search

DrrDom / crem

CReM: chemically reasonable mutations framework
BSD 3-Clause "New" or "Revised" License
206 stars 38 forks source link

Tutorials #2

Open rajathsalegame opened 4 years ago

rajathsalegame commented 4 years ago

Hi! I was wondering whether you might have some more jupyter tutorials that aren't uploaded on the current GitHub repository? Thanks for building this software, it's super cool!

DrrDom commented 4 years ago

You are welcome! Currently there is only this tutorial to demonstrate basic abilities. If you have some questions even general ones ask them here. Later I would be able to compile my answers in another tutorial.

rajathsalegame commented 4 years ago

I think general tutorials on database generation would be super helpful, in case people want to create their own custom workflows for fragment generation.

DrrDom commented 4 years ago

I expected that there is enough information in README to make an own fragment database.

  1. There is a script which makes everything. It takes input SMILES and returns a fragment database - https://github.com/DrrDom/crem/blob/master/crem/scripts/crem_create_frag_db.sh.

  2. It is also possible to make all steps by your own.

To speed up overall pipeline I use several nodes on a cluster to prepare context-fragment pairs and then combine them in one database. But this depends on a cluster scheduler and I did not include these scripts in the repo.

I'll think about some small examples on database generation for future tutorials which I plan to make at the annual winter workshop which we organize in Olomouc. We always make all materials publicly available, so they will be accessible for non-participants as well.

DrrDom commented 3 years ago

Forgot to mention. I added a simple tutorial how to use CReM in combination with machine learning models.The tutorial is in example dir.

rajathsalegame commented 3 years ago

Thanks! Will take a look.