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Install eMolFrag2 with:
pip install "git+https://github.com/deepdrugai/eMolFrag2.git"emolfrag$ emolfrag
usage: emolfrag -i INPUT [-o OUTPUT] [-l {DEBUG,INFO,WARNING,ERROR,CRITICAL}]
[-c CONFIG] [-a] [-n] [-t] [-d] [-h]
eMolFrag2 is a molecular fragmentation tool based on the BRICS algorithm written in Python.
Brought to you by LSU's DeepDrug.ai team.
options:
-i, --input INPUT Path containing source molecules for fragmentation.
Single file or directory.
-o, --output OUTPUT Path for output fragments. If the directory does not
exist, it will be created. Default output directory is
'out/output/'.
-l, --log {DEBUG,INFO,WARNING,ERROR,CRITICAL}
Set the logging level to print to console. Default is
INFO.
-c, --config CONFIG Configuration file: .emf extension required.)
-a, --all Output all fragments. Default is to output only TC-
unique fragments.
-n, --indiv Each fragment will be saved individually in separate
files. Default is to save in one unified file each for
bricks, linkers, and freeatoms.
-t, --trace Print trace file for reconstructing original
molecules.
-d, --debug Quick flag to set logging level to debug.
-h, --help Show this help message and exit.
Examples:
$ emolfrag -i data/test_data/ -o results/
$ emolfrag -i data/test_data/ -o results/ -a -nt
$ emolfrag -i data/test_data.smi -o results/
$ emolfrag -i data/test_data.sdf -o results/ -c config.emf
$ emolfrag -i data/test_data.mol2 -o results/ -an
Note: The default configuration assumes that your input contains RDKit Mol objects serialized as SMILES or MOL2 format.
You can customize the behavior by providing a .emf configuration file (-c option).Three dependencies are required for eMolFrag: rdkit, networkx and matplotlib. Optionally, colorlog is used for full color logging files.