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:
biobb_common.generic.biobb_object.BiobbObject
biobb_vs FPocketRunWrapper 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.
- 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:
- wrapped_software:
- name: fpocket
- version: >=3.1.4.2
- license: MIT
- ontology:
- name: EDAM
- schema: http://edamontology.org/EDAM.owl
-
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, **kwargs) → int[source]¶ Execute the
FPocketRun
class and execute thelaunch()
method.
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:
biobb_common.generic.biobb_object.BiobbObject
biobb_vs FPocketFilterPerforms 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.
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:
- wrapped_software:
- name: In house
- license: Apache-2.0
- ontology:
- name: EDAM
- schema: http://edamontology.org/EDAM.owl
-
launch
() → int[source]¶ Execute the
FPocketFilter
fpocket.fpocket_filter.FPocketFilter object.
- input_pockets_zip (str) –
-
fpocket.fpocket_filter.
fpocket_filter
(input_pockets_zip: str, input_summary: str, output_filter_pockets_zip: str, properties: dict = None, **kwargs) → int[source]¶ Execute the
FPocketFilter
class and execute thelaunch()
method.
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:
biobb_common.generic.biobb_object.BiobbObject
biobb_vs FPocketSelectSelects 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.
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:
- wrapped_software:
- name: In house
- license: Apache-2.0
- ontology:
- name: EDAM
- schema: http://edamontology.org/EDAM.owl
-
launch
() → int[source]¶ Execute the
FPocketSelect
fpocket.fpocket_select.FPocketSelect object.
- input_pockets_zip (str) –
-
fpocket.fpocket_select.
fpocket_select
(input_pockets_zip: str, output_pocket_pdb: str, output_pocket_pqr: str, properties: dict = None, **kwargs) → int[source]¶ Execute the
FPocketSelect
class and execute thelaunch()
method.