mjoh223 / HW2

BMI203 HW2

HW2

Skeleton for clustering project.

assignment

1. Implement a similarity metric
2. Implement a clustering method based on a partitioning algorithm
3. Implement a clustering method based on a hierarchical algorithm
4. Answer the questions given in the homework assignment

structure

The main file that you will need to modify is cluster.py and the corresponding test_cluster.py. utils.py contains helpful classes that you can use to represent Active Sites. io.py contains some reading and writing files for interacting with PDB files and writing out cluster info.

.
├── README.md
├── data
│   ...
├── hw2skeleton
│   ├── __init__.py
│   ├── __main__.py
│   ├── cluster.py
│   ├── io.py
│   └── utils.py
└── test
    ├── test_cluster.py
    └── test_io.py

usage

To use the package, first run

conda install --yes --file requirements.txt

to install all the dependencies in requirements.txt. Then the package's main function (located in hw2skeleton/__main__.py) can be run as follows

python -m hw2skeleton -P data test.txt

testing

Testing is as simple as running

python -m pytest

from the root directory of this project.

contributors

Original design by Scott Pegg. Refactored and updated by Tamas Nagy.