FFF_Template

To use this repository:

1. Use this template to create a new repository
2. Clone the newly repository on IRIS
3. Follow the steps indicated below

1. Dependencies

Skip this section if you have run a FFF campaign with this template before

SSH access to STFC/IRIS

Work directory

Set up xchem/slurm

Conda setup

Custom bashrc

Jupyter notebook server

BulkDock

HIPPO

Fragmenstein

Fragment Knitwork (optional)

Syndirella

EnamineCatalogs

Checklist

• you can ssh to IRIS (cepheus-slurm.diamond.ac.uk)
• you can source a file to set up conda
• you can connect to a Jupyter notebook on IRIS
• you can run python -m bulkdock status from the BulkDock directory
• you can import hippo from a notebook
• you can run fragmenstein --help
• you can ssh to the sw-graph VM (optional, only for Knitwork)
• you can run syndirella --help
• you have set up EnamineCatalogs

2. Setup

Download target

Setup target in BulkDock

Define merging opportunities

3. Compound Design

Fragmenstein

combine

Placement w/ BulkDock

Fragment Knitwork

fragment

knitting

Placement w/ BulkDock

4. Scaffold selection

Syndirella retrosynthesis

Review chemistry

HIPPO filtering

Fragalysis curation

5. Syndirella elaboration

6. HIPPO

Load elaborations

Quote reactants

Solve routes

Calculate interactions

Generate random recipes

Score random recipes

Optimise best recipes

Create proposal web page

7. Review & order

Review chemistry

Order reactants