Error calcultating chemical similarity

[felipeZ]

I am calling the chemical similarity method using these defaults together with the following input:

dict_similarity = {
    "mol_format": "smi",
    "ci_cutoff": 0.3617021276595745,
    "workdir": create_workdir('similarity'),
    "test_set": ["O1[C@@H](CCC1=O)CCC"],
    "reference_set": [
      "c1(c(cccc1Nc1c(cccc1)C(=O)O)C)C",
      "c12ccccc1nc1c(c2N)CCCC1",
      "c1ccc(c(c1)[N+](=O)[O-])[C@H]1C(=C(NC(=C1C(=O)OC)C)C)C(=O)OC",
      "c1cc(ccc1OCC)NC(=O)C",
      "c12c3c(ccc1c(=O)cc(o2)c1ccccc1)cccc3",
      "c1cc(cc(c1N/C=N/O)C)CCCC",
      "c1(cccnc1Nc1cc(ccc1)C(F)(F)F)C(=O)O",
      "c1ccc(c(c1C)OC[C@H](C)N)C",
      "c1(OC[C@H](CNC(C)C)O)c2c(ccc1)cccc2",
      "c12ccccc1cccc2",
      "c12ccccc1cccc2C",
      "c12ccccc1ccc(c2)C",
      "c12ccccc1ccc(c2)F",
      "c12ccccc1cc(cc2C)C",
      "c12ccccc1c(ccc2C)C",
      "c12cccc(c1cccc2Cl)Cl",
      "c12cc(ccc1cc(cc2)C)C",
      "C1CCC(=O)OCC1",
      "O1[C@@H](CCC1=O)C",
      "O1[C@@H](CCC1=O)CC",
      "O1[C@@H](CCC1=O)CCC",
      "O1[C@@H](CCC1=O)CCCCC",
      "O1[C@@H](CCC1=O)CCCCCC",
      "O1[C@@H](CCC1=O)CCCCCCC",
      "C1C[C@@H](OC(=O)C1)CCCCC",
      "c1c2c(ccc1)OC(=O)C2",
      "c1c2c(ccc1)CC(=O)C2",
      "c1c2c(ccc1)OCC2",
      "c1c2c(ccc1)oc(=O)[nH]2",
      "c1(ccccc1)c1ccccc1",
      "c1c(cccc1)c1ccc(cc1)Cl",
      "C1CCCC(C1)CCCC",
      "[C@@H]1(OC(=O)CC1)c1ccccc1",
      "c1(cc(oc(=O)c1)C)C",
      "C1CC(=O)N([C@H]1c1cccnc1)C"
    ]
}

The call produces the following error:

  File "MDStudio/components/lie_structures/lie_structures/wamp_services.py", line 36, in calculate_chemical_similarity
    return super(StructuresWampApi, self).calculate_chemical_similarity(request, claims)
  File "MDStudio/components/lie_structures/lie_structures/cheminfo_wamp/cheminfo_fingerprints_wamp.py", line 45, in calculate_chemical_similarity
    test_fps = [m.calcfp(fp_format) for m in test_mols]
  File "miniconda2/envs/mdstudio/lib/python2.7/site-packages/cinfony/pybel.py", line 380, in calcfp
    raise ValueError("%s is not a recognised Open Babel Fingerprint type" % fptype)
exceptions.ValueError: maccs is not a recognised Open Babel Fingerprint type

I have noticed that this method call was also failing using the prototype version (the code in master).

[marcvdijk]

That is strange, it should work as MACCS is supported by OpenBabel. Either something wrong in Cinfony, pybel or the OpenBabel installation. I will test on my side.

…

Op 20 apr. 2018, om 12:24 heeft felipe zapata ***@***.***> het volgende geschreven: Assigned #121 <https://github.com/MD-Studio/MDStudio/issues/121> to @marcvdijk <https://github.com/marcvdijk>. — You are receiving this because you were assigned. Reply to this email directly, view it on GitHub <https://github.com/MD-Studio/MDStudio/issues/121#event-1585850584>, or mute the thread <https://github.com/notifications/unsubscribe-auth/AEKUxZOS7Uvnn8dURvIywGOs1NvSLoAQks5tqbd7gaJpZM4TdOyg>.