Command: dock

sub commmand: vina

Introduction

The vina command is used to perform molecular docking using the Vina software. It allows users to run Vina in parallel for multiple tasks.

Parameters

  • -d or --dir: The directory containing the config files for docking tasks. Each sub-directory is considered a separate task. Default is the current directory.
  • -c or --config-name: The sub-string of name of the config file for each task. Default is config.txt.
  • -v or --vina-name: The name of the Vina executable to call. Default is vina.
  • --vina-args: Additional arguments to pass to the Vina executable. Default is --log ./log.txt.
  • -n or --n-workers: The number of tasks to run in parallel. Default is 1.

Behavior

  • The command first checks if the provided directory exists and is a valid directory.
  • It then finds all config files with the specified name in the directory and its subdirectories.
  • For each config file, it checks if the output file already exists. If it does, the task is skipped.
  • The command runs the Vina executable with the specified arguments for each task in parallel using a thread pool with the specified number of workers.
  • It waits for all tasks to complete before exiting.

Precautions

  • Ensure that the Vina executable is properly installed and accessible.
  • The config files should be in the correct format expected by Vina.
  • The number of workers should be adjusted based on the system's capabilities to avoid overloading.

Example

lazydock-cli dock vina -d ./docking_tasks --config-name config.txt -v vina --vina-args "--log ./log.txt --exhaustiveness 8" --n-workers 4

This command will run Vina docking for all tasks in the docking_tasks directory using 4 workers in parallel, with the specified Vina arguments.

sub commmand: hdock

Introduction

The hdock command is used to perform molecular docking using the HDOCK web server. It supports running docking tasks in batch mode.

Parameters

  • -d or --dir: The directory containing the config files or receptor/ligand files for docking tasks. Default is the current directory.
  • -r or --receptor: The sub-string of name of the receptor PDB file. If provided, it will override the config file.
  • -l or --ligand: The sub-string of name of the ligand PDB file. If provided, it will override the config file.
  • --config-name: The sub-string of name of the config file for each task. Default is config.txt.
  • -m or --method: The docking method to use. Currently, only web is supported. Default is web.
  • --email: The email address to use for the HDOCK web server.
  • -gui or --gui: A flag to show the browser GUI. Default is False.

Behavior

  • The command checks if the provided directory exists and is a valid directory.
  • It finds all config files or receptor/ligand file pairs in the directory and its subdirectories.
  • For each task, it checks if the output file already exists. If it does, the task is skipped.
  • The command runs the HDOCK docking using the web server for each task. If the GUI flag is set, it will open a browser window.
  • It waits for a random time between 3 to 5 minutes between tasks to avoid overloading the server.

Precautions

  • Ensure that the HDOCK web server is accessible.

Example

lazydock-cli dock hdock -d ./docking_tasks --config-name config.txt --email user@example.com

This command will run HDOCK docking for all tasks in the docking_tasks directory using the config files, with the specified email address.

sub commmand: hpepdock

Introduction

The hpepdock command is similar to hdock but specifically uses the HPEPDOCK web server for molecular docking.

Parameters

  • -d or --dir: The directory containing the config files or receptor/ligand files for docking tasks. Default is the current directory.
  • -r or --receptor: The sub-string of name of the receptor PDB file. If provided, it will override the config file.
  • -l or --ligand: The sub-string of name of the ligand PDB file. If provided, it will override the config file.
  • --config-name: The sub-string of name of the config file for each task. Default is config.txt.
  • -m or --method: The docking method to use. Currently, only web is supported. Default is web.
  • --email: The email address to use for the HPEPDOCK web server.
  • -gui or --gui: A flag to show the browser GUI. Default is False.

Behavior

  • The command checks if the provided directory exists and is a valid directory.
  • It finds all config files or receptor/ligand file pairs in the directory and its subdirectories.
  • For each task, it checks if the output file already exists. If it does, the task is skipped.
  • The command runs the HPEPDOCK docking using the web server for each task. If the GUI flag is set, it will open a browser window.
  • It waits for a random time between 3 to 5 minutes between tasks to avoid overloading the server.

Precautions

  • Ensure that the HPEPDOCK web server is accessible.

Example

lazydock-cli dock hpepdock -d ./docking_tasks --config-name config.txt --email user@example.com

This command will run HPEPDOCK docking for all tasks in the docking_tasks directory using the config files, with the specified email address.

sub commmand: dinc-ensemble

Introduction

The dinc-ensemble command is used to perform molecular docking using the DINC-Ensemble web server. It supports running docking tasks in batch mode and can use grid box parameters from config files.

Parameters

  • -d or --dir: The directory containing the config files or receptor/ligand files for docking tasks. Default is the current directory.
  • -r or --receptor: The sub-string of name of the receptor PDB file. If provided, it will override the config file.
  • -l or --ligand: The sub-string of name of the ligand PDB file. If provided, it will override the config file.
  • --config-name: The sub-string of name of the config file for each task. Default is config.txt.
  • -m or --method: The docking method to use. Currently, only web is supported. Default is web.
  • --email: The email address to use for the DINC-Ensemble web server. Required.
  • -gui or --gui: A flag to show the browser GUI. Default is False.
  • --use-config-box: A flag to use the grid box parameters from the config file. Default is False.

Behavior

  • The command checks if the provided directory exists and is a valid directory.
  • It finds all config files or receptor/ligand file pairs in the directory and its subdirectories.
  • For each task, it checks if the output file already exists. If it does, the task is skipped.
  • The command runs the DINC-Ensemble docking using the web server for each task. If the GUI flag is set, it will open a browser window.
  • It waits for a random time between 3 to 5 minutes between tasks to avoid overloading the server.
  • If the --use-config-box flag is set, it will use the grid box parameters from the config file for docking.

Precautions

  • Ensure that the DINC-Ensemble web server is accessible.
  • The email address is required and should be valid.
  • The config file should contain the correct grid box parameters if using the --use-config-box flag.

Example

lazydock-cli dock dinc-ensemble -d ./docking_tasks --config-name config.txt --email user@example.com --use-config-box

This command will run DINC-Ensemble docking for all tasks in the docking_tasks directory using the config files and grid box parameters, with the specified email address.

sub commmand: convert-result

Introduction The convert-result command is used to convert docking result files from various formats to PDB format.

Parameters

  • -d or --dir: The directory containing the input files to convert. Default is the current directory.
  • -n or --name: The sub-string of name of the input file to convert. Default is an empty string, which means all files in the directory will be considered.
  • -i or --input-type: The type of the input files. Multiple types can be specified separated by commas. Default is pdbqt,dlg.
  • -o or --output-type: The type of the output files. Currently, only pdb is supported. Default is pdb.
  • -s or --suffix: The suffix to add to the output file names. Default is an empty string.
  • -m or --method: The conversion method to use. Currently, lazydock and obabel are supported. Default is lazydock.
  • --n-workers: The number of tasks to run in parallel. Default is 4.

Behavior

  • The command checks if the provided directory exists and is a valid directory.
  • It finds all input files with the specified types in the directory and its subdirectories.
  • For each input file, it converts the file to the specified output type using the chosen method.
  • The command runs the conversion tasks in parallel using a process pool with the specified number of workers.
  • It waits for all tasks to complete before exiting.

Precautions

Ensure that the conversion tools (e.g., lazydock, obabel) are properly installed and accessible. The input files should be in the correct format expected by the conversion method.

Example

lazydock-cli dock convert-result -d ./docking_results -m lazydock --n-workers 2

This command will convert all pdbqt and dlg files in the docking_results directory to PDB format using the lazydock method with 2 workers in parallel.