CommonJobWriter is a command-line interface (CLI) tool designed to streamline and automate the execution of common tasks in research. It is built with Python and uses the prompt_toolkit library for user interaction.
CommonJobWriter provides a simple and intuitive interface for executing tasks such as:
- Stereochemical Enumeration (Unenumerated Stereocenter Only)
- Ligprep (SMILES to SDF, no epik, uses ligprep.inp)
- Glide Docking (SDF to SDF, makes glide.in)
The tool allows you to select tasks from a list, and it guides you through the necessary steps to execute each task. It also provides a mechanism for adding new tasks as needed.
To use CommonJobWriter, simply run the main.py script from your terminal:
python main.pyYou will be presented with a list of tasks. Enter the number corresponding to the task you want to execute.
I have several enhancements planned for CommonJobWriter to make it more versatile and user-friendly. Here are some of the key features I am planning to implement:
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Portability: I aim to make the tool portable to other servers. This will allow users to use CommonJobWriter on any server they have access to, increasing its utility and flexibility.
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Directory Independence: I plan to test and ensure the ability to run the tool from different directories. This will make it easier for users to integrate CommonJobWriter into their existing workflows.
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Input Presentation: I will be working on cleaning up the presentation of input commands to make the tool more intuitive and user-friendly.
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Additional Tasks: I plan to add more common tasks to the tool. Some of the tasks I am considering include:
- Running a Glide job with a premade
.infile - Integrating other scripts that handle file transfer to local machines
- Adding future Deep Docking related tasks
- Running a Glide job with a premade