Metadata-Version: 2.1
Name: PeptideConstructor
Version: 0.2.1
Summary: Create (DL-) peptide PDB files with specified secondary structures
Home-page: https://github.com/CharlesHahn/PeptideConstructor
Author: CharlesHahn
Author-email: 
License: UNKNOWN
Download-URL: https://github.com/CharlesHahn/PeptideConstructor/releases
Description: # PeptideConstructor: A simple Python library to generate model (DL-) peptides with different secondary structure.
        
        
        [![PyPI version](https://badge.fury.io/py/PeptideConstructor.svg)](https://badge.fury.io/py/PeptideConstructor)
        ![PyPI - Downloads](https://img.shields.io/pypi/dm/PeptideConstructor)
        ![PyPI - License](https://img.shields.io/pypi/l/PeptideConstructor)
        
        ![cover](./cover.png)
        
        
        ## Still working on this:
        
        - [x] add D amino acids support
        - [x] add command-line interface support
        - [ ] add support of more amino acids
        - [ ] add support of adding amino acids to existing protein
        - [ ] add energy minimization or conformation optimization support
        - [ ] further more, add DNA/RNA support
        
        ## Installation
        
        You can easily install PeptideConstructor with pip:
        
        ```
        pip install PeptideConstructor
        ```
        
        or just clone this repo and run:
        
        ```
        python setup.py build
        python setup.py install
        ```
        
        PeptideConstructor has two required dependency: 
        - `Biopython` for PDB IO.
        - `Numpy` for coordinates calculation.
        
        ## Usage
        
        After installation, `PCcli` command could be called in your terminal. `PCcli` could generage peptide PDB file from sequence in a simple way.
        
        For instance:
        
        ```
        PCcli -s AaDdKSQym -o test.pdb
        ```
        which will generage a test.pdb file in current directory which contains a peptide with sequence of `AaDdKSQym`, in which, uppercase indicates L amino acids and lowercase indicates D amino acids. 
        
        Also, secondary structure and capping of peptide could be applied through `PCcli`.
        
        ```
        PCcli -s AaDdKSQym -o test.pdb -ss a -cap 1
        ```
        
        **parameters** : 
        
        - `-s` : peptide sequence. Uppercases indicate L amino acids while lowercases indicate D amino acids
        - `-o` : output PDB file name
        - `-ss` : (optional) secondary structure you want:
          -  `l` for no secondary structure assignment (default)
          -  `a` for alpha helix 
          -  `b` for beta sheet 
          -  `la` for left hand helix 
          -  `lb` for mirror inverted beta sheet
        - `-cap` : (optional) cappings:
          - `0` for no cappings (default)
          - `1` for cappings (`ACE` in the N terminal and `NME` in the C terminal)
          - `2` for only adding `ACE` to the N termial 
          - `3` for only adding `NME` in the C terminal 
        
        **examples** : 
        
        Sure you could generage peptide in original way by writing codes.
        
        check examples/ directory for more examples of generating peptide by code.
        
         see [PeptideBuilder](https://github.com/clauswilke/PeptideBuilder) for more infomation.
        
        
        ## Post-processing Tools Recommandation:
        
        1. add hydrogens : reduce, PyMol, TINKER
        2. structure optimization: Avogadro/EM, PyMol/sculpt, ModRefiner, TINKER/minimize
        
        ## Contributing
        
        Pull requests are welcome on GitHub. However, to be accepted, contributions must:
        
        1. Be styled with [`black`](https://black.readthedocs.io/en/stable/)
        2. Be linted with `pylint`
        3. Be type-checked with `mypy`
        4. Pass the `pytest` unit tests
        
        Thus, before contributing code make sure the following commands exit without errors when run from the root directory of the PeptideConstructor project:
        
        - `pytest`
        - `black .`
        - `mypy PeptideConstructor/`
        - `pylint --rcfile=setup.cfg PeptideConstructor/`
        
        ## Others
        
        This repo is based on [Lun4m/PeptideBuilder.git](https://github.com/Lun4m/PeptideBuilder) and [clauswilke/PeptideBuilder.git](https://github.com/clauswilke/PeptideBuilder). 
        
        **Cite the original paper**:
        
        M. Z. Tien, D. K. Sydykova, A. G. Meyer, C. O. Wilke (2013). PeptideBuilder:
        A simple Python library to generate model peptides. PeerJ 1:e80.
        
Platform: cross-platform
Classifier: Development Status :: 4 - Beta
Classifier: License :: OSI Approved :: MIT License
Classifier: Programming Language :: Python
Classifier: Programming Language :: Python :: 3
Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
Classifier: Topic :: Scientific/Engineering :: Chemistry
Classifier: Intended Audience :: Science/Research
Description-Content-Type: text/markdown
Provides-Extra: test
