fpocket package

Submodules

fpocket.fpocket_run module

Module containing the FPocketRun class and the command line interface.

class fpocket.fpocket_run.FPocketRun(input_pdb_path, output_pockets_zip, output_summary, properties=None, **kwargs)[source]

Bases: BiobbObject

biobb_vs FPocketRun
Wrapper of the fpocket software.
Finds the binding site of the input_pdb_path file via the fpocket software.
Parameters:

  • input_pdb_path (str) – Path to the PDB structure where the binding site is to be found. File type: input. Sample file. Accepted formats: pdb (edam:format_1476).

  • output_pockets_zip (str) –

    Path to all the pockets found by fpocket in the input_pdb_path structure. File type: output. Sample file. Accepted formats: zip (edam:format_3987).

  • output_summary (str) –

    Path to the JSON summary file. File type: output. Sample file. Accepted formats: json (edam:format_3464).

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

    • min_radius (float) - (None) [0.1~1000|0.1] The minimum radius in Ångstroms an alpha sphere might have in a binding pocket.

    • max_radius (float) - (None) [2~1000|0.1] The maximum radius in Ångstroms of alpha spheres in a pocket.

    • num_spheres (int) - (None) [1~1000|1] Indicates how many alpha spheres a pocket must contain at least in order to figure in the results.

    • sort_by (str) - (‘druggability_score’) From which property the output will be sorted. Values: druggability_score (this score intends to assess the likeliness of the pocket to bind a small drug like molecule), score (fpocket score as defined in the fpocket paper), volume (volume of the pocket).

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

    • 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) - (‘fpocket/fpocket:latest’) 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_vs.fpocket.fpocket_run import fpocket_run
prop = {
    'min_radius': 3,
    'max_radius': 6,
    'num_spheres': 35,
    'sort_by': 'druggability_score'
}
fpocket_run(input_pdb_path='/path/to/myStructure.pdb',
        output_pockets_zip='/path/to/newPockets.zip',
        output_summary='/path/to/newSummary.json',
        properties=prop)
Info:
check_data_params(out_log, err_log)[source]

Checks all the input/output paths and parameters

launch() → int[source]

Execute the FPocketRun fpocket.fpocket_run.FPocketRun object.

fpocket.fpocket_run.fpocket_run(input_pdb_path: str, output_pockets_zip: str, output_summary: str, properties: dict | None = None, **kwargs) → int[source]

Execute the FPocketRun class and execute the launch() method.

fpocket.fpocket_run.main()[source]

Command line execution of this building block. Please check the command line documentation.

fpocket.fpocket_filter module

Module containing the FPocketFilter class and the command line interface.

class fpocket.fpocket_filter.FPocketFilter(input_pockets_zip, input_summary, output_filter_pockets_zip, properties=None, **kwargs)[source]

Bases: BiobbObject

biobb_vs FPocketFilter
Performs a search over the outputs of the fpocket building block.
Finds one or more binding sites in the outputs of the fpocket building block from given parameters.
Parameters:

  • input_pockets_zip (str) –

    Path to all the pockets found by fpocket. File type: input. Sample file. Accepted formats: zip (edam:format_3987).

  • input_summary (str) –

    Path to the JSON summary file returned by fpocket. File type: input. Sample file. Accepted formats: json (edam:format_3464).

  • output_filter_pockets_zip (str) –

    Path to the selected pockets after filtering. File type: output. Sample file. Accepted formats: zip (edam:format_3987).

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

    • score (list) - (None) List of two float numbers between 0 and 1 indicating the score range. Indicates the fpocket score after the evaluation of pocket prediction accuracy as defined in the fpocket paper.

    • druggability_score (list) - (None) List of two float numbers between 0 and 1 indicating the druggability_score range. It’s a value between 0 and 1, 0 signifying that the pocket is likely to not bind a drug like molecule and 1, that it is very likely to bind the latter.

    • volume (list) - (None) List of two float numbers indicating the volume range. Indicates the pocket volume.

    • 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.

Examples

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

from biobb_vs.fpocket.fpocket_filter import fpocket_filter
prop = {
    'score': [0.2, 1],
    'druggability_score': [0.2, 0.8],
    'volume': [100, 600.2]
}
fpocket_filter(input_pockets_zip='/path/to/myPockets.zip',
        input_summary='/path/to/mySummary.json',
        output_filter_pockets_zip='/path/to/newPockets.json',
        properties=prop)
Info:
check_data_params(out_log, err_log)[source]

Checks all the input/output paths and parameters

druggability_score_matcher(druggability_score)[source]
launch() → int[source]

Execute the FPocketFilter fpocket.fpocket_filter.FPocketFilter object.

score_matcher(score)[source]
volume_matcher(volume)[source]
fpocket.fpocket_filter.fpocket_filter(input_pockets_zip: str, input_summary: str, output_filter_pockets_zip: str, properties: dict | None = None, **kwargs) → int[source]

Execute the FPocketFilter class and execute the launch() method.

fpocket.fpocket_filter.main()[source]

Command line execution of this building block. Please check the command line documentation.

fpocket.fpocket_select module

Module containing the FPocketSelect class and the command line interface.

class fpocket.fpocket_select.FPocketSelect(input_pockets_zip, output_pocket_pdb, output_pocket_pqr, properties=None, **kwargs)[source]

Bases: BiobbObject

biobb_vs FPocketSelect
Selects a single pocket in the outputs of the fpocket building block.
Selects a single pocket in the outputs of the fpocket building block from a given parameter.
Parameters:

  • input_pockets_zip (str) –

    Path to the pockets found by fpocket. File type: input. Sample file. Accepted formats: zip (edam:format_3987).

  • output_pocket_pdb (str) –

    Path to the PDB file with the cavity found by fpocket. File type: output. Sample file. Accepted formats: pdb (edam:format_1476).

  • output_pocket_pqr (str) –

    Path to the PQR file with the pocket found by fpocket. File type: output. Sample file. Accepted formats: pqr (edam:format_1476).

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

    • pocket (int) - (1) [1~1000|1] Pocket id from the summary json given by the fpocket building block.

    • 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.

Examples

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

from biobb_vs.fpocket.fpocket_select import fpocket_select
prop = {
    'pocket': 2
}
fpocket_select(input_pockets_zip='/path/to/myPockets.zip',
        output_pocket_pdb='/path/to/myCavity.pdb',
        output_pocket_pqr='/path/to/myPocket.pqr',
        properties=prop)
Info:
check_data_params(out_log, err_log)[source]

Checks all the input/output paths and parameters

launch() → int[source]

Execute the FPocketSelect fpocket.fpocket_select.FPocketSelect object.

fpocket.fpocket_select.fpocket_select(input_pockets_zip: str, output_pocket_pdb: str, output_pocket_pqr: str, properties: dict | None = None, **kwargs) → int[source]

Execute the FPocketSelect class and execute the launch() method.

fpocket.fpocket_select.main()[source]

Command line execution of this building block. Please check the command line documentation.