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] [-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. 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.
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 

properties:
  remove_tmp: true

Docker config file 

properties:
  container_image: quay.io/biocontainers/biobb_vs:5.2.1--pyhdfd78af_0
  container_path: docker
  container_user_id: '1001'
  container_volume_path: /tmp

Singularity config file 

properties:
  container_image: https://depot.galaxyproject.org/singularity/biobb_vs:5.2.1--pyhdfd78af_0
  container_path: singularity
  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": "quay.io/biocontainers/biobb_vs:5.2.1--pyhdfd78af_0",
    "container_volume_path": "/tmp",
    "container_user_id": "1001"
  }
}

Singularity config file 

{
  "properties": {
    "container_path": "singularity",
    "container_image": "https://depot.galaxyproject.org/singularity/biobb_vs:5.2.1--pyhdfd78af_0",
    "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] [-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. 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.
sandbox_path (string): (./) Parent path to the sandbox directory.

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] [-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. 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. The box is centred on the mean of the selected coordinates, so a set of points that is asymmetric about its centre may extend slightly beyond the box faces. Choose an offset large enough to absorb that asymmetry, yet small enough not to enlarge the box past what the binding site needs, since a larger box spreads the same sampling effort over more space.
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 

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

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] [-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. 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. The box is centred on the mean of the selected coordinates, so a set of points that is asymmetric about its centre may extend slightly beyond the box faces. Choose an offset large enough to absorb that asymmetry, yet small enough not to enlarge the box past what the binding site needs, since a larger box spreads the same sampling effort over more space.
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 

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

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] [-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. 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.
sandbox_path (string): (./) Parent path to the sandbox directory.

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

Fpocket_filter

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

Get help

Command:

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. 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.
sandbox_path (string): (./) Parent path to the sandbox directory.

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_run

Wrapper of the fpocket software.

Get help

Command:

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. 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.
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 

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

Docker config file 

properties:
  container_image: quay.io/biocontainers/biobb_vs:5.2.1--pyhdfd78af_0
  container_path: docker
  container_user_id: '1001'
  container_volume_path: /tmp
  max_radius: 6
  min_radius: 3
  num_spheres: 35
  sort_by: druggability_score

Singularity config file 

properties:
  container_image: https://depot.galaxyproject.org/singularity/biobb_vs:5.2.1--pyhdfd78af_0
  container_path: singularity
  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": "quay.io/biocontainers/biobb_vs:5.2.1--pyhdfd78af_0",
    "container_volume_path": "/tmp",
    "container_user_id": "1001"
  }
}

Singularity config file 

{
  "properties": {
    "min_radius": 3,
    "max_radius": 6,
    "num_spheres": 35,
    "sort_by": "druggability_score",
    "container_path": "singularity",
    "container_image": "https://depot.galaxyproject.org/singularity/biobb_vs:5.2.1--pyhdfd78af_0",
    "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] [-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. 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.
sandbox_path (string): (./) Parent path to the sandbox directory.

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

Gnina_run

Wrapper of the gnina software.

Get help

Command:

gnina_run -h

usage: gnina_run [-h] [-c CONFIG] --input_ligand_path INPUT_LIGAND_PATH --input_receptor_path INPUT_RECEPTOR_PATH [--input_box_path INPUT_BOX_PATH] [--input_autobox_path INPUT_AUTOBOX_PATH] --output_sdf_path OUTPUT_SDF_PATH [--output_summary_path OUTPUT_SUMMARY_PATH] [--output_log_path OUTPUT_LOG_PATH]

Performs docking of a ligand to a receptor with CNN rescoring via the gnina 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:
  --input_ligand_path INPUT_LIGAND_PATH
                        Path to the input ligand. It may hold several ligands and it must hold genuine 3D coordinates, as gnina samples torsions but never bond lengths, bond angles or ring conformations. Accepted formats: sdf, mol2, pdb, pdbqt.
  --input_receptor_path INPUT_RECEPTOR_PATH
                        Path to the input receptor. Every atom of this file is treated as rigid receptor, so any crystal ligand must be removed beforehand.  Provide a PDBQT file for full control over protonation, as PDBQT input is passed to gnina unmodified. Charges are not taken into account, just hydrogen donor/acceptor character which depends on the protonation state. Accepted formats: pdb, pdbqt.
  --output_sdf_path OUTPUT_SDF_PATH
                        Path to the output file with the docked poses and their scores as SD data fields. Use a .sdf.gz extension to obtain gzip compressed output. Accepted formats: sdf, gz.

optional arguments:
  --input_box_path INPUT_BOX_PATH
                        Path to the PDB file with the box center and size annotated as a REMARK, as written by the box and box_residues building blocks. Mutually exclusive with input_autobox_path. Accepted formats: pdb.
  --input_autobox_path INPUT_AUTOBOX_PATH
                        Path to a reference structure whose bounding coordinates define the docking box, for example a crystal ligand, an fpocket pocket or the whole receptor. It only needs atoms with Cartesian coordinates, it does not need to be a real molecule. Mutually exclusive with input_box_path. Accepted formats: sdf, mol2, pdb, pdbqt, pqr.
  --output_summary_path OUTPUT_SUMMARY_PATH
                        Path to the JSON summary file, holding one entry per output pose with the ligand it belongs to and every score gnina assigned to it. Accepted formats: json.
  --output_log_path OUTPUT_LOG_PATH
                        Path to the log file written by gnina. Accepted formats: log.

I / O Arguments

Syntax: input_argument (datatype) : Definition

Config input / output arguments for this building block:

input_ligand_path (string): Path to the input ligand. It may hold several ligands and it must hold genuine 3D coordinates, as gnina samples torsions but never bond lengths, bond angles or ring conformations. File type: input. Sample file. Accepted formats: SDF, MOL2, PDB, PDBQT
input_receptor_path (string): Path to the input receptor. Every atom of this file is treated as rigid receptor, so any crystal ligand must be removed beforehand. Provide a PDBQT file for full control over protonation, as PDBQT input is passed to gnina unmodified. File type: input. Sample file. Accepted formats: PDB, PDBQT
input_box_path (string): Path to the PDB file with the box center and size annotated as a REMARK, as written by the box and box_residues building blocks. Mutually exclusive with input_autobox_path. File type: input. Sample file. Accepted formats: PDB
input_autobox_path (string): Path to a reference structure whose bounding coordinates define the docking box, for example a crystal ligand, an fpocket pocket or the whole receptor. It only needs atoms with Cartesian coordinates, it does not need to be a real molecule. Mutually exclusive with input_box_path. File type: input. Sample file. Accepted formats: SDF, MOL2, PDB, PDBQT, PQR
output_sdf_path (string): Path to the output file with the docked poses and their scores as SD data fields. Use a .sdf.gz extension to obtain gzip compressed output. File type: output. Sample file. Accepted formats: SDF, GZ
output_summary_path (string): Path to the JSON summary file, holding one entry per output pose with the ligand it belongs to and every score gnina assigned to it. File type: output. Sample file. Accepted formats: JSON
output_log_path (string): Path to the log file written by gnina. 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) Number of CPU cores to use. Keep it lower than or equal to exhaustiveness, and always set it explicitly on a shared machine.
exhaustiveness (integer): (8) Number of independent Monte Carlo search chains. This is the main sampling knob, but it gives diminishing returns past the default for a targeted pocket.
num_modes (integer): (9) Maximum number of binding modes written out.
min_rmsd_filter (number): (1.0) RMSD in Angstroms below which a pose is dropped as redundant with a better ranked one.
num_mc_saved (integer): (None) Number of top poses retained in each Monte Carlo chain, gnina defaults to 50 when unset.
seed (integer): (None) Explicit random seed. Docking is stochastic, so set it for reproducible runs.
scoring (string): (None) Built-in empirical scoring function, gnina uses its own default when unset.
cnn_scoring (string): (None) Where the convolutional neural network is used in the pipeline, gnina defaults to rescore when unset.
cnn (string): (None) Name of a built-in convolutional neural network model, or a name ending in _ensemble to evaluate every built-in model sharing that prefix. gnina defaults to an ensemble of three models when unset.
pose_sort_order (string): (None) How the internal pose pool is sorted before the redundancy filter and the num_modes cutoff are applied, so it can surface a different set of poses and not merely reorder them. gnina defaults to CNNscore when unset.
autobox_add (number): (None) Buffer in Angstroms added on every side of the box derived from input_autobox_path, gnina defaults to 4 when unset. A larger box does not slow gnina down, but it does loosen the constraint on sampling.
autobox_extend (boolean): (None) Enlarge the box derived from input_autobox_path when needed so the input ligand can rotate freely inside it, gnina enables this when unset.
minimize (boolean): (False) Energy minimize the poses given in input_ligand_path instead of searching for new ones.
score_only (boolean): (False) Score the poses given in input_ligand_path without searching or minimizing.
local_only (boolean): (False) Restrict the search to a local one inside the box.
no_gpu (boolean): (False) Disable GPU acceleration even when a GPU is available.
device (integer): (None) Index of the GPU device to use.
quiet (boolean): (False) Suppress the gnina output messages.
binary_path (string): (gnina) Path to the gnina executable in your local computer. gnina is not distributed with this package, install it from its binary release or run it through a container.
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): (gnina/gnina:latest) Container image definition.
container_volume_path (string): (/data) 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 -c) Path to default shell inside the container.

YAML

Common config file 

properties:
  cnn_scoring: none
  cpu: 4
  exhaustiveness: 4
  no_gpu: true
  num_modes: 3
  scoring: vinardo
  seed: 42

Docker config file 

properties:
  cnn_scoring: none
  container_image: gnina/gnina:latest
  container_path: docker
  container_user_id: '1001'
  container_volume_path: /data
  cpu: 4
  seed: 42

Command line

gnina_run --config config_gnina_run.yml --input_ligand_path gnina_ligand.sdf --input_receptor_path vina_receptor.pdbqt --input_box_path vina_box.pdb --output_sdf_path ref_output_gnina.sdf --output_summary_path ref_output_summary.json --output_log_path ref_output_gnina.log

JSON

Common config file 

{
  "properties": {
    "cnn_scoring": "none",
    "scoring": "vinardo",
    "exhaustiveness": 4,
    "num_modes": 3,
    "cpu": 4,
    "seed": 42,
    "no_gpu": true
  }
}

Docker config file 

{
  "properties": {
    "cnn_scoring": "none",
    "cpu": 4,
    "seed": 42,
    "container_path": "docker",
    "container_image": "gnina/gnina:latest",
    "container_volume_path": "/data",
    "container_user_id": "1001"
  }
}

Command line

gnina_run --config config_gnina_run.json --input_ligand_path gnina_ligand.sdf --input_receptor_path vina_receptor.pdbqt --input_box_path vina_box.pdb --output_sdf_path ref_output_gnina.sdf --output_summary_path ref_output_summary.json --output_log_path ref_output_gnina.log

Gnina_select_pose

Selects a single pose in the output of the gnina_run building block.

Get help

Command:

gnina_select_pose -h

usage: gnina_select_pose [-h] [-c CONFIG] -i INPUT_SDF_PATH -o OUTPUT_SDF_PATH

Selects a single pose in the output of the gnina_run building block.

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_SDF_PATH, --input_sdf_path INPUT_SDF_PATH
                        Path to the SDF file with the docked poses written by the gnina_run building block. Accepted formats: sdf, gz.
  -o OUTPUT_SDF_PATH, --output_sdf_path OUTPUT_SDF_PATH
                        Path to the output SDF file with the selected pose. Accepted formats: sdf, gz.

I / O Arguments

Syntax: input_argument (datatype) : Definition

Config input / output arguments for this building block:

input_sdf_path (string): Path to the SDF file with the docked poses written by the gnina_run building block. File type: input. Sample file. Accepted formats: SDF, GZ
output_sdf_path (string): Path to the output SDF file with the selected pose. File type: output. Sample file. Accepted formats: SDF, GZ

Config

Syntax: input_parameter (datatype) - (default_value) Definition

Config parameters for this building block:

pose (integer): (1) Rank of the pose to extract, counted over the poses left after ligand has been applied and sort_by has been honoured.
ligand (integer): (None) Index of the ligand whose poses are considered, following the order of the ligands in the file gnina docked. All poses in the file are considered when unset.
sort_by (string): (None) Score to reorder the poses by before one is picked. The poses are taken in the order gnina wrote them when unset, which is already gnina’s own ranking. Note that this reorders only the poses present in the file, so it is not equivalent to the pose_sort_order property of gnina_run, which reorders the whole internal pool before the redundancy filter and the num_modes cutoff discard poses.
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 

properties:
  pose: 1

Command line

gnina_select_pose --config config_gnina_select_pose.yml --input_sdf_path gnina_poses.sdf --output_sdf_path ref_output_pose.sdf

JSON

Common config file 

{
  "properties": {
    "pose": 1
  }
}

Command line

gnina_select_pose --config config_gnina_select_pose.json --input_sdf_path gnina_poses.sdf --output_sdf_path ref_output_pose.sdf