BioBB VS Command Line Help

Generic usage:

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

Extract_model_pdbqt

Extracts a model from a PDBQT file with several models.

Get help

Command:

extract_model_pdbqt -h
/anaconda3/envs/biobb_dev_37/lib/python3.7/site-packages/Bio/SubsMat/__init__.py:131: BiopythonDeprecationWarning: Bio.SubsMat has been deprecated, and we intend to remove it in a future release of Biopython. As an alternative, please consider using Bio.Align.substitution_matrices as a replacement, and contact the Biopython developers if you still need the Bio.SubsMat module.
  BiopythonDeprecationWarning,
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

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
/anaconda3/envs/biobb_dev_37/lib/python3.7/site-packages/Bio/SubsMat/__init__.py:131: BiopythonDeprecationWarning: Bio.SubsMat has been deprecated, and we intend to remove it in a future release of Biopython. As an alternative, please consider using Bio.Align.substitution_matrices as a replacement, and contact the Biopython developers if you still need the Bio.SubsMat module.
  BiopythonDeprecationWarning,
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

Autodock_vina_run

Wrapper of the AutoDock Vina software.

Get help

Command:

autodock_vina_run -h
/bin/sh: 1: autodock_vina_run: not found

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:

  • vina_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..

YAML

Common config file

properties:
  remove_tmp: true

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
  }
}

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

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

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

Fpocket_run

Wrapper of the fpocket software.

Get help

Command:

fpocket_run -h
/bin/sh: 1: fpocket_run: not found

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. .
  • fpocket_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..

YAML

Common config file

properties:
  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"
  }
}

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

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
/anaconda3/envs/biobb_dev_37/lib/python3.7/site-packages/Bio/SubsMat/__init__.py:131: BiopythonDeprecationWarning: Bio.SubsMat has been deprecated, and we intend to remove it in a future release of Biopython. As an alternative, please consider using Bio.Align.substitution_matrices as a replacement, and contact the Biopython developers if you still need the Bio.SubsMat module.
  BiopythonDeprecationWarning,
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

Bindingsite

This class finds the binding site of the input_pdb.

Get help

Command:

bindingsite -h
/anaconda3/envs/biobb_dev_37/lib/python3.7/site-packages/Bio/SubsMat/__init__.py:131: BiopythonDeprecationWarning: Bio.SubsMat has been deprecated, and we intend to remove it in a future release of Biopython. As an alternative, please consider using Bio.Align.substitution_matrices as a replacement, and contact the Biopython developers if you still need the Bio.SubsMat module.
  BiopythonDeprecationWarning,
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