Tool to extract protein-ligand interaction fingerprints from a Fragalysis target.
It's recommended that you work in a conda environment. To create a new environment and install the required packages, run the following commands:
$ git clone https://github.com/roncv/FragFeatures.git
$ conda create -n fragfeatures -c conda-forge python=3.11
$ conda activate fragfeatures
$ conda install -c conda-forge numpy rdkit pandas openmm
$ pip install molparse
$ cd FragFeatures
$ pip install .
FragFeatures can be used as a command line tool or as a Python package. The executable provided is fragfeat, which is added to your PATH upon installation of the package with pip.
FragFeatures comes with two submodules:
$ conda activate fragfeatures
$ fragfeat --help
usage: fragfeat [-h] ...
Open-source toolkit for extracting fragment features from protein-
ligand complexes.
options:
-h, --help show this help message and exit
Subcommands:
prepare-duck Prepare an experiment for DUck.
summarise-duck Summarise the output of a DUck experiment.
The modules accept inputs as command line arguments, yaml functionality is yet to be implemented.
To extract features from a target and prepare a directory for simulation, you can use the prepare-duck module. This module requires the following arguments:
$ fragfeat prepare-duck --help
usage: fragfeat prepare-duck [-h]
[-c COMPOUND_SELECTION [COMPOUND_SELECTION ...]]
[-e EXPERIMENT_NAME] [-t TARGET_DIR]
[-a] [-v]
options:
-h, --help show this help message and exit
-c COMPOUND_SELECTION [COMPOUND_SELECTION ...], --compound-selection COMPOUND_SELECTION [COMPOUND_SELECTION ...]
Compound selection for the experiment.
-e EXPERIMENT_NAME, --experiment-name EXPERIMENT_NAME
Name of the experiment.
-t TARGET_DIR, --target-dir TARGET_DIR
Path to the Fragalysis target's directory.
-a, --all-compounds Select all available compounds from a
target.
-v, --verbose Increase verbosity. Use -v for verbose and
-vv for additional verbosity.
Example:
$ fragfeat prepare-duck -c <compound_code(s)> -e Experiment -t /path/to/target/dir -v