How to extract template and retrosynthesis from scratch

[sitanshubhunia]

Respected Sir, Thanks for this valuable repo. Requesting you to guide how I start from scratch for a given set of reaction smiles ->extract template -> retrosynthesis. If possible please guide me with steps. I am not from a chemistry background just simple a technical guy.

Regards, Sitanshu

[shuan4638]

Going through the demo noteboook should be helpful to understand how to use it. Let me know if you need further help.

[sitanshubhunia]

Thanks Sir for your reply. Trying to create virtual environment on windows 10, but stuck on "conda install -c conda-forge rdkit -y" For ref. I have attached screen shot.

[shuan4638]

Did you try pip install rdkit?

[sitanshubhunia]

Again thanks Sir. Now virtual env. is created.

Let me try to other steps

[sitanshubhunia]

Sorry to disturb you again and again. I admitted that due to lack of my knowledge I am getting this error. If possible please help me for further steps.

[shuan4638]

Did you install dgl package in the same envinroment?

[sitanshubhunia]

Yes sir. FYI I have attached screen shots. Obviously I am doing something wrong. But not figure it out where .......

dgl

---

dgllife

ipynb

The list of commands

conda create -c conda-forge -n rdenvNew python=3.7 -y conda activate rdenvNew conda install pytorch cudatoolkit=10.2 -c pytorch -y pip install rdkit [ as per your advice and successfully installed] pip install dgl pip install dgllife

[shuan4638]

Can you make sure the Jupiter notebook you are running is using the same virtual environment you install those packages?

[sitanshubhunia]

Thanks Sir. I have to add two more pip install

1. pip install jupyter
2. pip install torch

jupyter is now running from same env.

### After that I am getting following

After change device = torch.device('cpu')

I am getting following error

My Environment is Windows 11 Pro

Directory structure

[shuan4638]

@sitanshubhunia Did you solve the problem?

[sitanshubhunia]

No @shuan4638 Sir. I am unable to solve it.

I am also stuck in step 3 [3] Train LocalRetro model

### Stuck in this step. Nothing is saved in model folder.

[shuan4638]

@sitanshubhunia The training process takes time, you may see the model file after the first epoch. You'll be able to use the python notebook once you obtain the model file.

[sitanshubhunia]

@shuan4638 Sir thanks for reply. Yes it's running. Still now ....

I hope, I can run this after all steps done...

[sitanshubhunia]

@shuan4638 Sir, Finally I have successfully run Retrosynthesis.ipynb.

Requesting you to give the steps how to proceed, if I have only reaction smiles then how I able to use this model extract templates , generate other files and retrosynthesis.

I understand that this type of questions may be annoying to you.

This is not an issue. Just questions🙏

Thanks for your valuable works.

[shuan4638]

LocalRetro is not the model to generate reaction template. Reaction template can be directly generated by the extract_from_reaction function defined here. Playing with this function should be helpful.