# BioBB VS Command Line Help Generic usage: ```python biobb_command [-h] --config CONFIG --input_file(s) --output_file ``` ----------------- ## Autodock_vina_run Wrapper of the AutoDock Vina software. ### Get help Command: ```python autodock_vina_run -h ``` usage: autodock_vina_run [-h] [-c CONFIG] --input_ligand_pdbqt_path INPUT_LIGAND_PDBQT_PATH --input_receptor_pdbqt_path INPUT_RECEPTOR_PDBQT_PATH --input_box_path INPUT_BOX_PATH --output_pdbqt_path OUTPUT_PDBQT_PATH [--output_log_path OUTPUT_LOG_PATH] Prepares input ligand for an Autodock Vina Virtual Screening. options: -h, --help show this help message and exit -c CONFIG, --config CONFIG This file can be a YAML file, JSON file or JSON string required arguments: --input_ligand_pdbqt_path INPUT_LIGAND_PDBQT_PATH Path to the input PDBQT ligand. Accepted formats: pdbqt. --input_receptor_pdbqt_path INPUT_RECEPTOR_PDBQT_PATH Path to the input PDBQT receptor. Accepted formats: pdbqt. --input_box_path INPUT_BOX_PATH Path to the PDB containig the residues belonging to the binding site. Accepted formats: pdb. --output_pdbqt_path OUTPUT_PDBQT_PATH Path to the output PDBQT file. Accepted formats: pdbqt. optional arguments: --output_log_path OUTPUT_LOG_PATH Path to the log file. Accepted formats: log. ### I / O Arguments Syntax: input_argument (datatype) : Definition Config input / output arguments for this building block: * **input_ligand_pdbqt_path** (*string*): Path to the input PDBQT ligand. File type: input. [Sample file](https://github.com/bioexcel/biobb_vs/raw/master/biobb_vs/test/data/vina/vina_ligand.pdbqt). Accepted formats: PDBQT * **input_receptor_pdbqt_path** (*string*): Path to the input PDBQT receptor. File type: input. [Sample file](https://github.com/bioexcel/biobb_vs/raw/master/biobb_vs/test/data/vina/vina_receptor.pdbqt). Accepted formats: PDBQT * **input_box_path** (*string*): Path to the PDB containig the residues belonging to the binding site. File type: input. [Sample file](https://github.com/bioexcel/biobb_vs/raw/master/biobb_vs/test/data/vina/vina_box.pdb). Accepted formats: PDB * **output_pdbqt_path** (*string*): Path to the output PDBQT file. File type: output. [Sample file](https://github.com/bioexcel/biobb_vs/raw/master/biobb_vs/test/reference/vina/ref_output_vina.pdbqt). Accepted formats: PDBQT * **output_log_path** (*string*): Path to the log file. File type: output. [Sample file](https://github.com/bioexcel/biobb_vs/raw/master/biobb_vs/test/reference/vina/ref_output_vina.log). Accepted formats: LOG ### Config Syntax: input_parameter (datatype) - (default_value) Definition Config parameters for this building block: * **cpu** (*integer*): (1) the number of CPUs to use.. * **exhaustiveness** (*integer*): (8) exhaustiveness of the global search (roughly proportional to time).. * **num_modes** (*integer*): (9) maximum number of binding modes to generate.. * **min_rmsd** (*integer*): (1) minimum RMSD between output poses.. * **energy_range** (*integer*): (3) maximum energy difference between the best binding mode and the worst one displayed (kcal/mol).. * **binary_path** (*string*): (vina) path to vina in your local computer.. * **remove_tmp** (*boolean*): (True) Remove temporal files.. * **restart** (*boolean*): (False) Do not execute if output files exist.. * **sandbox_path** (*string*): (./) Parent path to the sandbox directory.. * **container_path** (*string*): (None) Container path definition.. * **container_image** (*string*): (biocontainers/autodock-vina:v1.1.2-5b1-deb_cv1) Container image definition.. * **container_volume_path** (*string*): (/tmp) Container volume path definition.. * **container_working_dir** (*string*): (None) Container working directory definition.. * **container_user_id** (*string*): (None) Container user_id definition.. * **container_shell_path** (*string*): (/bin/bash) Path to default shell inside the container.. ### YAML #### [Common config file](https://github.com/bioexcel/biobb_vs/blob/master/biobb_vs/test/data/config/config_autodock_vina_run.yml) ```python properties: remove_tmp: true ``` #### [Docker config file](https://github.com/bioexcel/biobb_vs/blob/master/biobb_vs/test/data/config/config_autodock_vina_run_docker.yml) ```python properties: container_image: biocontainers/autodock-vina:v1.1.2-5b1-deb_cv1 container_path: docker container_user_id: '1001' container_volume_path: /tmp ``` #### Command line ```python autodock_vina_run --config config_autodock_vina_run.yml --input_ligand_pdbqt_path vina_ligand.pdbqt --input_receptor_pdbqt_path vina_receptor.pdbqt --input_box_path vina_box.pdb --output_pdbqt_path ref_output_vina.pdbqt --output_log_path ref_output_vina.log ``` ### JSON #### [Common config file](https://github.com/bioexcel/biobb_vs/blob/master/biobb_vs/test/data/config/config_autodock_vina_run.json) ```python { "properties": { "remove_tmp": true } } ``` #### [Docker config file](https://github.com/bioexcel/biobb_vs/blob/master/biobb_vs/test/data/config/config_autodock_vina_run_docker.json) ```python { "properties": { "container_path": "docker", "container_image": "biocontainers/autodock-vina:v1.1.2-5b1-deb_cv1", "container_volume_path": "/tmp", "container_user_id": "1001" } } ``` #### Command line ```python autodock_vina_run --config config_autodock_vina_run.json --input_ligand_pdbqt_path vina_ligand.pdbqt --input_receptor_pdbqt_path vina_receptor.pdbqt --input_box_path vina_box.pdb --output_pdbqt_path ref_output_vina.pdbqt --output_log_path ref_output_vina.log ``` ## Bindingsite This class finds the binding site of the input_pdb. ### Get help Command: ```python bindingsite -h ``` usage: bindingsite [-h] [-c CONFIG] --input_pdb_path INPUT_PDB_PATH --input_clusters_zip INPUT_CLUSTERS_ZIP -o OUTPUT_PDB_PATH Finds the binding site of the input_pdb file based on the ligands' location of similar structures (members of the sequence identity cluster) options: -h, --help show this help message and exit -c CONFIG, --config CONFIG This file can be a YAML file, JSON file or JSON string required arguments: --input_pdb_path INPUT_PDB_PATH Path to the PDB structure where the binding site is to be found. Accepted formats: pdb. --input_clusters_zip INPUT_CLUSTERS_ZIP Path to the ZIP file with all the PDB members of the identity cluster. Accepted formats: zip. -o OUTPUT_PDB_PATH, --output_pdb_path OUTPUT_PDB_PATH Path to the PDB containig the residues belonging to the binding site. Accepted formats: pdb. ### I / O Arguments Syntax: input_argument (datatype) : Definition Config input / output arguments for this building block: * **input_pdb_path** (*string*): Path to the PDB structure where the binding site is to be found. File type: input. [Sample file](https://github.com/bioexcel/biobb_vs/raw/master/biobb_vs/test/data/utils/bindingsite.pdb). Accepted formats: PDB * **input_clusters_zip** (*string*): Path to the ZIP file with all the PDB members of the identity cluster. File type: input. [Sample file](https://github.com/bioexcel/biobb_vs/raw/master/biobb_vs/test/data/utils/bindingsite.zip). Accepted formats: ZIP * **output_pdb_path** (*string*): Path to the PDB containig the residues belonging to the binding site. File type: output. [Sample file](https://github.com/bioexcel/biobb_vs/raw/master/biobb_vs/test/reference/utils/ref_output_bindingsite.pdb). Accepted formats: PDB ### Config Syntax: input_parameter (datatype) - (default_value) Definition Config parameters for this building block: * **ligand** (*string*): (None) Ligand to be found in the protein structure. If no ligand provided, the largest one will be selected, if more than one.. * **radius** (*number*): (5.0) Cut-off distance (Ångstroms) around ligand atoms to consider a protein atom as a binding site atom.. * **max_num_ligands** (*integer*): (15) Total number of superimposed ligands to be extracted from the identity cluster. For populated clusters, the restriction avoids to superimpose redundant structures. If 0, all ligands extracted will be considered.. * **matrix_name** (*string*): (BLOSUM62) Substitution matrices for use in alignments. . * **gap_open** (*number*): (-10.0) Gap open penalty.. * **gap_extend** (*number*): (-0.5) Gap extend penalty.. * **remove_tmp** (*boolean*): (True) Remove temporal files.. * **restart** (*boolean*): (False) Do not execute if output files exist.. * **sandbox_path** (*string*): (./) Parent path to the sandbox directory.. ### YAML #### [Common config file](https://github.com/bioexcel/biobb_vs/blob/master/biobb_vs/test/data/config/config_bindingsite.yml) ```python properties: gap_extend: -0.5 gap_open: -10.0 ligand: PGA matrix_name: BLOSUM62 max_num_ligands: 15 radius: 5 ``` #### Command line ```python bindingsite --config config_bindingsite.yml --input_pdb_path bindingsite.pdb --input_clusters_zip bindingsite.zip --output_pdb_path ref_output_bindingsite.pdb ``` ### JSON #### [Common config file](https://github.com/bioexcel/biobb_vs/blob/master/biobb_vs/test/data/config/config_bindingsite.json) ```python { "properties": { "ligand": "PGA", "matrix_name": "BLOSUM62", "gap_open": -10.0, "gap_extend": -0.5, "max_num_ligands": 15, "radius": 5 } } ``` #### Command line ```python bindingsite --config config_bindingsite.json --input_pdb_path bindingsite.pdb --input_clusters_zip bindingsite.zip --output_pdb_path ref_output_bindingsite.pdb ``` ## Box This class sets the center and the size of a rectangular parallelepiped box around a set of residues or a pocket. ### Get help Command: ```python box -h ``` usage: box [-h] [-c CONFIG] -i INPUT_PDB_PATH -o OUTPUT_PDB_PATH Sets the center and the size of a rectangular parallelepiped box around a set of residues from a given PDB or a pocket from a given PQR. options: -h, --help show this help message and exit -c CONFIG, --config CONFIG This file can be a YAML file, JSON file or JSON string required arguments: -i INPUT_PDB_PATH, --input_pdb_path INPUT_PDB_PATH PDB file containing a selection of residue numbers or PQR file containing the pocket. Accepted formats: pdb, pqr. -o OUTPUT_PDB_PATH, --output_pdb_path OUTPUT_PDB_PATH PDB including the annotation of the box center and size as REMARKs. Accepted formats: pdb. ### I / O Arguments Syntax: input_argument (datatype) : Definition Config input / output arguments for this building block: * **input_pdb_path** (*string*): PDB file containing a selection of residue numbers or PQR file containing the pocket. File type: input. [Sample file](https://github.com/bioexcel/biobb_vs/raw/master/biobb_vs/test/data/utils/input_box.pqr). Accepted formats: PDB, PQR * **output_pdb_path** (*string*): PDB including the annotation of the box center and size as REMARKs. File type: output. [Sample file](https://github.com/bioexcel/biobb_vs/raw/master/biobb_vs/test/reference/utils/ref_output_box.pdb). Accepted formats: PDB ### Config Syntax: input_parameter (datatype) - (default_value) Definition Config parameters for this building block: * **offset** (*number*): (2.0) Extra distance (Angstroms) between the last residue atom and the box boundary.. * **box_coordinates** (*boolean*): (False) Add box coordinates as 8 ATOM records.. * **remove_tmp** (*boolean*): (True) Remove temporal files.. * **restart** (*boolean*): (False) Do not execute if output files exist.. * **sandbox_path** (*string*): (./) Parent path to the sandbox directory.. ### YAML #### [Common config file](https://github.com/bioexcel/biobb_vs/blob/master/biobb_vs/test/data/config/config_box.yml) ```python properties: box_coordinates: true offset: 2 ``` #### Command line ```python box --config config_box.yml --input_pdb_path input_box.pqr --output_pdb_path ref_output_box.pdb ``` ### JSON #### [Common config file](https://github.com/bioexcel/biobb_vs/blob/master/biobb_vs/test/data/config/config_box.json) ```python { "properties": { "offset": 2, "box_coordinates": true } } ``` #### Command line ```python box --config config_box.json --input_pdb_path input_box.pqr --output_pdb_path ref_output_box.pdb ``` ## Box_residues This class sets the center and the size of a rectangular parallelepiped box around a set of residues. ### Get help Command: ```python box_residues -h ``` usage: box_residues [-h] [-c CONFIG] -i INPUT_PDB_PATH -o OUTPUT_PDB_PATH Sets the center and the size of a rectangular parallelepiped box around a selection of residues found in a given PDB. options: -h, --help show this help message and exit -c CONFIG, --config CONFIG This file can be a YAML file, JSON file or JSON string required arguments: -i INPUT_PDB_PATH, --input_pdb_path INPUT_PDB_PATH PDB protein structure for which the box will be build. Its size and center will be set around the 'resid_list' property once mapped against this PDB. Accepted formats: pdb. -o OUTPUT_PDB_PATH, --output_pdb_path OUTPUT_PDB_PATH PDB including the annotation of the box center and size as REMARKs. Accepted formats: pdb. ### I / O Arguments Syntax: input_argument (datatype) : Definition Config input / output arguments for this building block: * **input_pdb_path** (*string*): PDB protein structure for which the box will be build. Its size and center will be set around the 'resid_list' property once mapped against this PDB. File type: input. [Sample file](https://github.com/bioexcel/biobb_vs/raw/master/biobb_vs/test/data/utils/input_box_residues.pdb). Accepted formats: PDB * **output_pdb_path** (*string*): PDB including the annotation of the box center and size as REMARKs. File type: output. [Sample file](https://github.com/bioexcel/biobb_vs/raw/master/biobb_vs/test/reference/utils/ref_output_box_residues.pdb). Accepted formats: PDB ### Config Syntax: input_parameter (datatype) - (default_value) Definition Config parameters for this building block: * **resid_list** (*array*): (None) List with all the residue numbers to form a cavity or binding site. Mandatory property.. * **offset** (*number*): (2.0) Extra distance (Angstroms) between the last residue atom and the box boundary.. * **box_coordinates** (*boolean*): (False) Add box coordinates as 8 ATOM records.. * **residue_offset** (*integer*): (0) Residue id offset.. * **remove_tmp** (*boolean*): (True) Remove temporal files.. * **restart** (*boolean*): (False) Do not execute if output files exist.. * **sandbox_path** (*string*): (./) Parent path to the sandbox directory.. ### YAML #### [Common config file](https://github.com/bioexcel/biobb_vs/blob/master/biobb_vs/test/data/config/config_box_residues.yml) ```python properties: box_coordinates: true offset: 2 resid_list: - 718 - 743 - 745 - 762 - 766 - 796 - 790 - 791 - 793 - 794 - 788 ``` #### Command line ```python box_residues --config config_box_residues.yml --input_pdb_path input_box_residues.pdb --output_pdb_path ref_output_box_residues.pdb ``` ### JSON #### [Common config file](https://github.com/bioexcel/biobb_vs/blob/master/biobb_vs/test/data/config/config_box_residues.json) ```python { "properties": { "resid_list": [ 718, 743, 745, 762, 766, 796, 790, 791, 793, 794, 788 ], "offset": 2, "box_coordinates": true } } ``` #### Command line ```python box_residues --config config_box_residues.json --input_pdb_path input_box_residues.pdb --output_pdb_path ref_output_box_residues.pdb ``` ## Extract_model_pdbqt Extracts a model from a PDBQT file with several models. ### Get help Command: ```python extract_model_pdbqt -h ``` usage: extract_model_pdbqt [-h] [-c CONFIG] -i INPUT_PDBQT_PATH -o OUTPUT_PDBQT_PATH Extracts a model from a PDBQT file with several models. options: -h, --help show this help message and exit -c CONFIG, --config CONFIG This file can be a YAML file, JSON file or JSON string required arguments: -i INPUT_PDBQT_PATH, --input_pdbqt_path INPUT_PDBQT_PATH Input PDBQT file. Accepted formats: pdbqt. -o OUTPUT_PDBQT_PATH, --output_pdbqt_path OUTPUT_PDBQT_PATH Output PDBQT file. Accepted formats: pdbqt. ### I / O Arguments Syntax: input_argument (datatype) : Definition Config input / output arguments for this building block: * **input_pdbqt_path** (*string*): Input PDBQT file. File type: input. [Sample file](https://github.com/bioexcel/biobb_vs/raw/master/biobb_vs/test/data/utils/models.pdbqt). Accepted formats: PDBQT * **output_pdbqt_path** (*string*): Output PDBQT file. File type: output. [Sample file](https://github.com/bioexcel/biobb_vs/raw/master/biobb_vs/test/reference/utils/ref_extract_model.pdbqt). Accepted formats: PDBQT ### Config Syntax: input_parameter (datatype) - (default_value) Definition Config parameters for this building block: * **model** (*integer*): (1) Model number to extract from input_pdbqt_path.. * **remove_tmp** (*boolean*): (True) Remove temporal files.. * **restart** (*boolean*): (False) Do not execute if output files exist.. * **sandbox_path** (*string*): (./) Parent path to the sandbox directory.. ### YAML #### [Common config file](https://github.com/bioexcel/biobb_vs/blob/master/biobb_vs/test/data/config/config_extract_model_pdbqt.yml) ```python properties: model: 1 ``` #### Command line ```python extract_model_pdbqt --config config_extract_model_pdbqt.yml --input_pdbqt_path models.pdbqt --output_pdbqt_path ref_extract_model.pdbqt ``` ### JSON #### [Common config file](https://github.com/bioexcel/biobb_vs/blob/master/biobb_vs/test/data/config/config_extract_model_pdbqt.json) ```python { "properties": { "model": 1 } } ``` #### Command line ```python extract_model_pdbqt --config config_extract_model_pdbqt.json --input_pdbqt_path models.pdbqt --output_pdbqt_path ref_extract_model.pdbqt ``` ## Fpocket_filter Performs a search over the outputs of the fpocket building block. ### Get help Command: ```python fpocket_filter -h ``` usage: fpocket_filter [-h] [-c CONFIG] --input_pockets_zip INPUT_POCKETS_ZIP --input_summary INPUT_SUMMARY -o OUTPUT_FILTER_POCKETS_ZIP Finds one or more binding sites in the outputs of the fpocket building block from given parameters. options: -h, --help show this help message and exit -c CONFIG, --config CONFIG This file can be a YAML file, JSON file or JSON string required arguments: --input_pockets_zip INPUT_POCKETS_ZIP Path to all the pockets found by fpocket. Accepted formats: zip. --input_summary INPUT_SUMMARY Path to the JSON summary file returned by fpocket. Accepted formats: json. -o OUTPUT_FILTER_POCKETS_ZIP, --output_filter_pockets_zip OUTPUT_FILTER_POCKETS_ZIP Path to the selected pockets after filtering. Accepted formats: zip. ### I / O Arguments Syntax: input_argument (datatype) : Definition Config input / output arguments for this building block: * **input_pockets_zip** (*string*): Path to all the pockets found by fpocket. File type: input. [Sample file](https://github.com/bioexcel/biobb_vs/raw/master/biobb_vs/test/data/fpocket/input_pockets.zip). Accepted formats: ZIP * **input_summary** (*string*): Path to the JSON summary file returned by fpocket. File type: input. [Sample file](https://github.com/bioexcel/biobb_vs/raw/master/biobb_vs/test/data/fpocket/input_summary.json). Accepted formats: JSON * **output_filter_pockets_zip** (*string*): Path to the selected pockets after filtering. File type: output. [Sample file](https://github.com/bioexcel/biobb_vs/raw/master/biobb_vs/test/reference/fpocket/ref_output_filter_pockets.zip). Accepted formats: ZIP ### Config Syntax: input_parameter (datatype) - (default_value) Definition Config parameters for this building block: * **score** (*array*): (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** (*array*): (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** (*array*): (None) List of two float numbers indicating the volume range. Indicates the pocket volume.. * **remove_tmp** (*boolean*): (True) Remove temporal files.. * **restart** (*boolean*): (False) Do not execute if output files exist.. * **sandbox_path** (*string*): (./) Parent path to the sandbox directory.. ### YAML #### [Common config file](https://github.com/bioexcel/biobb_vs/blob/master/biobb_vs/test/data/config/config_fpocket_filter.yml) ```python properties: druggability_score: - 0.2 - 0.9 score: - 0.2 - 1 volume: - 100 - 600 ``` #### Command line ```python fpocket_filter --config config_fpocket_filter.yml --input_pockets_zip input_pockets.zip --input_summary input_summary.json --output_filter_pockets_zip ref_output_filter_pockets.zip ``` ### JSON #### [Common config file](https://github.com/bioexcel/biobb_vs/blob/master/biobb_vs/test/data/config/config_fpocket_filter.json) ```python { "properties": { "score": [ 0.2, 1 ], "druggability_score": [ 0.2, 0.9 ], "volume": [ 100, 600 ] } } ``` #### Command line ```python fpocket_filter --config config_fpocket_filter.json --input_pockets_zip input_pockets.zip --input_summary input_summary.json --output_filter_pockets_zip ref_output_filter_pockets.zip ``` ## Fpocket_run Wrapper of the fpocket software. ### Get help Command: ```python fpocket_run -h ``` usage: fpocket_run [-h] [-c CONFIG] -i INPUT_PDB_PATH --output_pockets_zip OUTPUT_POCKETS_ZIP --output_summary OUTPUT_SUMMARY Finds the binding site of the input_pdb_path file via the fpocket software options: -h, --help show this help message and exit -c CONFIG, --config CONFIG This file can be a YAML file, JSON file or JSON string required arguments: -i INPUT_PDB_PATH, --input_pdb_path INPUT_PDB_PATH Path to the PDB structure where the binding site is to be found. Accepted formats: pdb. --output_pockets_zip OUTPUT_POCKETS_ZIP Path to all the pockets found by fpocket in the input_pdb_path structure. Accepted formats: zip. --output_summary OUTPUT_SUMMARY Path to the JSON summary file. Accepted formats: json. ### I / O Arguments Syntax: input_argument (datatype) : Definition Config input / output arguments for this building block: * **input_pdb_path** (*string*): Path to the PDB structure where the binding site is to be found. File type: input. [Sample file](https://github.com/bioexcel/biobb_vs/raw/master/biobb_vs/test/data/fpocket/fpocket_input.pdb). Accepted formats: PDB * **output_pockets_zip** (*string*): Path to all the pockets found by fpocket in the input_pdb_path structure. File type: output. [Sample file](https://github.com/bioexcel/biobb_vs/raw/master/biobb_vs/test/reference/fpocket/ref_output_pockets.zip). Accepted formats: ZIP * **output_summary** (*string*): Path to the JSON summary file. File type: output. [Sample file](https://github.com/bioexcel/biobb_vs/raw/master/biobb_vs/test/reference/fpocket/ref_output_summary.json). Accepted formats: JSON ### Config Syntax: input_parameter (datatype) - (default_value) Definition Config parameters for this building block: * **min_radius** (*number*): (None) The minimum radius in Ångstroms an alpha sphere might have in a binding pocket.. * **max_radius** (*number*): (None) The maximum radius in Ångstroms of alpha spheres in a pocket.. * **num_spheres** (*integer*): (None) Indicates how many alpha spheres a pocket must contain at least in order to figure in the results.. * **sort_by** (*string*): (druggability_score) From which property the output will be sorted. . * **binary_path** (*string*): (fpocket) path to fpocket in your local computer.. * **remove_tmp** (*boolean*): (True) Remove temporal files.. * **restart** (*boolean*): (False) Do not execute if output files exist.. * **sandbox_path** (*string*): (./) Parent path to the sandbox directory.. * **container_path** (*string*): (None) Container path definition.. * **container_image** (*string*): (fpocket/fpocket:latest) Container image definition.. * **container_volume_path** (*string*): (/tmp) Container volume path definition.. * **container_working_dir** (*string*): (None) Container working directory definition.. * **container_user_id** (*string*): (None) Container user_id definition.. * **container_shell_path** (*string*): (/bin/bash) Path to default shell inside the container.. ### YAML #### [Common config file](https://github.com/bioexcel/biobb_vs/blob/master/biobb_vs/test/data/config/config_fpocket_run.yml) ```python properties: max_radius: 6 min_radius: 3 num_spheres: 35 sort_by: druggability_score ``` #### [Docker config file](https://github.com/bioexcel/biobb_vs/blob/master/biobb_vs/test/data/config/config_fpocket_run_docker.yml) ```python properties: container_image: fpocket/fpocket:latest container_path: docker container_user_id: '1001' container_volume_path: /tmp max_radius: 6 min_radius: 3 num_spheres: 35 sort_by: druggability_score ``` #### Command line ```python fpocket_run --config config_fpocket_run.yml --input_pdb_path fpocket_input.pdb --output_pockets_zip ref_output_pockets.zip --output_summary ref_output_summary.json ``` ### JSON #### [Common config file](https://github.com/bioexcel/biobb_vs/blob/master/biobb_vs/test/data/config/config_fpocket_run.json) ```python { "properties": { "min_radius": 3, "max_radius": 6, "num_spheres": 35, "sort_by": "druggability_score" } } ``` #### [Docker config file](https://github.com/bioexcel/biobb_vs/blob/master/biobb_vs/test/data/config/config_fpocket_run_docker.json) ```python { "properties": { "min_radius": 3, "max_radius": 6, "num_spheres": 35, "sort_by": "druggability_score", "container_path": "docker", "container_image": "fpocket/fpocket:latest", "container_volume_path": "/tmp", "container_user_id": "1001" } } ``` #### Command line ```python fpocket_run --config config_fpocket_run.json --input_pdb_path fpocket_input.pdb --output_pockets_zip ref_output_pockets.zip --output_summary ref_output_summary.json ``` ## Fpocket_select Selects a single pocket in the outputs of the fpocket building block. ### Get help Command: ```python fpocket_select -h ``` usage: fpocket_select [-h] [-c CONFIG] -i INPUT_POCKETS_ZIP --output_pocket_pdb OUTPUT_POCKET_PDB --output_pocket_pqr OUTPUT_POCKET_PQR Selects a single pocket in the outputs of the fpocket building block from a given parameter. options: -h, --help show this help message and exit -c CONFIG, --config CONFIG This file can be a YAML file, JSON file or JSON string required arguments: -i INPUT_POCKETS_ZIP, --input_pockets_zip INPUT_POCKETS_ZIP Path to the pockets found by fpocket. Accepted formats: zip. --output_pocket_pdb OUTPUT_POCKET_PDB Path to the PDB file with the cavity found by fpocket. Accepted formats: pdb. --output_pocket_pqr OUTPUT_POCKET_PQR Path to the PQR file with the pocket found by fpocket. Accepted formats: pqr. ### I / O Arguments Syntax: input_argument (datatype) : Definition Config input / output arguments for this building block: * **input_pockets_zip** (*string*): Path to the pockets found by fpocket. File type: input. [Sample file](https://github.com/bioexcel/biobb_vs/raw/master/biobb_vs/test/data/fpocket/input_pockets.zip). Accepted formats: ZIP * **output_pocket_pdb** (*string*): Path to the PDB file with the cavity found by fpocket. File type: output. [Sample file](https://github.com/bioexcel/biobb_vs/raw/master/biobb_vs/test/reference/fpocket/ref_output_pocket.pdb). Accepted formats: PDB * **output_pocket_pqr** (*string*): Path to the PQR file with the pocket found by fpocket. File type: output. [Sample file](https://github.com/bioexcel/biobb_vs/raw/master/biobb_vs/test/reference/fpocket/ref_output_pocket.pqr). Accepted formats: PQR ### Config Syntax: input_parameter (datatype) - (default_value) Definition Config parameters for this building block: * **pocket** (*integer*): (1) Pocket id from the summary json given by the fpocket building block.. * **remove_tmp** (*boolean*): (True) Remove temporal files.. * **restart** (*boolean*): (False) Do not execute if output files exist.. * **sandbox_path** (*string*): (./) Parent path to the sandbox directory.. ### YAML #### [Common config file](https://github.com/bioexcel/biobb_vs/blob/master/biobb_vs/test/data/config/config_fpocket_select.yml) ```python properties: pocket: 4 ``` #### Command line ```python fpocket_select --config config_fpocket_select.yml --input_pockets_zip input_pockets.zip --output_pocket_pdb ref_output_pocket.pdb --output_pocket_pqr ref_output_pocket.pqr ``` ### JSON #### [Common config file](https://github.com/bioexcel/biobb_vs/blob/master/biobb_vs/test/data/config/config_fpocket_select.json) ```python { "properties": { "pocket": 4 } } ``` #### Command line ```python fpocket_select --config config_fpocket_select.json --input_pockets_zip input_pockets.zip --output_pocket_pdb ref_output_pocket.pdb --output_pocket_pqr ref_output_pocket.pqr ```