Sample input and output with sample command

[Danissss]

Hi
I ran this command ./DeepCCS predict -mp ../saved_models/default/ -ap ../saved_models/default/ -i "CN1C=NC(C[C@H](N)C(O)=O)=C1" -o result.csv, and it gives this error NameError: free variable 'table' referenced before assignment in enclosing scope

Could you give some sample input and output (with sample command)?

[ElinaFF]

Hi @Danissss
The error in your command is with the "-i" option. You gave it a string ( "CN1C=NC(CC@HC(O)=O)=C1") instead of a file.

So you juste have to create a file with at least the two necessary columns as the first line : SMILES,Adducts, and then put as lines the SMILES you want to predict with their adducts. In your case it could be CN1C=NC(C[C@H](N)C(O)=O)=C1,M+H if you want the CCS of this molecule to be calculated for the M+H ionization.

So the final command line would be ./DeepCCS predict -mp ../saved_models/default/ -ap ../saved_models/default/ -i test.csv -o result.csv , where test.csv is the file with your SMILES.

Hope it helps !
Élina

[Danissss]

Thanks for the clarification!

[Danissss]

I suggest to provide the sample test file as error indicates ValueError: Supplied file must contain at leat 2 columns named 'SMILES' and 'Adducts'. use the provided template if needed.

// test.csv
SMILES,Adducts
CN1C=NC(C[C@H](N)C(O)=O)=C1,M+H

Also, I need to use

import sys
sys.path.insert("some relative path")

to make the relative import works.

OS: MacOS Catalina
Python: 3.6
Env: Anaconda