MT

Installation on Merlin

Create a conda env:

module load anaconda
conda env create -f environment.yml --prefix=/data/project/bio/schertler/Flurin/mtenv

Activate (command line)

conda activate /data/project/bio/schertler/Flurin/mtenv

To just the environment to show up in jupyter, you may need to run (within the environment)

python -m ipykernel install --user --name mtenv --display-name "Python [conda env:mtenv]"

Clone the repo

git clone git@github.com:flurinh/mt.git
Install the env into jupyter. (needs testing)

conda activate /data/project/bio/schertler/Flurin/mtenv python -m ipykernel install --user --name mtenv --display-name "Python [conda env:mtenv]"

I'm not sure whether this is necessary or sufficient to make the environemnt show up in jupyterhub. See merlin-jupyter docs

New dendencies should be added to environment.yml. After adding something, update:

conda env update -f environment.yml

Name		Name	Last commit message	Last commit date
Latest commit History 72 Commits
.idea		.idea
analysis		analysis
models		models
neuralnet		neuralnet
papers		papers
plots		plots
processing		processing
pymol-lic		pymol-lic
.gitignore		.gitignore
CifProcessor.ipynb		CifProcessor.ipynb
DataLoader.ipynb		DataLoader.ipynb
DataToNet.ipynb		DataToNet.ipynb
GPCR and GPCR_G protein complex data processing (GRN annotation).ipynb		GPCR and GPCR_G protein complex data processing (GRN annotation).ipynb
ICL4_data.ipynb		ICL4_data.ipynb
Local graph representation of the GPCR’s G protein binding region.ipynb		Local graph representation of the GPCR’s G protein binding region.ipynb
Pair-wise distance and helix-helix angle analysis.ipynb		Pair-wise distance and helix-helix angle analysis.ipynb
README.md		README.md
Training and analysis Graph neural network.ipynb		Training and analysis Graph neural network.ipynb
WALKTHROUGH.py		WALKTHROUGH.py
affinities.ipynb		affinities.ipynb
environment.yml		environment.yml
helixangle.ipynb		helixangle.ipynb
master thesis gpcr-g protein-complex plots.ipynb		master thesis gpcr-g protein-complex plots.ipynb
writetocif.ipynb		writetocif.ipynb