https://github.com/xiaohan2012/epitope-similarity
Epitope similarity between two structures
https://github.com/xiaohan2012/epitope-similarity
Last synced: 15 days ago
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Epitope similarity between two structures
- Host: GitHub
- URL: https://github.com/xiaohan2012/epitope-similarity
- Owner: xiaohan2012
- License: mit
- Created: 2014-03-01T14:19:24.000Z (over 11 years ago)
- Default Branch: master
- Last Pushed: 2015-01-07T11:43:00.000Z (over 10 years ago)
- Last Synced: 2025-04-02T09:17:36.013Z (3 months ago)
- Language: Python
- Size: 313 KB
- Stars: 0
- Watchers: 0
- Forks: 0
- Open Issues: 3
-
Metadata Files:
- Readme: README.md
- License: LICENSE
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README
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 any specification: `python get_sim_score.py --query-pdb test/data/sample1.pdb --against-pdb test/data/sample2.pdb`
2. With epitope specification: `python get_sim_score.py --query-pdb test/data/sample1.pdb --query-epitope 211,213,214,224,225,226,227,228,229 --against-pdb test/data/sample2.pdb --against-epitope 216,217,218,219,220,221`
3. With spinimage parametrization: `python get_sim_score.py --query-pdb test/data/sample1.pdb --against-pdb test/data/sample2.pdb --spin-image-radius-step=2 --spin-image-height-step=5 --sphere-radius-step=2`
4. With cutoff parametrization: `python get_sim_score.py --query-pdb test/data/sample1.pdb --against-pdb test/data/sample2.pdb --cutoff=10`
You can specify the fingerprint path and skip the fp calcualtion step by using the option --query-fp and --against_fp, for example:
`python get_sim_score.py --query-pdb test/data/sample1.pdb --against-pdb test/data/sample2.pdb --query-fp=fp/h2-v2/sample1.pdb.fp --against-fp=fp/h2-v2/sample2.pdb.fp`