Advanced Features¶

Ring Conformer Sampling¶

Improve docking of compounds containing saturated rings by sampling multiple starting conformers.

easydock -i input.smi -o output.db --program vina --config config.yml -c 4 --ring_sample

How it works:

1. Generate multiple representative conformers for saturated rings
2. Dock each initial conformer independently
3. Store only the best scoring conformer

Containerized Programs¶

Non-server docking programs (Gnina, QVina, etc.) can be launched through a container by writing the full container command as script_file. For example, Gnina in Apptainer:

script_file: apptainer exec -B /path/to/data:/path/to/data container.sif gnina
protein: /path/to/data/protein.pdbqt
protein_setup: /path/to/data/grid.txt
exhaustiveness: 8
scoring: default
cnn_scoring: rescore
cnn: dense_ensemble
n_poses: 10
addH: False
ncpu: 1
seed: 0

Important: Mount directories containing input files:

• Apptainer: -B /path/to/data:/path/to/data
• Docker: -v /path/to/data:/path/to/data

Distributed Computing¶

Distribute docking across multiple servers using Dask.

Setup¶

1. Create hostfile:

With SLURM:

srun hostname | sort | uniq > NODEFILE

With PBS:

# Use $PBS_NODEFILE directly

2. Start Dask cluster and run docking:

dask ssh --hostfile $PBS_NODEFILE --nworkers 15 --nthreads 1 &
sleep 10
easydock -i input.smi -o output.db --program vina --config config.yml \
         --sdf --hostfile $PBS_NODEFILE --dask_report

Parameters:

• --hostfile: File with server IP addresses
• --nworkers: Number of workers per host (molecules docked in parallel per host)
• --nthreads: Can be any value; actual CPUs taken from config
• --dask_report: Generate HTML performance report

Check file limit:

ulimit -n

Reusing Databases¶

Create Clean Copy¶

Create a copy of an existing database removing all docking data:

make_clean_copy -i original.db -o clean.db

This preserves: - Initialized molecules - Stereoisomers - Protonation states - Setup parameters

Use the clean copy for docking with different proteins, programs or settings skipping the ligand initialization stage.

Database Upgrading¶

Databases created before version 1.3.0 use an older internal schema. When you open such a database, EasyDock detects the schema version and prompts you to upgrade:

Database 'output.db' uses schema version 0 (current: 1).
Upgrade now? [y/N] (auto-abort in 2 minutes):

Type y and press Enter to proceed. The upgrade rewrites the setup table to the new key/value format; all molecule data and docking results are preserved. If no response is received within 2 minutes, the run aborts automatically.

Boron-Containing Compounds¶

EasyDock automatically handles boron-containing compounds for programs that don't natively support boron:

1. Replaces boron with carbon before docking
2. Returns boron atoms after docking

No special flags needed - this happens automatically as implemented in individual docking pipelines.

Custom Configuration Arguments¶

Two ways to pass arguments to external programs in config.yml:

Method 1: Individual Config Entries¶

exhaustiveness: 8
n_poses: 5

Method 2: In script_file Value¶

script_file: /path/to/qvina2 --exhaustiveness 8 --num_modes 5