| Name | pdb-profiling JSON |
| Version |
0.4.4
JSON |
| download |
| home_page | https://github.com/NatureGeorge/pdb-profiling |
| Summary | Profiling Protein Structures from Protein Data Bank and integrate various resources.🏄♂️ |
| upload_time | 2023-03-30 06:20:16 |
| maintainer | ZeFeng Zhu |
| docs_url | None |
| author | |
| requires_python | >=3.7 |
| license | MIT |
| keywords |
|
| VCS |
 |
| bugtrack_url |
|
| requirements |
No requirements were recorded.
|
| Travis-CI |
|
| coveralls test coverage |
No coveralls.
|
# pdb-profiling
[](https://zenodo.org/badge/latestdoi/247475852)
[](https://github.com/naturegeorge/pdb-profiling/blob/master/LICENSE)
[](https://pypi.org/project/pdb-profiling/)
[](https://github.com/naturegeorge/pdb-profiling/blob/master/pdb_profiling/__init__.py)
[](https://pypi.org/project/pdb-profiling/)
[](https://github.com/NatureGeorge/pdb-profiling/releases/)
[](https://github.com/naturegeorge/pdb-profiling)
[](https://coveralls.io/github/NatureGeorge/pdb-profiling?branch=master)
Profiling Protein Structures from Protein Data Bank and integrate various resources.
## Features
* `Collection`: Implement various API to collect the well-organized metadata of PDB in real time.
* `Integration`: Provide a unified call for API-interface and return-data-form as well as subsequent data processing.
* `Detection`: Reorganize metadata to evaluate a PDB structure in Entry-Assembly/Model-Entity-Chain-Residue level and integrated with UniProt-KB.
* `Interaction`: Include UniProt Isoform Interaction in Asymmetric unit plus Biological Assembly level.
* `Selection`: Define the representative set of PDB structures in Monomeric|Homomeric|Heteromeric states.
* `Mapping`: Provide interface for both entry-identifier/accession-level and residue-level bidirectional mapping.
## Install
> Notice: require Python Environment >= 3.7, Platform Independent
Install by `pip` command.
### *Before your Installation
* Make sure that your 64-bit machine is installed with 64-bit Python.
* To avoid some unexpected issues, you should upgrade your `pip` beforehand:
```bash
python -m pip install --upgrade pip
```
### Official Installation
```bash
python -m pip install pdb-profiling
```
If you have already installed an older version of `pdb-profiling`, use the following command to install the latest version:
```bash
python -m pip install --upgrade pdb-profiling
```
### Build From Source (optional, for non-windows environment)
```bash
python -m pip install cython
python -m pip install numpy
git clone https://github.com/NatureGeorge/pdb-profiling.git
python setup.py build_ext --inplace # Need GCC or Other Compiler For C
python setup.py install # or "sudo python setup.py install" or "python setup.py install --user"
```
## Documentation
<https://pdb-profiling.netlify.app/>
## Examples
### Basic Usage
* [Command Line Example](https://github.com/NatureGeorge/pdb-profiling/discussions/2)
* [Retrieve Bound Molecule Data From PDBe](https://github.com/NatureGeorge/pdb-profiling/discussions/3)
* ...
### Large-Scale-Example
* [ExAC](https://github.com/NatureGeorge/pdb-profiling/blob/master/examples/exac_example.md)
## Resources
* PDBe Entry-Based API
* PDBe Aggregated API (PDBe Graph API)
* PDBe ModelServer API
* SWISS-MODEL Repository API
* UniProt API
* EBI Proteins API
* RCSB Data API
* RCSB Search API
* Eutils API (minimum usage)
* ...
> click [here](https://pdb-profiling.netlify.app/docs/5-reference/) for more details
## Related Resources
> Using similar data resources but meant to achieve different goals.
<details>
<summary>Click to view</summary>
* `RCSB`: [Build Customize Tabular Reports of PDB Data](https://www.rcsb.org/news?year=2020&article=5f6529e207302466657ec0e9&feature=true)
* [MolArt](https://github.com/davidhoksza/MolArt)
</details>
## Copyright Notice
This project is developed by [Zefeng Zhu](https://github.com/NatureGeorge) and hold by [Minghui Group](https://lilab.jysw.suda.edu.cn/).
## License
The `pdb_profiling.cython.py_qcprot` module is derived from the [cython wrapper contributed by Bernhard Thiel](https://github.com/Bernhard10/py_qcprot) and is distributed under the terms of a BSD-3-Clause License. And it also contains the dependent C-code from <http://theobald.brandeis.edu/QCP/> written by Pu Liu and Douglas Theobald (with slight modification by Bernhard Thiel) and is licensed under a BSD-3-Clause License.
The `pdb_profiling` is distributed under the terms of the MIT License.
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"description": "# pdb-profiling\n\n[](https://zenodo.org/badge/latestdoi/247475852)\n[](https://github.com/naturegeorge/pdb-profiling/blob/master/LICENSE)\n[](https://pypi.org/project/pdb-profiling/)\n[](https://github.com/naturegeorge/pdb-profiling/blob/master/pdb_profiling/__init__.py)\n[](https://pypi.org/project/pdb-profiling/)\n[](https://github.com/NatureGeorge/pdb-profiling/releases/)\n[](https://github.com/naturegeorge/pdb-profiling)\n[](https://coveralls.io/github/NatureGeorge/pdb-profiling?branch=master)\n\n\n\nProfiling Protein Structures from Protein Data Bank and integrate various resources.\n\n## Features\n\n* `Collection`: Implement various API to collect the well-organized metadata of PDB in real time.\n* `Integration`: Provide a unified call for API-interface and return-data-form as well as subsequent data processing.\n* `Detection`: Reorganize metadata to evaluate a PDB structure in Entry-Assembly/Model-Entity-Chain-Residue level and integrated with UniProt-KB.\n* `Interaction`: Include UniProt Isoform Interaction in Asymmetric unit plus Biological Assembly level.\n* `Selection`: Define the representative set of PDB structures in Monomeric|Homomeric|Heteromeric states.\n* `Mapping`: Provide interface for both entry-identifier/accession-level and residue-level bidirectional mapping.\n\n## Install\n\n> Notice: require Python Environment >= 3.7, Platform Independent\n\nInstall by `pip` command.\n\n### *Before your Installation\n\n* Make sure that your 64-bit machine is installed with 64-bit Python.\n* To avoid some unexpected issues, you should upgrade your `pip` beforehand:\n\n```bash\npython -m pip install --upgrade pip\n```\n\n### Official Installation\n\n```bash\npython -m pip install pdb-profiling\n```\n\nIf you have already installed an older version of `pdb-profiling`, use the following command to install the latest version:\n\n```bash\npython -m pip install --upgrade pdb-profiling\n```\n\n### Build From Source (optional, for non-windows environment)\n\n```bash\npython -m pip install cython\npython -m pip install numpy\ngit clone https://github.com/NatureGeorge/pdb-profiling.git\npython setup.py build_ext --inplace # Need GCC or Other Compiler For C\npython setup.py install # or \"sudo python setup.py install\" or \"python setup.py install --user\"\n```\n\n## Documentation\n\n<https://pdb-profiling.netlify.app/>\n\n## Examples\n\n### Basic Usage\n\n* [Command Line Example](https://github.com/NatureGeorge/pdb-profiling/discussions/2)\n* [Retrieve Bound Molecule Data From PDBe](https://github.com/NatureGeorge/pdb-profiling/discussions/3)\n* ...\n\n### Large-Scale-Example\n\n* [ExAC](https://github.com/NatureGeorge/pdb-profiling/blob/master/examples/exac_example.md)\n\n## Resources\n\n* PDBe Entry-Based API\n* PDBe Aggregated API (PDBe Graph API)\n* PDBe ModelServer API\n* SWISS-MODEL Repository API\n* UniProt API\n* EBI Proteins API\n* RCSB Data API\n* RCSB Search API\n* Eutils API (minimum usage)\n* ...\n\n> click [here](https://pdb-profiling.netlify.app/docs/5-reference/) for more details\n\n## Related Resources\n\n> Using similar data resources but meant to achieve different goals.\n\n<details>\n\n<summary>Click to view</summary>\n\n* `RCSB`: [Build Customize Tabular Reports of PDB Data](https://www.rcsb.org/news?year=2020&article=5f6529e207302466657ec0e9&feature=true)\n* [MolArt](https://github.com/davidhoksza/MolArt)\n\n</details>\n\n## Copyright Notice\n\nThis project is developed by [Zefeng Zhu](https://github.com/NatureGeorge) and hold by [Minghui Group](https://lilab.jysw.suda.edu.cn/).\n\n## License\n\nThe `pdb_profiling.cython.py_qcprot` module is derived from the [cython wrapper contributed by Bernhard Thiel](https://github.com/Bernhard10/py_qcprot) and is distributed under the terms of a BSD-3-Clause License. And it also contains the dependent C-code from <http://theobald.brandeis.edu/QCP/> written by Pu Liu and Douglas Theobald (with slight modification by Bernhard Thiel) and is licensed under a BSD-3-Clause License.\n\nThe `pdb_profiling` is distributed under the terms of the MIT License.\n",
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