From 33993eca356636f267717fe2f617a6a91d549a2d Mon Sep 17 00:00:00 2001 From: bries Date: Sun, 26 Nov 2023 10:24:27 +0100 Subject: [PATCH] addin gsettigns section --- rbfe_tutorial/cli_tutorial.md | 39 ++++++++++++++++++++++++++++++----- 1 file changed, 34 insertions(+), 5 deletions(-) diff --git a/rbfe_tutorial/cli_tutorial.md b/rbfe_tutorial/cli_tutorial.md index 410d221..fe12a3f 100644 --- a/rbfe_tutorial/cli_tutorial.md +++ b/rbfe_tutorial/cli_tutorial.md @@ -101,8 +101,15 @@ how these simulation are set up: minimum distance of 1.2 nm from the solute to the edge of the box. 4. The protocol used is OpenFE's OpenMM-based Hybrid Topology RFE protocol, with [default settings](https://docs.openfree.energy/en/stable/reference/api/openmm_rfe.html#protocol-settings). -### Customize you Networkplanning with Settings - MORE HERE -You can exchange settings in for the network planning using a `.yaml` file. +## Customize you Campaign Setup + +OpenFE contains many different options and methods for setting up a calculation campaign. +The options can be easily accessed and modified with providing a settings +file in the `.yaml` format. +Let's assume you want to exchange the LOMAP atom mapper with the Kartograf +atom mapper and the Minimal Spanning Tree +Network Planner with the Maximal Network Planner, then you could do the following: +1. provide a file like `settings.yaml` with the desired changes: ```yaml mapper: method: kartograf @@ -110,13 +117,14 @@ mapper: network: method: generate_maximal_network ``` -this you can simply loop in to your CLI command with the `-s` option and a e.g. -`settings.yaml` file: + +2. Plan your rbfe network with an additional `-s` flag for passing the settings: ```bash openfe plan-rbfe-network -M tyk2_ligands.sdf -p tyk2_protein.pdb -o network_setup -s settings.yaml ``` -you will be able to check your set Settings in the stdout of your shell: +3. The output of the CLI program will now reflect the made changes: + ```text RBFE-NETWORK PLANNER ______________________ @@ -134,6 +142,27 @@ Using Options: Networker: functools.partial() ``` +That concludes the straightforward process of tailoring your OpenFE setup to your specifications. +Additionally, we've provided a snippet for generating YAML files with +various of the current options for your convenience. + +Option Examples: + +```yaml +mapper: + method: lomap + # method: kartograf + +network: + method: generate_minimal_spanning_network + # method: generate_radial_network + # method: generate_maximal_network + # method: generate_minimal_redundant_network +``` + + +**Customize away!** + ## Running the simulations For this tutorial, we have precalculated data that you can load, since