BioBB VS Command Line Help¶

Generic usage:

biobb_command [-h] --config CONFIG --input_file(s) <input_file(s)> --output_file <output_file>

Autodock_vina_run¶

Wrapper of the AutoDock Vina software.

Get help¶

Command:

autodock_vina_run -h

usage: autodock_vina_run [-h] [--config 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.

optional arguments:
  -h, --help            show this help message and exit
  --config CONFIG       Configuration file
  --output_log_path OUTPUT_LOG_PATH
                        Path to the log file. Accepted formats: log.

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.

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. Accepted formats: PDBQT
input_receptor_pdbqt_path (string): Path to the input PDBQT receptor. File type: input. Sample file. Accepted formats: PDBQT
input_box_path (string): Path to the PDB containig the residues belonging to the binding site. File type: input. Sample file. Accepted formats: PDB
output_pdbqt_path (string): Path to the output PDBQT file. File type: output. Sample file. Accepted formats: PDBQT
output_log_path (string): Path to the log file. File type: output. Sample file. 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..
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..
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 ¶

properties:
  remove_tmp: true

Docker config file ¶

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¶

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 ¶

{
  "properties": {
    "remove_tmp": true
  }
}

Docker config file ¶

{
  "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¶

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:

bindingsite -h

usage: bindingsite [-h] [--config CONFIG] --input_pdb_path INPUT_PDB_PATH --input_clusters_zip INPUT_CLUSTERS_ZIP --output_pdb_path 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)

optional arguments:
  -h, --help            show this help message and exit
  --config CONFIG       Configuration file

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.
  --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. 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. Accepted formats: ZIP
output_pdb_path (string): Path to the PDB containig the residues belonging to the binding site. File type: output. Sample file. 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..

YAML¶

Common config file ¶

properties:
  gap_extend: -0.5
  gap_open: -10.0
  ligand: PGA
  matrix_name: blosum62
  max_num_ligands: 15
  radius: 5

Command line¶

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 ¶

{
  "properties": {
    "ligand": "PGA",
    "matrix_name": "blosum62",
    "gap_open": -10.0,
    "gap_extend": -0.5,
    "max_num_ligands": 15,
    "radius": 5
  }
}

Command line¶

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:

box -h

usage: box [-h] [--config CONFIG] --input_pdb_path INPUT_PDB_PATH --output_pdb_path 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.

optional arguments:
  -h, --help            show this help message and exit
  --config CONFIG       Configuration file

required arguments:
  --input_pdb_path INPUT_PDB_PATH
                        PDB file containing a selection of residue numbers or PQR file containing the pocket. Accepted formats: pdb, pqr.
  --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. 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. 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..

YAML¶

Common config file ¶

properties:
  box_coordinates: true
  offset: 2

Command line¶

box --config config_box.yml --input_pdb_path input_box.pqr --output_pdb_path ref_output_box.pdb

JSON¶

Common config file ¶

{
  "properties": {
    "offset": 2,
    "box_coordinates": true
  }
}

Command line¶

box --config config_box.json --input_pdb_path input_box.pqr --output_pdb_path ref_output_box.pdb

Fpocket_filter¶

Performs a search over the outputs of the fpocket building block.

Get help¶

Command:

fpocket_filter -h

usage: fpocket_filter [-h] [--config CONFIG] --input_pockets_zip INPUT_POCKETS_ZIP --input_summary INPUT_SUMMARY --output_filter_pockets_zip OUTPUT_FILTER_POCKETS_ZIP

Finds one or more binding sites in the outputs of the fpocket building block from given parameters.

optional arguments:
  -h, --help            show this help message and exit
  --config CONFIG       Configuration file

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.
  --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. Accepted formats: ZIP
input_summary (string): Path to the JSON summary file returned by fpocket. File type: input. Sample file. Accepted formats: JSON
output_filter_pockets_zip (string): Path to the selected pockets after filtering. File type: output. Sample file. 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..

YAML¶

Common config file ¶

properties:
  druggability_score:
  - 0.2
  - 0.9
  score:
  - 0.2
  - 1
  volume:
  - 100
  - 600

Command line¶

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 ¶

{
  "properties": {
    "score": [
      0.2,
      1
    ],
    "druggability_score": [
      0.2,
      0.9
    ],
    "volume": [
      100,
      600
    ]
  }
}

Command line¶

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

Box_residues¶

This class sets the center and the size of a rectangular parallelepiped box around a set of residues.

Get help¶

Command:

box_residues -h

usage: box_residues [-h] [--config CONFIG] --input_pdb_path INPUT_PDB_PATH --output_pdb_path OUTPUT_PDB_PATH

Sets the center and the size of a rectangular parallelepiped box around a selection of residues found in a given PDB.

optional arguments:
  -h, --help            show this help message and exit
  --config CONFIG       Configuration file

required arguments:
  --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.
  --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. Accepted formats: PDB
output_pdb_path (string): PDB including the annotation of the box center and size as REMARKs. File type: output. Sample file. 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..

YAML¶

Common config file ¶

properties:
  box_coordinates: true
  offset: 2
  resid_list:
  - 718
  - 743
  - 745
  - 762
  - 766
  - 796
  - 790
  - 791
  - 793
  - 794
  - 788

Command line¶

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 ¶

{
  "properties": {
    "resid_list": [
      718,
      743,
      745,
      762,
      766,
      796,
      790,
      791,
      793,
      794,
      788
    ],
    "offset": 2,
    "box_coordinates": true
  }
}

Command line¶

box_residues --config config_box_residues.json --input_pdb_path input_box_residues.pdb --output_pdb_path ref_output_box_residues.pdb

Fpocket_run¶

Wrapper of the fpocket software.

Get help¶

Command:

fpocket_run -h

usage: fpocket_run [-h] [--config CONFIG] --input_pdb_path 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

optional arguments:
  -h, --help            show this help message and exit
  --config CONFIG       Configuration file

required arguments:
  --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. 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. Accepted formats: ZIP
output_summary (string): Path to the JSON summary file. File type: output. Sample file. 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..
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 ¶

properties:
  max_radius: 6
  min_radius: 3
  num_spheres: 35
  sort_by: druggability_score

Docker config file ¶

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¶

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 ¶

{
  "properties": {
    "min_radius": 3,
    "max_radius": 6,
    "num_spheres": 35,
    "sort_by": "druggability_score"
  }
}

Docker config file ¶

{
  "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¶

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:

fpocket_select -h

usage: fpocket_select [-h] [--config CONFIG] --input_pockets_zip 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.

optional arguments:
  -h, --help            show this help message and exit
  --config CONFIG       Configuration file

required arguments:
  --input_pockets_zip INPUT_POCKETS_ZIP
                        Path to all 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. Accepted formats: ZIP
output_pocket_pdb (string): Path to the PDB file with the cavity found by fpocket. File type: output. Sample file. Accepted formats: PDB
output_pocket_pqr (string): Path to the PQR file with the pocket found by fpocket. File type: output. Sample file. 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..

YAML¶

Common config file ¶

properties:
  pocket: 4

Command line¶

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 ¶

{
  "properties": {
    "pocket": 4
  }
}

Command line¶

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

Extract_model_pdbqt¶

Extracts a model from a PDBQT file with several models.

Get help¶

Command:

extract_model_pdbqt -h

usage: extract_model_pdbqt [-h] [--config CONFIG] --input_pdbqt_path INPUT_PDBQT_PATH --output_pdbqt_path OUTPUT_PDBQT_PATH

Extracts a model from a PDBQT file with several models.

optional arguments:
  -h, --help            show this help message and exit
  --config CONFIG       Configuration file

required arguments:
  --input_pdbqt_path INPUT_PDBQT_PATH
                        Input PDBQT file. Accepted formats: pdbqt.
  --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. Accepted formats: PDBQT
output_pdbqt_path (string): Output PDBQT file. File type: output. Sample file. 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..

YAML¶

Common config file ¶

properties:
  model: 1

Command line¶

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 ¶

{
  "properties": {
    "model": 1
  }
}

Command line¶

extract_model_pdbqt --config config_extract_model_pdbqt.json --input_pdbqt_path models.pdbqt --output_pdbqt_path ref_extract_model.pdbqt