smina package

Submodules

smina.smina_run module

Module containing the sminaRun class and the command line interface.

class smina.smina_run.SminaRun(input_ligands_sdf_path, input_receptor_pdbqt_path, input_site_coords_path, output_sdf_path, output_log_path=None, properties=None, **kwargs)[source]

Bases: BiobbObject

biobb_lsvs SminaRun
Wrapper of the smina molecular docking software.
This class performs docking of ligands to a predefined site on a target protein via the smina software.
Parameters:

  • input_ligands_sdf_path (str) – Path to the input SDF ligands. File type: input. Sample file. Accepted formats: sdf (edam:format_3814).

  • input_receptor_pdbqt_path (str) –

    Path to the input PDBQT receptor. File type: input. Sample file. Accepted formats: pdbqt (edam:format_1476).

  • input_site_coords_path (str) –

    Path to the yaml-file containing the binding site size and coordinates. File type: input. Sample file. Accepted formats: yml (edam:format_1476).

  • output_sdf_path (str) –

    Path to the output SDF file. File type: output. Sample file. Accepted formats: sdf (edam:format_1476).

  • output_log_path (str) (Optional) –

    Path to the log file. File type: output. Sample file. Accepted formats: log (edam:format_2330).

  • properties (dic - Python dictionary object containing the tool parameters, not input/output files) –

    • cpu (int) - (1) [1~1000|1] the number of CPUs to use.

    • exhaustiveness (int) - (8) [1~10000|1] exhaustiveness of the global search (roughly proportional to time).

    • num_modes (int) - (9) [1~1000|1] maximum number of binding modes to generate.

    • min_rmsd_filter (int) - (1) [1~1000|1] minimum RMSD between output poses.

    • energy_range (int) - (3) [1~1000|1] maximum energy difference between the best binding mode and the worst one displayed (kcal/mol).

    • binary_path (string) - (‘smina’) path to smina in your local computer.

    • scoring (string) - (‘vinardo’) scoring function to be used.

    • seed (int) - (1234) [-9999999-9999999] random number generator seed.

    • remove_tmp (bool) - (True) [WF property] Remove temporal files.

    • restart (bool) - (False) [WF property] Do not execute if output files exist.

    • sandbox_path (str) - (“./”) [WF property] Parent path to the sandbox directory.

    • container_path (str) - (None) Container path definition.

    • container_image (str) - (‘biocontainers/smina:v1.1.2-5b1-deb_cv1’) Container image definition.

    • container_volume_path (str) - (‘/tmp’) Container volume path definition.

    • container_working_dir (str) - (None) Container working directory definition.

    • container_user_id (str) - (None) Container user_id definition.

    • container_shell_path (str) - (‘/bin/bash’) Path to default shell inside the container.

Examples

This is a use example of how to use the building block from Python:

from biobb_lsvs.smina.smina_run import smina_run
prop = {
    'binary_path': 'smina'
}
smina_run(input_ligands_sdf_path='/path/to/myLigands.sdf',
                input_receptor_pdbqt_path='/path/to/myReceptor.pdbqt',
                input_site_coords_path='/path/to/mySiteCoords.yml',
                output_sdf_path='/path/to/newStructure.sdf',
                output_log_path='/path/to/newLog.log',
                properties=prop)
Info:
check_data_params(out_log, err_log)[source]

Checks all the input/output paths and parameters

launch() → int[source]

Execute the sminaRun_run smina.smina_run.sminaRun_run object.

parse_site_coords()[source]

Parse box centroid position and side lengths from site_coord.yml

smina.smina_run.smina_run(input_ligands_sdf_path: str, input_receptor_pdbqt_path: str, input_site_coords_path: str, output_sdf_path: str, output_log_path: str | None = None, properties: dict | None = None, **kwargs) → int[source]
biobb_lsvs SminaRun
Wrapper of the smina molecular docking software.
This class performs docking of ligands to a predefined site on a target protein via the smina software.
Parameters:

  • input_ligands_sdf_path (str) –

    Path to the input SDF ligands. File type: input. Sample file. Accepted formats: sdf (edam:format_3814).

  • input_receptor_pdbqt_path (str) –

    Path to the input PDBQT receptor. File type: input. Sample file. Accepted formats: pdbqt (edam:format_1476).

  • input_site_coords_path (str) –

    Path to the yaml-file containing the binding site size and coordinates. File type: input. Sample file. Accepted formats: yml (edam:format_1476).

  • output_sdf_path (str) –

    Path to the output SDF file. File type: output. Sample file. Accepted formats: sdf (edam:format_1476).

  • output_log_path (str) (Optional) –

    Path to the log file. File type: output. Sample file. Accepted formats: log (edam:format_2330).

  • properties (dic - Python dictionary object containing the tool parameters, not input/output files) –

    • cpu (int) - (1) [1~1000|1] the number of CPUs to use.

    • exhaustiveness (int) - (8) [1~10000|1] exhaustiveness of the global search (roughly proportional to time).

    • num_modes (int) - (9) [1~1000|1] maximum number of binding modes to generate.

    • min_rmsd_filter (int) - (1) [1~1000|1] minimum RMSD between output poses.

    • energy_range (int) - (3) [1~1000|1] maximum energy difference between the best binding mode and the worst one displayed (kcal/mol).

    • binary_path (string) - (‘smina’) path to smina in your local computer.

    • scoring (string) - (‘vinardo’) scoring function to be used.

    • seed (int) - (1234) [-9999999-9999999] random number generator seed.

    • remove_tmp (bool) - (True) [WF property] Remove temporal files.

    • restart (bool) - (False) [WF property] Do not execute if output files exist.

    • sandbox_path (str) - (“./”) [WF property] Parent path to the sandbox directory.

    • container_path (str) - (None) Container path definition.

    • container_image (str) - (‘biocontainers/smina:v1.1.2-5b1-deb_cv1’) Container image definition.

    • container_volume_path (str) - (‘/tmp’) Container volume path definition.

    • container_working_dir (str) - (None) Container working directory definition.

    • container_user_id (str) - (None) Container user_id definition.

    • container_shell_path (str) - (‘/bin/bash’) Path to default shell inside the container.

Examples

This is a use example of how to use the building block from Python:

from biobb_lsvs.smina.smina_run import smina_run
prop = {
    'binary_path': 'smina'
}
smina_run(input_ligands_sdf_path='/path/to/myLigands.sdf',
                input_receptor_pdbqt_path='/path/to/myReceptor.pdbqt',
                input_site_coords_path='/path/to/mySiteCoords.yml',
                output_sdf_path='/path/to/newStructure.sdf',
                output_log_path='/path/to/newLog.log',
                properties=prop)
Info: