plpla/deepccs

CCS prediction using deep neural network

deepccs's Issues

Interface train function dataset names are inconsistents

Command line arguments don't match the code.

DeepCCS: command not found

Hi, I recently wanted to try using DeepCCS.
I installed all the packages that you mentioned on my python environment according to your installation instructions.

Then I executed the installation command in the core path. After that, I added an .xlsx file named "input" in the interface path, with the first column being SMILES and the second column being Adducts.

When I executed "DeepCCS predict -i INPUT.xlsx", the system prompted me with "DeepCCS: command not found".

I checked that the Python version is 3.6.13 and all the relevant packages are also installed.

I can't find the problem, so I'm asking for your help on how to resolve it.

Prediction yields no result for some SMILES w/o throwing error

Some of the SMILES inputs I provide do not yield a result or error. The output file contains blank spaces upon finishing. An example SMILES is below.

CC(C)CCCC@@HCCCC@@HCCCC@@HCCOCC@@HOCCC@HCCCC@HCCCC@HCCCC(C)C

Add sample test file to the repo

Fix DeepCCS logo on github page

Sample input and output with sample command

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)?

Add support for xlsx files

Input file

What is the separator(s) expected in the input file? Space, comma or tab? Should there be a header line with "SMILES" and "Adducts" column headers? Perhaps a simple example input file or more detailed description in the README would be nice? Excited to take DeepCCS for a spin...

Datasets used to train this

Hi

I'm doing my own research into creating a model to predict the CCS, are the datasets you used publicly available, and if so would you be able to show me where to find them?

Thank you
Arthur

Add default model adducts to the documentation

DeepCCS model training could perform the encoder train-transform