Pose Quality Assessment¶

easydock_bust runs PoseBusters on docked molecules stored in an EasyDock database and records pass/fail results in a bust table. The fast protocol is used. Results are stored in the database as a single indicator: True - if all checks were passed, false - if at least one check was failed. These results can then be used to filter output with get_sdf_from_easydock --bust.

Installation¶

pip install posebusters

Basic Usage¶

easydock_bust -i output.db -p protein.pdb -c 4

On the first run, the protein structure is stored in the database and reused automatically. You do not need to supply -p again on subsequent runs unless you want to replace the protein.

Arguments¶

-i / --input (required)

EasyDock SQLite database.

-p / --protein

Protein PDB file with all hydrogen atoms. Required on the first run; stored in the database and reused on subsequent runs. Providing a different file replaces the stored structure and clears all previously computed bust results.

-d / --ids (default: all docked)

Molecule IDs to process. Can be a space-separated list or a path to a text file with one ID per line.

--poses (default: 1)

Pose numbers to check, 1-based.

-c / --ncpu (default: all CPUs)

Number of CPUs.

-o / --output (default: stdout)

Output file path.

--full

Write all individual PoseBusters check columns to the output. When set, all molecules are re-processed from scratch to produce the full report.

Output Format¶

Tab-separated file with columns: id, stereo_id, pose, result.

id      stereo_id  pose  result
mol_1   0          1     True
mol_2   0          1     False
mol_3   1          1     True

With --full, additional boolean columns for each individual PoseBusters check are appended.

Examples¶

Check all docked molecules (top pose only)¶

easydock_bust -i output.db -p protein.pdb -c 4

Check multiple poses¶

easydock_bust -i output.db -p protein.pdb --poses 1 2 3 -c 4

Write full PoseBusters report to file¶

easydock_bust -i output.db --poses 1 -c 4 --full -o bust_report.tsv

Process specific molecules¶

easydock_bust -i output.db -p protein.pdb -d mol_1 mol_2 mol_3 -c 4

Or from a file:

easydock_bust -i output.db -p protein.pdb -d id_list.txt -c 4

Resumable runs¶

Already-processed molecules are skipped automatically (unless --full is used). You can re-run the same command to add new molecules without reprocessing existing ones:

# First run: processes all docked molecules
easydock_bust -i output.db -p protein.pdb -c 4

# Later: only new molecules are processed
easydock_bust -i output.db -c 4

Filtering Output with get_sdf_from_easydock¶

After running easydock_bust, use the --bust flag to keep only poses that passed:

get_sdf_from_easydock -i output.db -o output.sdf --bust

For specific poses:

get_sdf_from_easydock -i output.db -o output.sdf --poses 1 2 --bust

See Data Retrieval for more filtering options.