diff --git a/README.md b/README.md index 239060f..ecfd1d2 100644 --- a/README.md +++ b/README.md @@ -64,6 +64,47 @@ python calc_props.py -b tests/b-lactams.smi -o tests/b-lactam.csv python calc_props.py -b tests/b-lactams.smi ``` +Installing as a package +----------------------- + +```sh +# Download package and goto package directory +git clone https://github.com/HergenrotherLab/entry-cli +cd entry-cli + +# Make conda environment 'entry-cli-env' +make init + +# Install package +make install + +# To uninstall the package later, run 'make uninstall' +``` + +After installing the package, the application is available from the command line: + +```sh +usage: entry-cli [-h] [-s SMILES string | -b Batch file] [-o Output file] + +Performs calculation of physiochemical properties of potential antibiotics. +SMILES strings are parsed, conformers are generated, and properties +calculated. Properties include: chemical formula, molecular weight, rotatable +bonds, globularity, and PBF. + +optional arguments: + -h, --help show this help message and exit + -s SMILES string, --smiles SMILES string + -b Batch file, --batch Batch file + -o Output file, --output Output file + Defaults to csv file with same name as input +``` + +Alternatively, the functions can be imported as a python module. + +```python +from entry_cli.calc_props import smiles_to_ob, average_properties +``` + Citing ------