# Directory Structure ### General The root folder of AdaptiveFlow contains the following folders: * `input-files/` * `output-files/` * `workflow/` * `tools/` * `cfn/` The following image shows the four folders within the AFLP root directory and their relationships:

Shown are the four first-level folders within the root folder of the AdaptiveFlow root directory and their relationships. Arrows indicate flow of information and/or directives. During the set-up of the workflow by the user, the tools folder is prepared and configured. After that, the other workflow folders are prepared automatically with the command afvs_prepare_folders.py and afvs_prepare_workflow.py. afvs_prepare_workflow.py will in particular prepare the workflow folder. The workflow folder is used by AdaptiveFlow to run and organize the workflow, which actually processes the input-files (including the ligand database) and generates the output database.

### The `input-files` Folder The `input-files` folder contains files that are not part of the AdaptiveFlow code, but are provided by the user as input files. E.g. in the case of AFVS, it will contain the configuration files for the docking programs. The only exception is the input ligand database, which can be stored in any location (even outside the AdaptiveFlow root folder) and can be specified in the control file. The reason for this circumstance is that the input ligand database might not only be used for one particular workflow, but multiple instances. Since ligand databases for AdaptiveFlow can be very large, it can be practical to store them only in a single centralized location. ### The `output-files` Folder The `output-files` folder is intended for the final output files generated by AdaptiveFlow during the workflow. For AFLP the `output-files` folder would contain the prepared ligands. In the case of AFVS it would contain the docking results and related output files. ### The `workflow` Folder The `workflow` folder contains all the intermediate and runtime files which are needed and generated by AdaptiveFlow itself. ### The `tools` Folder The `tools` folder is not used by AdaptiveFlow during the runtime, but it is used by the user. It is used for setting up, starting, controlling, and monitoring the workflow. The `tools` folder is also the primary working directory of AdaptiveFlow, meaning that all AdaptiveFlow user commands (the commands starting with `aflp_ or afvs_`) have to be run from this folder. Also, the batch jobs which are run by AdaptiveFlow use the `tools` folder as their working directory. All paths specified in the configuration files of AdaptiveFlow are relative to the `tools` folder. --- # Agent Instructions: Querying This Documentation If you need additional information that is not directly available in this page, you can query the documentation dynamically by asking a question. Perform an HTTP GET request on the current page URL with the `ask` query parameter: ``` GET https://docs.virtual-flow.org/documentation-af/documentation/backgrounds-and-principles/directory-structure.md?ask= ``` The question should be specific, self-contained, and written in natural language. The response will contain a direct answer to the question and relevant excerpts and sources from the documentation. Use this mechanism when the answer is not explicitly present in the current page, you need clarification or additional context, or you want to retrieve related documentation sections.