63-somnfeature-request---cdxml-file-as-user-input

[ckouder]

Resolves #62
Resolves #63
Resolves #64

Staging environment is updated with this PR

Testing Procedure #62

Go to - https://mmli.fastapi.staging.mmli1.ncsa.illinois.edu/docs#/Somn/check_reaction_sites_somn_all_reaction_sites_get

• Valid chemical

  • with chiral BrC1=C(C=CC=C1)CO[C@@H]2CCCCO2, role el
    expected output: ..."has_chiral": true...,
  • without chiral BrC1=C(C=CC=C1)CO[CH]2CCCCO2, role el
    expected output: ..."has_chiral": false...,

• Invalid chemical

  • BrC1=C(C=CC=C1)CO[CH]2CCCCO, role el
    expected output: ... "detail": "Invalid SMILES string: BrC1=C(C=CC=C1)CO[C@@H]2CCCCO" ...

• Chemical which failed 3d testing

  • TBD
  • expected output: ... "detail": "Unable to generate 3D coordinates for XXX" ...

Testing Procedure #63

It is a very rare case and we haven't produced any example for it. However, the feature has been tested with force casting error type to 3d-gen

Testing procedure #64

Go to - https://mmli.fastapi.staging.mmli1.ncsa.illinois.edu/docs#/Somn/check_reaction_sites_somn_all_reaction_sites_get

Number of heavy atoms = number of non-hydrogen atoms

• Valid chemical

  • without hydrogenBrC1=C(C=CC=C1), role el
    expected output: ..."num_heavy_atoms": 7...,
  • with hydrogen BrC1=C(C=CC=C1)CO[C@@H]2CCCCO2, role el
    expected output: ..."num_heavy_atoms": 15...,

• Invalid chemical

  • BrC1=C(C=CC=C1)CO[CH]2CCCCO, role el
    expected output: ... "detail": "Invalid SMILES string: BrC1=C(C=CC=C1)CO[C@@H]2CCCCO" ...

• Chemical which failed 3d testing

  • TBD
  • expected output: ... "detail": "Unable to generate 3D coordinates for XXX" ...

[ckouder]

blocked at #63 - detailed in issue page

[David-Bianchi]

Thanks Bingji!