Metadata-Version: 2.1
Name: moleculekit
Version: 0.8.3
Summary: A molecule reading/writing and manipulation package.
Home-page: https://github.com/acellera/moleculekit/
Author: Acellera
Author-email: info@acellera.com
License: UNKNOWN
Description: # MoleculeKit
        
        [![Build Status](https://dev.azure.com/stefdoerr/moleculekit/_apis/build/status/Acellera.moleculekit?branchName=master)](https://dev.azure.com/stefdoerr/moleculekit/_build/latest?definitionId=1&branchName=master)
        [![Language Grade: Python](https://img.shields.io/lgtm/grade/python/g/Acellera/moleculekit.svg?logo=lgtm&logoWidth=18)](https://lgtm.com/projects/g/Acellera/moleculekit/context:python) 
        [![Conda](https://anaconda.org/acellera/moleculekit/badges/version.svg)](https://anaconda.org/acellera/moleculekit)
        [![codecov](https://codecov.io/gh/Acellera/moleculekit/branch/master/graph/badge.svg)](https://codecov.io/gh/Acellera/moleculekit)
        
        A molecule manipulation library
        
        # Getting started
        
        We recommend installing Miniconda on your machine to better manage python packages and environments.
        
        You can install moleculekit either in the "base" conda environment or in a new conda environment. We recommend the second.
        
        
        ### Install it into the base conda environment
        
        #### With conda
        
        ```
        (base) user@computer:~$ conda install moleculekit -c acellera
        ```
        
        #### With pip
        
        ```
        (base) user@computer:~$ pip install moleculekit
        ```
        
        ### Create a new conda environment
        
        The advantage of conda environments is that you can keep each of your python packages separate with all of their dependencies.
        This helps avoid conflicts between python packages (i.e. one requires python 2.7 and the other one python 3.6) which might be hard to resolve.
        
        To create a new conda environment named "moleculekit" you run the following command
        
        ```
        (base) user@computer:~$ conda create -n moleculekit
        ```
        
        Then you activate that conda environment with
        
        ```
        (base) user@computer:~$ conda activate moleculekit
        (moleculekit) user@computer:~$ 
        ```
        
        As you can see the environment changed now.
        Now you can use the same above install commands to install into the new conda environment.
        
        ### Optional dependencies of moleculekit
        
        Moleculekit has a small number of optional dependencies which are needed for some of it's functionalities. They were not added to the default dependencies to keep moleculekit a fast and small installation and to avoid unnecessary conflicts with other software. However if you want to leverage all of it's functionality you can install the rest of the dependencies with the following command:
        
        ```
        (moleculekit) user@computer:~$ wget https://raw.githubusercontent.com/Acellera/moleculekit/master/extra_requirements.txt
        (moleculekit) user@computer:~$ conda install --file extra_requirements.txt -c acellera
        ``` 
        
        ### Using moleculekit in ipython
        
        Install ipython in the correct conda enviroment using the following command. If you have installed the extra dependencies as above, you can skip this step since it already installs ipython.
        
        ```
        (moleculekit) user@computer:~$ conda install ipython
        ```
        
        Now you can start an ipython console with
        
        ```
        (moleculekit) user@computer:~$ ipython
        ```
        
        In the ipython console you can now import any of the modules of moleculekit and use it as normal.
        
        ```python
        from moleculekit.molecule import Molecule
        
        mol = Molecule('3ptb')
        mol.view()
        ```
        
        ### Issues
        
        For any bugs or questions on usage feel free to use the issue tracker of this github repo.
        For the official documentation of moleculekit head over to https://software.acellera.com/docs/latest/moleculekit/index.html 
        
        ### Dev
        
        If you are using moleculekit without installing it by using the PYTHONPATH env var you will need to compile the C++ extensions in-place with the following command:
        
        ```
        python setup.py build_ext --inplace
        ```
        
        ## Citing MoleculeKit
        
        If you use this software in your publication please cite:
        
        Stefan Doerr, Matthew J. Harvey, Frank Noé, and Gianni De Fabritiis. 
        **HTMD: High-throughput molecular dynamics for molecular discovery.** 
        *Journal of Chemical Theory and Computation*, **2016**, *12* (4), pp 1845–1852.
        [doi:10.1021/acs.jctc.6b00049](http://pubs.acs.org/doi/abs/10.1021/acs.jctc.6b00049)
        
        
Platform: UNKNOWN
Classifier: Programming Language :: Python :: 3
Classifier: Operating System :: POSIX :: Linux
Description-Content-Type: text/markdown
