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README.md

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Sparsehc-dm is a python wrapper for sparcehc distance matrix clustering algorithm, integrated with STXXL[![DOI for Citing STXXL](https://img.shields.io/badge/DOI-10.1002%2Fspe.v38%3A6-blue.svg)](http://dx.doi.org/10.1002/spe.v38:6) for on-disk sorting. SparseHC [![DOI for Citing SparseHC](https://img.shields.io/badge/DOI-10.1016%2Fj.procs.2014.05.001-blue.svg)](http://dx.doi.org/10.1016/j.procs.2014.05.001) is a memory-efficient hierarchical agglomerative clustering implementation. It has close to linear memory complexity, enabling clustering of ~900000 structures/points on 32GB RAM.
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Usage example:
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#### Usage example:
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```python
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import mdtraj as md
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from sparsehc_dm import sparsehc_dm
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Z=sparsehc_dm.linkage(m,"complete")
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```
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###Instalation
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####Prerequisites: boost graph and stxxl library
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### Instalation
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#### Prerequisites: boost graph and stxxl library
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```
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sudo apt-get install libboost-graph-dev libstxxl-dev libstxxl1
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```
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####Building:
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#### Building:
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```
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git clone https://github.com/Burning-Daylight/sparsehc-dm.git sparsehc-dm
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cd sparsehc-dm
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cmake ..
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make
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sudo make install
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```
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```

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