemistry / Markey Cancer Center / Resource Center for Stable Isotope Resolved Metabolomics Not just a scientist, but a fencer as well. My foil is sharp, but my mind sharper still. --------------------------------------------------------------- Email: hunter.moseley@uky.edu (work) hunter.moseley@gmail.com (personal) Phone: 859-218-2964 (office) 859-218-2965 (lab) 859-257-7715 (fax) Web: http://bioinformatics.cesb.uky.edu/ Address: CC434 Roach Building, 800 Rose Street, Lexington, KY 40536-0093