| # Software setup |
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| This directory contains installation instructions for the third-party docking software used by the OpenBind docking workflow. |
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| GNINA, Smina, and DiffDock are **not included** in this repository and must be installed separately. The paths to the installed software, optional Singularity/Apptainer images, and Slurm profiles are configured in [`../configs/docking/software_settings.yaml`](../configs/docking/software_settings.yaml). |
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| ## Expected directory structure |
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| A local installation can follow this structure: |
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| ```text |
| software/ |
| ├── gnina/ |
| │ ├── gnina |
| │ └── gnina_singularity.sif # optional |
| ├── smina/ |
| │ └── smina |
| └── DiffDock/ |
| ├── inference.py |
| ├── default_inference_args.yaml |
| └── diffdock_singularity.sif # optional |
| ``` |
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| The exact locations are configurable, so this structure is recommended rather than required. |
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| ## Software and Slurm configuration |
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| Update [`../configs/docking/software_settings.yaml`](../configs/docking/software_settings.yaml) after installation. For example: |
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| ```yaml |
| methods: |
| diffdock: |
| executable: software/DiffDock/ |
| singularity: software/DiffDock/diffdock_singularity.sif |
| profile: gpu |
| |
| gnina: |
| executable: software/gnina/gnina |
| singularity: software/gnina/gnina_singularity.sif |
| profile: gpu |
| |
| smina: |
| executable: software/smina/smina |
| profile: cpu |
| ``` |
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| Relative paths are resolved from the OpenBind docking repository root. |
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| The `profiles` section accepts Slurm options as key-value pairs and passes them through as `#SBATCH` directives. Add the settings required by your cluster, for example `partition`, `account`, `cluster`, or `qos`. Boolean `true` values are emitted as flag-only options, while `false`, empty, and `null` values are omitted. |
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| ```yaml |
| profiles: |
| gpu: |
| cpus-per-task: 8 |
| mem: 16G |
| time: "24:00:00" |
| gres: gpu:1 |
| account: my-project |
| partition: gpu |
| exclusive: true |
| ``` |
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| No site-specific partition, account, or cluster is set in the repository defaults. |
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| ## Optional Singularity / Apptainer environments |
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| Optional Singularity/Apptainer images can be used for GNINA and DiffDock. These images provide reproducible runtime dependency environments for the locally installed software; the executable or DiffDock source tree is still provided separately through `software_settings.yaml`. |
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| They are primarily useful for: |
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| - HPC environments; |
| - CUDA compatibility; |
| - avoiding dependency conflicts; and |
| - improving reproducibility across systems. |
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| If a Singularity image is configured for a GPU Slurm profile, the OpenBind launcher adds GPU support when the profile requests a GPU resource. |
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| ## GNINA |
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| **Recommended version:** `v1.3.2` |
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| Create the software directory: |
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| ```bash |
| mkdir -p software/gnina |
| ``` |
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| Download the precompiled GNINA binary: |
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| ```bash |
| wget https://github.com/gnina/gnina/releases/download/v1.3.2/gnina.1.3.2 |
| mv gnina.1.3.2 software/gnina/gnina |
| chmod +x software/gnina/gnina |
| ``` |
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| ### Optional Singularity image |
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| ```bash |
| singularity pull software/gnina/gnina_singularity.sif \ |
| oras://ghcr.io/jnelen/gnina_singularity:v1 |
| ``` |
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| ## Smina |
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| Download Smina from its project page and place the executable at: |
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| ```text |
| software/smina/smina |
| ``` |
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| Then make it executable: |
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| ```bash |
| chmod +x software/smina/smina |
| ``` |
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| ## DiffDock |
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| Clone DiffDock into `software/`: |
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| ```bash |
| cd software |
| git clone https://github.com/gcorso/DiffDock.git |
| cd .. |
| ``` |
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| Follow the official DiffDock installation instructions to install its Python dependencies and model files. For reproducible benchmark runs, record and reuse the exact DiffDock version or commit used for the calculation. |
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| ### Important: configure the number of generated poses |
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| DiffDock reads inference settings from: |
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| ```text |
| software/DiffDock/default_inference_args.yaml |
| ``` |
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| The value of `samples_per_complex` in this file **must match** `methods.diffdock.num_modes` in the OpenBind docking experiment YAML. |
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| For the supplied A71EV2A benchmark configuration: |
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| ```yaml |
| methods: |
| diffdock: |
| num_modes: 40 |
| ``` |
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| set the DiffDock configuration to: |
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| ```yaml |
| samples_per_complex: 40 |
| ``` |
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| This manual change is required because the current DiffDock inference implementation loads `default_inference_args.yaml` after parsing command-line arguments. As a result, the YAML value for `samples_per_complex` overrides a value supplied on the command line. |
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| The OpenBind runner checks this setting before starting DiffDock and raises a clear error if the two values do not match. This prevents a run configured for, for example, 40 poses from silently producing the DiffDock YAML default instead. |
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| If you change `methods.diffdock.num_modes` for another experiment, update `samples_per_complex` in `default_inference_args.yaml` to the same value before submitting the jobs. |
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| ### Optional Singularity image |
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| ```bash |
| singularity pull software/DiffDock/diffdock_singularity.sif \ |
| oras://ghcr.io/jnelen/diffdock_singularity:v1 |
| ``` |
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| ## Final checks |
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| Before submitting a benchmark, confirm that: |
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| - the configured executable and installation paths exist; |
| - any configured Singularity/Apptainer images exist; |
| - the required Slurm profile contains the settings needed by your cluster; |
| - GNINA and Smina binaries are executable; and |
| - DiffDock `samples_per_complex` matches `methods.diffdock.num_modes` in the experiment configuration. |
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| For method-specific installation or advanced configuration, refer to the corresponding upstream documentation. |
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