# BioBB LSVS Command Line Help Generic usage: ```python biobb_command [-h] --config CONFIG --input_file(s) --output_file ``` ----------------- ## Smina_run Wrapper of the smina molecular docking software. ### Get help Command: ```python 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](https://github.com/bioexcel/biobb_lsvs/raw/master/biobb_lsvs/test/data/smina/smina_ligands.sdf). Accepted formats: SDF * **input_receptor_pdbqt_path** (*string*): Path to the input PDBQT receptor. File type: input. [Sample file](https://github.com/bioexcel/biobb_lsvs/raw/master/biobb_lsvs/test/data/smina/smina_receptor.pdbqt). 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](https://github.com/bioexcel/biobb_lsvs/raw/master/biobb_lsvs/test/data/smina/smina_site_coords.yml). Accepted formats: YML * **output_sdf_path** (*string*): Path to the output SDF file. File type: output. [Sample file](https://github.com/bioexcel/biobb_lsvs/raw/master/biobb_lsvs/test/reference/smina/ref_output_smina.sdf). Accepted formats: SDF * **output_log_path** (*string*): Path to the log file. File type: output. [Sample file](https://github.com/bioexcel/biobb_lsvs/raw/master/biobb_lsvs/test/reference/smina/ref_output_smina.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_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](https://github.com/bioexcel/biobb_lsvs/blob/master/biobb_lsvs/test/data/config/config_smina_run.yml) ```python properties: check_extensions: true cpu: 2 exhaustiveness: 2 num_modes: 1 remove_tmp: true ``` #### [Docker config file](https://github.com/bioexcel/biobb_lsvs/blob/master/biobb_lsvs/test/data/config/config_smina_run_docker.yml) ```python properties: container_image: biocontainers/smina:v1.1.2-5b1-deb_cv1 container_path: docker container_user_id: '1001' container_volume_path: /tmp ``` #### Command line ```python 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](https://github.com/bioexcel/biobb_lsvs/blob/master/biobb_lsvs/test/data/config/config_smina_run.json) ```python { "properties": { "cpu": 2, "exhaustiveness": 2, "num_modes": 1, "check_extensions": true, "remove_tmp": true } } ``` #### [Docker config file](https://github.com/bioexcel/biobb_lsvs/blob/master/biobb_lsvs/test/data/config/config_smina_run_docker.json) ```python { "properties": { "container_path": "docker", "container_image": "biocontainers/smina:v1.1.2-5b1-deb_cv1", "container_volume_path": "/tmp", "container_user_id": "1001" } } ``` #### Command line ```python 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 ```