ReactionMechanismGenerator / ReactionMechanismGenerator/ARC

ARC predicts a wrong optical isomers number

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

Description

Describe the bug
ARC uses the S. Patchkovskii brute force algorithm for determining symmetry and number of chiral centers. It gets the number of chiral centers wrong as reported here.
It also got it wrong for simle species such as [CH2]O.

How to reproduce
run:

from arc.common import determine_symmetry
from arc.species.converter import str_to_xyz


xyz = """
    O       0.75746700   -0.40970800    0.18629600
    C      -0.45247600    0.03076900   -0.24291600
    H      -1.23388100   -0.71100600   -0.17890300
    H      -0.49120400    0.82353200   -0.98028600
    H       1.42009400    0.26641200    0.03880800
"""


symmetry, optical_isomers = determine_symmetry(str_to_xyz(xyz))
print(optical_isomers)

Expected behavior
We should use the RDKit method implemented in the conformers module in ARC to perceive chirality.

Contributor guide

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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 with determine_symmetry and str_to_xyz using the provided [CH2]O reproduction, then inspect the conformers module where ARC already implements RDKit-based chirality perception. Replace the incorrect optical-isomer calculation with that method and confirm the reproduction reports the expected number of optical isomers.

Written by the indexing model from the issue text.

Assessment

Tech stack
python
Domain
backend
Issue type
Bug
Difficulty
3/5
Estimated time
1-2 days
Activity status
Stale
Clarity
Mostly clear
Newbie friendliness
35/100

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