openbabel / openbabel/openbabel

Allylic Radicals: Open Babel Error in Do 3D coordinate generation failed

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Description

Environment Information

Open Babel version: Open Babel 3.1.0 -- Jun 13 2022 -- 01:49:04
Operating system and version: MacOS Ventura 13.2.1

Expected Behavior

I expect to generate a 3D geometry for the allylic radical below:

obabel -:"C/C=C(C)/[CH2]" --gen3D --ff MMFF94 -h -oxyz

Actual Behavior

When I attempt to generate the 3D geometry for the allylic radical, I obtain an error instead:

obabel -:"C/C=C(C)/[CH2]" --gen3D --ff MMFF94 -h -oxyz
==============================
*** Open Babel Error  in Do
  3D coordinate generation failed
14

C          0.00000        0.00000        0.00000
C          0.00000        0.00000        0.00000
C          0.00000        0.00000        0.00000
C          0.00000        0.00000        0.00000
C          0.00000        0.00000        0.00000
H          0.00000        0.00000        0.00000
H          0.00000        0.00000        0.00000
H          0.00000        0.00000        0.00000
H          0.00000        0.00000        0.00000
H          0.00000        0.00000        0.00000
H          0.00000        0.00000        0.00000
H          0.00000        0.00000        0.00000
H          0.00000        0.00000        0.00000
H          0.00000        0.00000        0.00000
1 molecule converted

Changing the alkene geometry (obabel -:"C/C=C(C)\[CH2]" --gen3D --ff MMFF94 -h -oxyz) or removing the alkene geometry entirely (obabel -:"CC=C(C)[CH2]" --gen3D --ff MMFF94 -h -oxyz) has no impact; I get the same error.

The corresponding anion seems fine (including with the other alkene geometry):

obabel -:"C/C=C(C)/[CH2-]" --gen3D --ff MMFF94 -h -oxyz
14

C          0.93745        0.00500        0.09536
C          2.42550       -0.10483        0.03668
C          3.12936       -1.25052        0.00992
C          2.51958       -2.62452        0.04605
C          4.57019       -1.21118       -0.07364
H          0.64233        1.06012        0.10304
H          0.54410       -0.45593        1.00624
H          0.47811       -0.45886       -0.78226
H          2.95568        0.84895        0.00129
H          1.42593       -2.60389        0.06982
H          2.85452       -3.16324        0.93934
H          2.81401       -3.20125       -0.83735
H          5.10498       -0.27298        0.02505
H          5.10141       -2.05996       -0.48980
1 molecule converted

I can get a structure for the original allylic radical by enumerating the Hs on the radical explicitly, like so, with no alkene geometry specified:

obabel -:"CC=C(C)[C]([H])[H]" --gen3D --ff MMFF94 -h -oxyz
14

C          0.96609       -0.13361        0.10476
C          2.44475       -0.13741       -0.11041
C          3.09441        0.53782       -1.07856
C          2.42731        1.41491       -2.10109
C          4.53079        0.44165       -1.18629
H          5.08925       -0.26795       -0.58627
H          5.08002        1.18435       -1.75434
H          0.71893       -0.72475        0.99267
H          0.44834       -0.58446       -0.74721
H          0.59124        0.88077        0.26961
H          3.01264       -0.74417        0.59270
H          1.33640        1.40950       -2.01873
H          2.67599        1.07752       -3.11348
H          2.76034        2.45275       -1.99086
1 molecule converted

Any idea what might be going on here? The closest related issue I could find was #2317.

Thanks so much for any assistance!

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First steps

  1. Read the whole issue, then the project's contributing guide.
  2. Comment on the issue to say you are picking it up — it saves two people doing the same work.
  3. Fork the repository and make your change on a branch.
  4. Open a pull request that references the issue number.

Research direction

Start by reproducing the reported obabel --gen3D --ff MMFF94 command for the allylic radical and compare it with the working anion and explicitly hydrogenated forms. Read the handling of radical input and 3D coordinate generation, using issue #2317 as the related reference. Done means the original radical command generates valid, nonzero 3D coordinates without the reported error.

Written by the indexing model from the issue text.

Assessment

Tech stack
cpp
Domain
cli
Issue type
Bug
Difficulty
4/5
Estimated time
3-5 days
Activity status
Stale
Clarity
Mostly clear
Newbie friendliness
35/100

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