Homework 2: Clustering

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
│   ...
├── functions
│   ├── __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 functions/__main__.py) can be run as follows

python -m functions -P data test.txt

The -P flag is for the partition method, the -H flag is for heirarchical, and the -A flag runs both methods, then compares the two clusters using the Rand Index and measures the Quality of the clusters using the Sum of Distances Method

testing

Testing is as simple as running

python -m pytest

from the root directory of this project.