ReactionMechanismGenerator / ReactionMechanismGenerator/ARC

Updating to 6.6.0 XTB

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Type: Feature
Dominant language
Python
Stars
51
Forks
25
Avg merge
4d 5h
Merged PRs (30d)
15

Description

Currently we use xtb 6.3.3

If we are to update to 6.6.0 we need to modify our mol.sdf files into the correct format for xtb 6.6.0 to calculate and return normal termination

Here is an example mol.sdf file that works on 6.3.3

     RDKit          3D

 10  9  0  0  0  0  0  0  0  0999 V2000
    1.1517   -0.3760   -0.5231 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.2893    0.4500    0.3115 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1415   -0.0561    0.2592 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.1386   -1.3376   -0.1854 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.1151   -0.0555   -0.4352 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.6517    0.4342    1.3447 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.3279    1.4855   -0.0414 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2133   -1.0839    0.6308 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7870    0.5726    0.8809 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5327   -0.0332   -0.7636 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  1  4  1  0
  1  5  1  0
  2  3  1  0
  2  6  1  0
  2  7  1  0
  3  8  1  0
  3  9  1  0
  3 10  1  0
M  END
$$$$

However, this will not run on xtb 6.6.0

########################################################################
[ERROR] Program stopped due to fatal error
-2- reading geometry input 'mol.sdf' failed
-1- Error: Cannot read topology from connection table
  --> mol.sdf:15:13-15
   |
15 |   1  2  1  0
   |             ^^^ unexpected value
   |
########################################################################
abnormal termination of xtb
ERROR STOP 

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  3. Fork the repository and make your change on a branch.
  4. Open a pull request that references the issue number.

Research direction

Locate the code that generates the mol.sdf input and reproduce the reported failure with xtb 6.6.0. Compare the generated connection table with the format accepted by that version; done when the calculation reaches normal termination while preserving compatibility with the existing workflow.

Written by the indexing model from the issue text.

Assessment

Tech stack
python
Domain
tooling
Issue type
Bug
Difficulty
3/5
Estimated time
1-2 days
Activity status
Quiet
Clarity
Mostly clear
Newbie friendliness
48/100

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