diff --git a/rbfe_tutorial/cli_tutorial.md b/rbfe_tutorial/cli_tutorial.md index e888de9..fe12a3f 100644 --- a/rbfe_tutorial/cli_tutorial.md +++ b/rbfe_tutorial/cli_tutorial.md @@ -101,6 +101,67 @@ 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 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 + +network: + method: generate_maximal_network +``` + +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 +``` + +3. The output of the CLI program will now reflect the made changes: + +```text +RBFE-NETWORK PLANNER +______________________ + +Parsing in Files: + Got input: + Small Molecules: SmallMoleculeComponent(name=lig_ejm_54) SmallMoleculeComponent(name=lig_jmc_23) SmallMoleculeComponent(name=lig_ejm_47) SmallMoleculeComponent(name=lig_jmc_27) SmallMoleculeComponent(name=lig_ejm_46) SmallMoleculeComponent(name=lig_ejm_31) SmallMoleculeComponent(name=lig_ejm_42) SmallMoleculeComponent(name=lig_ejm_50) SmallMoleculeComponent(name=lig_ejm_45) SmallMoleculeComponent(name=lig_jmc_28) SmallMoleculeComponent(name=lig_ejm_55) SmallMoleculeComponent(name=lig_ejm_43) SmallMoleculeComponent(name=lig_ejm_48) + Protein: ProteinComponent(name=) + Cofactors: [] + Solvent: SolventComponent(name=O, Na+, Cl-) + +Using Options: + Mapper: + Mapping Scorer: + 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