What is it?
A toolkit to interface https://tldr.docking.org/, a webserver home to a collection of docking optimization and benchmark molecular docking programs.
Installation
Installation is super easy and pip installable. Please make sure you have Python 3.6 installed.
$ pip install tldr-tools
The API_KEY, as found on the top right corner under tldr.docking.org, must be set as an environmental variable before usage. The API_KEY can be assigned in .env under the package root, or directly set in terminal.
# Method 1: Add under .env (recommended for for python notebooks)
$ echo "API_KEY=SOMESECRETKEY" > .env
# Method 2: Manually setting API_KEY (recommended for interactive jobs)
export API_KEY="SOMESECRETKEY"
Usage
To view the current implemented modules in tldr-tools, please run:
$ tldr-submit --list-modules
For example, if running decoy generation is desired:
tldr-submit --module decoys --activesism input_files/actives.ism --decoygenin input_files/decoy_generation.in --memo "Decoy generation for ADA, replicate 1"
Or, you can build a ligand using DOCK38:
tldr-submit --module build --input chaff_tools/aggregator_advisor_hf_test.txt --memo "aa_hf_test"
Documenting runs with the optional memo parameter is encouraged.
Pass in a job number to check on a status of a run:
tldr-status --job-number 14886
Once a run is successful, you can download the output to a local directory:
tldr-download --job-number 14886 --output some_folder
Does tldr-tools work in Colab and Jupyter Notebook?
Yep, you use tldr-tools as follow:
from tldr_tools.tldr_submit import * # Import to submit new jobs
from tldr_tools.tldr_endpoint import * # Import for APIManager() which is responsible for handling requests (api_token and headers)
from tldr_tools.tldr_status import * # Import to check on status
api_manager = APIManager()
module_name = "build"
kwargs = {
"input": "aggregator_advisor_hf_test.txt",
"memo": "aa_hf_test"
}
# Submit the module
job_number = submit_module(api_manager, module_name, **kwargs)
Extending tldr-tools
Community and expansion is encouraged and made easy with this codebase. Adding new modules that are newly introduced on https://tldr.docking.org/ is painless, and is as simple as adding a new Endpoint and required/optional list of files.
1 maintainer
Release files for tldr-tools 0.2.4.4
For a detailed explanation of source distributions (sdists) and built distributions (wheels), please see the package formats documentation.
Source distribution (sdist)
| File | Size | Uploaded | |
|---|---|---|---|
| tldr_tools-0.2.4.4.tar.gz | 17.7 kB | Details |
Built distribution (wheel)
| File | Interpreter | ABI | Platform | Reset |
|---|---|---|---|---|
| tldr_tools-0.2.4.4-py3-none-any.whl | Python 3 | none | any | Details |
Total release size: 45.1 kB
Release files / tldr_tools-0.2.4.4.tar.gz
| Download URL | tldr_tools-0.2.4.4.tar.gz |
|---|---|
| Size | 17.7 kB |
| Tags | Source |
|
SHA-256 checksum How to use checksums |
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No |
| Uploaded via |
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Release files / tldr_tools-0.2.4.4-py3-none-any.whl
| Download URL | tldr_tools-0.2.4.4-py3-none-any.whl |
|---|---|
| Size | 27.4 kB |
| Tags | Python 3 |
|
SHA-256 checksum How to use checksums |
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BLAKE2b-256 checksum How to use checksums |
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Uploaded using Trusted Publishing? What is trusted publishing? |
No |
| Uploaded via |
twine/6.1.0 CPython/3.12.7
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