BioBB LSVS Command Line Help

Generic usage:

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

---

Smina_run

Wrapper of the smina molecular docking software.

Get help

Command:

smina_run -h

usage: smina_run [-h] [-c CONFIG] --input_ligands_sdf_path INPUT_LIGANDS_SDF_PATH --input_receptor_pdbqt_path INPUT_RECEPTOR_PDBQT_PATH --input_site_coords_path INPUT_SITE_COORDS_PATH --output_sdf_path OUTPUT_SDF_PATH [--output_log_path OUTPUT_LOG_PATH]

Prepares input ligand for an smina 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
  --output_log_path OUTPUT_LOG_PATH
                        Path to the log file. Accepted formats: log.

required arguments:
  --input_ligands_sdf_path INPUT_LIGANDS_SDF_PATH
                        Path to the input SDF ligands. Accepted formats: sdf.
  --input_receptor_pdbqt_path INPUT_RECEPTOR_PDBQT_PATH
                        Path to the input PDBQT receptor. Accepted formats: pdbqt.
  --input_site_coords_path INPUT_SITE_COORDS_PATH
                        Path to the yaml-file containing the binding site size and coordinates. Accepted formats: yml.
  --output_sdf_path OUTPUT_SDF_PATH
                        Path to the output SDF file. Accepted formats: sdf.

I / O Arguments

Syntax: input_argument (datatype) : Definition

Config input / output arguments for this building block:

• input_ligands_sdf_path (string): Path to the input SDF ligands. File type: input. Sample file. Accepted formats: SDF

• input_receptor_pdbqt_path (string): Path to the input PDBQT receptor. File type: input. Sample file. Accepted formats: PDBQT

• input_site_coords_path (string): Path to the yaml-file containing the binding site size and coordinates. File type: input. Sample file. Accepted formats: YML

• output_sdf_path (string): Path to the output SDF file. File type: output. Sample file. Accepted formats: SDF

• 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_filter (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): (smina) path to smina in your local computer..

• scoring (string): (vinardo) scoring function to be used..

• seed (integer): (1234) random number generator seed..

• 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/smina: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:
  check_extensions: true
  cpu: 2
  exhaustiveness: 2
  num_modes: 1
  remove_tmp: true

Docker config file

properties:
  container_image: biocontainers/smina:v1.1.2-5b1-deb_cv1
  container_path: docker
  container_user_id: '1001'
  container_volume_path: /tmp

Command line

smina_run --config config_smina_run.yml --input_ligands_sdf_path smina_ligands.sdf --input_receptor_pdbqt_path smina_receptor.pdbqt --input_site_coords_path smina_site_coords.yml --output_sdf_path ref_output_smina.sdf --output_log_path ref_output_smina.log

JSON

Common config file

{
  "properties": {
    "cpu": 2,
    "exhaustiveness": 2,
    "num_modes": 1,
    "check_extensions": true,
    "remove_tmp": true
  }
}

Docker config file

{
  "properties": {
    "container_path": "docker",
    "container_image": "biocontainers/smina:v1.1.2-5b1-deb_cv1",
    "container_volume_path": "/tmp",
    "container_user_id": "1001"
  }
}

Command line

smina_run --config config_smina_run.json --input_ligands_sdf_path smina_ligands.sdf --input_receptor_pdbqt_path smina_receptor.pdbqt --input_site_coords_path smina_site_coords.yml --output_sdf_path ref_output_smina.sdf --output_log_path ref_output_smina.log