<commit_before>epitope-similarity
==================

Epitope similarity calculation between two structures

#Before you run

`> pip install -r requirements.txt`
	
#How to use

1. Without epitope specification: `python get_sim_score.py --query-pdb data/sample1.pdb  --against-pdb data/sample2.pdb`
2. With specification: `python get_sim_score.py --query-pdb data/sample1.pdb  --query-epitope 211,213,214,224,225,226,227,228,229 --against-pdb data/sample2.pdb --against-epitope 216,217,218,219,220,221`
3. With spinimage configuration: `python get_sim_score.py --query-pdb data/sample1.pdb  --against-pdb data/sample2.pdb  --spin-image-radius-range=20,40 --spin-image-radius-step=2 --spin-image-height-range=10,60 --spin-image-height-step=5 --sphere-radius-range=20,40 --sphere-radius-step=2`<commit_msg>added the virtualenv part in the README.md<commit_after>epitope-similarity
==================

Epitope similarity calculation between two structures

#Before you run

```
> cd epitope-similarity
> virtualenv venv
> source venv/bin/activate
> pip install -r requirements.txt
```

#Check if everything is ok

`> python test/similarity_test.py`

	
#How to use

1. Without epitope specification: `python get_sim_score.py --query-pdb data/sample1.pdb  --against-pdb data/sample2.pdb`
2. With specification: `python get_sim_score.py --query-pdb data/sample1.pdb  --query-epitope 211,213,214,224,225,226,227,228,229 --against-pdb data/sample2.pdb --against-epitope 216,217,218,219,220,221`
3. With spinimage configuration: `python get_sim_score.py --query-pdb data/sample1.pdb  --against-pdb data/sample2.pdb  --spin-image-radius-range=20,40 --spin-image-radius-step=2 --spin-image-height-range=10,60 --spin-image-height-step=5 --sphere-radius-range=20,40 --sphere-radius-step=2`
{'fraction_non_alphanumeric': 0.156056338028169, 'fraction_numerical': 0.07774647887323943, 'mean_word_length': 4.6380952380952385, 'pattern_counts': {'":': 0, '<': 3, '<?xml version=': 0, '>': 9, 'https://': 0, 'lorem ipsum': 0, 'www.': 0, 'xml': 0}, 'pii_count': 0, 'substrings_counts': 0, 'word_list_counts': {'cursed_substrings.json': 0, 'profanity_word_list.json': 0, 'sexual_word_list.json': 0, 'zh_pornsignals.json': 0}}
{'dir': 'git-commits-cleaned', 'id': '7669485', 'n_tokens_mistral': 728, 'n_tokens_neox': 610, 'n_words': 130}