Data Retrieval¶

Using --sdf Flag¶

The simplest way to extract top poses during or after docking:

easydock -o output.db --sdf

Features: - Returns top scoring pose for each molecule - Automatically selects best among enumerated stereoisomers - Creates SDF file of the same name as a database in the same directory - Includes docking scores in SDF properties

Using get_sdf_from_easydock¶

More flexible extraction tool with extensive filtering options.

Basic Extraction¶

Extract top poses with docking scores:

get_sdf_from_easydock -i output.db -o output.sdf --fields docking_score

Extract as SMILES:

get_sdf_from_easydock -i output.db -o output.smi --fields id docking_score

Specific Molecules¶

By molecule ID:

get_sdf_from_easydock -i output.db -o output.sdf -d mol_1 mol_4 mol_10

From file:

# Create id_list.txt with one ID per line
get_sdf_from_easydock -i output.db -o output.sdf -d id_list.txt

Specific Poses¶

Extract second pose:

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

Extract multiple poses:

get_sdf_from_easydock -i output.db -o output.sdf --poses 1 2 3

Filtered Extraction¶

Score threshold:

get_sdf_from_easydock -i output.db -o output.sdf \
    --fields docking_score \
    --add_sql 'docking_score < -10'

Additional Fields¶

Extract additional database fields:

get_sdf_from_easydock -i output.db -o output.sdf --fields docking_score id stereo_id

Combining Options¶

Extract specific molecules with score filter:

get_sdf_from_easydock -i output.db -o output.sdf \
    -d mol_1 mol_2 mol_3 \
    --poses 1 2 \
    --fields docking_score \
    --add_sql 'docking_score < -9'

Advanced Flags¶

PoseBusters Filter (--bust)¶

Return only poses that passed the PoseBusters check. Bust results must be pre-computed with easydock_bust before using this flag (see Pose Quality Assessment).

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

Combined with explicit poses — each pose is filtered independently:

get_sdf_from_easydock -i output.db -o output.sdf --poses 1 2 3 --bust

Keep Stereo ID in Names (-s / --keep_stereo_id)¶

By default, the stereo ID suffix automatically injected by EasyDock during the preparation step (e.g. _0, _1, etc) is stripped from molecule names in the output. Use this flag to preserve it:

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

Debug SQL (--debug)¶

Print the final SQL query to stdout before execution. Useful for troubleshooting custom --add_sql expressions:

get_sdf_from_easydock -i output.db -o output.sdf --add_sql 'docking_score < -10' --debug

Enumerated Stereoisomer Handling¶