Error file with multiple ligands

[Sofea Arina Bt Shazali]

Hi, i have this error can you help me identify why?i really need this program. very much appreciated.
i sent an input sdf file with multiple ligands(15000) i tested out with a sdf file with 4 ligands(of the same format with the 15000 ligand file) and it worked out fine.

Loading molecules from forRealThisTime.sdf…
Traceback (most recent call last):
File "run_gypsum_dl.py", line 312, in <module>
prepare_molecules(INPUTS)
File "C:\Users\Sofea\Documents\SIV3001_FYP\gypsum_dl-1.1.8\gypsum_dl\Start.py", line 204, in prepare_molecules
smiles_data = load_sdf_file(src)
File "C:\Users\Sofea\Documents\SIV3001_FYP\gypsum_dl-1.1.8\gypsum_dl\Steps\IO\LoadFiles.py", line 125, in load_sdf_file
smiles = Chem.MolToSmiles(mol, isomericSmiles=True, canonical=True)
Boost.Python.ArgumentError: Python argument types in
rdkit.Chem.rdmolfiles.MolToSmiles(NoneType)
did not match C++ signature:
MolToSmiles(class RDKit::ROMol mol, bool isomericSmiles=True, bool kekuleSmiles=False, int rootedAtAtom=-1, bool canonical=True, bool allBondsExplicit=False, bool allHsExplicit=False, bool doRandom=False)

[ikk6]

Hello.
Are you sure your "large" file is properly formatted?

[Sofea Arina Bt Shazali]

hi thank you for the quick reply,
im not sure if this is the best indicator, but all the molecules in the "large" file can be read in a chemical database manager which is DataWarrior . can you advice me any other ways i can check?

[ikk6]

Well, I imagine you could pass it to openbabel to try and convert it. Something like:
obabel large_file.sdf -Onew.smi -m
Then check whether the number of the output files is equal to the number of compounds in the input file.

[Sofea Arina Bt Shazali]

if thats the case then yes , i’ve actually run this file on openbabel before running it on gypsum to append the coconut_id to title.
i’ve also just tried the method u mentioned and it did return the same number of molecules. Should i share with you the file?

[ikk6]

As long as it is okay to share this data, please do. I will try to reproduce the error.

[Sofea Arina Bt Shazali]

here’s the link, thank you for your help. I’ve been trying to figure it out but no clue
https://drive.google.com/file/d/1b2c9JBcOPJIpoaPJJp_KwGrPUX2K66ZL/view?usp=sharing

[ikk6]

What’s the exact command did you run?

[Sofea Arina Bt Shazali]

this is the command
python run_gypsum_dl.py –use_durrant_lab_filters –source ligandFile.sdf

[Sofea Arina Bt Shazali]

python run_gypsum_dl.py –use_durrant_lab_filters –source ligandFile.sdf

[Jacob Durrant]

Hi Sofea. Much thanks for your interest in Gypsum-DL. ikk6 and I spent some time today trying to get to the bottom of the problem. We just released version 1.1.9, which should avoid errors like those you’re seeing.

Gypsum-DL is primarily designed to work with SMI (SMILES) files. Internally, it uses RDKit to convert SDF files to SMI files. If RDKit can’t process an SDF entry, Gypsum-DL won’t be able to either. Some of your SDF entries cause RDKit problems. I think it’s because there are no charges on some nitrogen atoms. For example, this entry:

CNP0017802
 OpenBabel04082123302D

 11 11  0  0  0  0  0  0  0  0999 V2000
    2.5980    0.0000    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.7320   -0.5000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.7320   -1.5000    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.8660    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000   -0.5000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9135   -0.0932    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5826   -0.8364    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0826   -1.7024    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1045   -1.4945    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.6386   -2.1636    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5771   -0.7318    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  2  0  0  0  0
  2  3  1  0  0  0  0
  2  4  1  0  0  0  0
  4  5  1  0  0  0  0
  5  6  2  0  0  0  0
  5  9  1  0  0  0  0
  6  7  1  0  0  0  0
  7  8  1  0  0  0  0
  7 11  1  0  0  0  0
  8  9  2  0  0  0  0
  9 10  1  0  0  0  0
M  END
>  <coconut_id>
CNP0017802

>  <SMILES>
O=C(O)CC1=CN(C=N1C)C

$$$$

With the latest update, Gypsum-DL will now warn you that it’s skipping an entry like this, rather than throwing an error.

As a side note, if you just use a SMI file, Gypsum won’t get RDKit involved at this step, so you can avoid the problem entirely. You could create an SMI file using open babel like this: obabel -isdf ligandFile.sdf -osmi > mysmi.smi

Much thanks for bringing this bug to our attention! Take care.

[Sofea]

Hi. I’ve managed to run the software thank you very much for the help and information. Its very helpful to know which ligands that have problem in the file.Also thank you for creating such a useful software. Have a good day!

[Jacob Durrant]

Thank you, Sofea, for pointing out a useful new feature to include! Best of luck with your project.

[Author]

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