Metadata-Version: 2.1
Name: pdb-profiling
Version: 0.1.4
Summary: Profiling Protein Structures from Protein Data Bank and integrate various resources.
Home-page: https://github.com/NatureGeorge/pdb-profiling
Author-email: 1730416009@stu.suda.edu.cn
Maintainer: ZeFeng Zhu
Maintainer-email: 1730416009@stu.suda.edu.cn
License: MIT
Platform: UNKNOWN
Classifier: Operating System :: OS Independent
Classifier: Programming Language :: Python :: 3.6
Classifier: Programming Language :: Python :: 3.7
Classifier: Programming Language :: Python :: 3.8
Requires-Python: >=3.6.*
Description-Content-Type: text/markdown
Requires-Dist: aiofiles
Requires-Dist: aioftp
Requires-Dist: aiohttp
Requires-Dist: aiosqlite
Requires-Dist: databases
Requires-Dist: furl
Requires-Dist: neo4j
Requires-Dist: numpy
Requires-Dist: orjson
Requires-Dist: orm
Requires-Dist: pandas
Requires-Dist: pyexcel
Requires-Dist: smart-open
Requires-Dist: tablib
Requires-Dist: tenacity
Requires-Dist: textdistance
Requires-Dist: tqdm
Requires-Dist: unsync

# pdb-profiling

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![cover](https://user-images.githubusercontent.com/43134199/93692609-f28f5f00-fb27-11ea-95db-6fa32771394f.png)

Profiling Protein Structures from Protein Data Bank and integrate various resources.

## Goal

* Gather helpful/insightful indexes to evaluate a PDB structure's usefulness in:
  * Entry level
  * Assembly level
  * Model level
  * Entity level
  * Chain level
  * Residue level
* Define the representative set of protein structures:
  * of a cluster with nearly identical sequences
  * of UniProt Entry
  * of UniProt Isoform
  * or any other assigned structure dataset
* Provide interface for ID/residue mapping
* Apply mature and robust API to collect well-organized data
  * PDBe REST API
    * <https://www.ebi.ac.uk/pdbe/api/doc/pdb.html>
    * <https://www.ebi.ac.uk/pdbe/api/doc/pisa.html>
    * <https://www.ebi.ac.uk/pdbe/api/doc/sifts.html>
  * PDBe Graph API (Neo4j Graph DataBase)
    * <https://www.ebi.ac.uk/pdbe/graph-api/pdbe_doc/>
  * PDBe CoordinateServer API
    * <https://www.ebi.ac.uk/pdbe/coordinates/index.html>
  * PDBe ModelServer API
    * <https://www.ebi.ac.uk/pdbe/model-server/>
  * SWISS-MODEL Repository API
    * <https://swissmodel.expasy.org/docs/smr_openapi>
  * EBI Proteins API
    * <https://www.ebi.ac.uk/proteins/api/doc/>
  * Interactome3D API
    * <https://interactome3d.irbbarcelona.org/>
  * ModBase API (?)
* Download data from PDB Archive against unexpected needs
  * wwwPDB&RCSB: <https://ftp.wwpdb.org/pub/pdb/data/structures/>
  * EBI: <http://ftp.ebi.ac.uk/pub/databases/pdb/data/structures/>

## Install

```bash
pip install pdb-profiling
```

## Examples

See `examples/...`

1. [Introduction](https://nbviewer.jupyter.org/github/NatureGeorge/pdb-profiling/blob/master/examples/Introduction.ipynb)
2. [Batch](https://nbviewer.jupyter.org/github/NatureGeorge/pdb-profiling/blob/master/examples/Batch.ipynb)
3. [DisplayPDB](https://nbviewer.jupyter.org/github/NatureGeorge/pdb-profiling/blob/master/examples/DisplayPDB.ipynb)
3. ...

## Copyright Notice

This project is developed by [Zefeng Zhu](https://github.com/NatureGeorge) and hold by [Minghui Group](https://lilab.jysw.suda.edu.cn/).

