Skip to main content

A package for quantifying cyclic molecule conformations.

Project description

==========
Tessellate
==========


.. image:: https://img.shields.io/pypi/v/tessellate.svg
:target: https://pypi.python.org/pypi/tessellate

.. image:: https://readthedocs.org/projects/tessellate/badge/?version=latest
:target: https://tessellate.readthedocs.io/en/latest/?badge=latest
:alt: Documentation Status

A package for quantifying cyclic molecule conformations.


* Free software: Apache Software License 2.0
* Documentation: https://tessellate.readthedocs.io.

Using
-----

`make install; tessellate data/example-builtin --input-format=builtin --output-format=json `
`make install; tessellate data/*DNA --input-format=pdblist --output-format=json `

Usecase 1 - timeseries data
---------------------------

`make install; tessellate data/usecase-timeseries --input-format=builtin --output-format=json --output-dir=output-usecase-timeseries`

Usecase 2 - RNA and DNA
-----------------------
`make install; tessellate data/usecase-*DNA --input-format=pdblist --output-format=json --output-dir=output-usecase-rnadna`

Usecase 3 - Alpha Cyclodextrin
------------------------------
`make install; tessellate data/usecase-*CD --input-format=pdblist --output-format=json --output-dir=output-usecase-cyclodextrin`

Run All Usecases
----------------

```
tessellate data/usecase-timeseries --input-format=builtin --output-format=json --output-dir=output-usecase-timeseries
tessellate data/usecase-*DNA --input-format=pdblist --output-format=json --output-dir=output-usecase-rnadna
tessellate data/usecase-*CD --input-format=pdblist --output-format=json --output-dir=output-usecase-cyclodextrin
```


Viewing Data
------------

Try out Montage to create reports for these datasets.
For example:
```
USECASE_DATA=output-usecase-cyclodextrin
multiqc $USECASE_DATA -m comp_tessellate -f # -f to overwrite existing reports
google-chrome multiqc_report.html
```

Compare all outputs
```
multiqc output* -m comp_tessellate -f # -f to overwrite existing reports
google-chrome multiqc_report.html
```





Features
--------

* Improve testing and documentation. Port existing tests over.
* Tables
* Merge in tcl scripts and VMD examples


Development
-----------
Bump version numbers using bumpversion
X=thecurrentversion
`bumpversion --current-version X minor`

To bump from x.y.z to x.y.a use patch as the part:
`bumpversion --current-version X patch`

Uploading to PyPi
-----------------
Use twine
conda install -c conda-forge twine
make install
make dist
twine upload dist/*

Read the Docs
-------------
Docs are here. RTD is authorised to acces GitHub repos. The RTD service hook builds doc on push.

Credits
---------


This package incorporates work from existing packages (all originally developed by Chris B. Barnett.)
* https://bitbucket.org/scientificomputing/triangular-tessellation-class http://git.cem.uct.ac.za/analysis-pucker/triangular-tessellation-class
* https://bitbucket.org/scientificomputing/ring-analytics-webserver https://bitbucket.org/rxncor/rad-dev http://git.cem.uct.ac.za/analysis-pucker/ring-analytics-dash
* https://bitbucket.org/scientificomputing/triangular-tessellation-in-vmd http://git.cem.uct.ac.za/analysis-pucker/triangular-decomposition-timeseries-in-VMD

This package was created with Cookiecutter_ and the `audreyr/cookiecutter-pypackage`_ project template.

.. _Cookiecutter: https://github.com/audreyr/cookiecutter
.. _`audreyr/cookiecutter-pypackage`: https://github.com/audreyr/cookiecutter-pypackage



=======
History
=======

0.3.1 (2017-11-24)
------------------
* Usecase, documentation update. Update requirements for PyPi.

0.3.0 (2017-11-23)
------------------
* First release on PyPi

0.2.0 (2017-11-23)
------------------
* Alpha version that can read PDBlists and builtin, can write json
* Include examples and much verbose logging

0.1.0 (2017-11-21)
------------------

* Alpha version. Basic function


Project details


Download files

Download the file for your platform. If you're not sure which to choose, learn more about installing packages.

Source Distribution

tessellate-0.3.3.tar.gz (41.3 kB view hashes)

Uploaded Source

Built Distribution

tessellate-0.3.3-py2.py3-none-any.whl (30.7 kB view hashes)

Uploaded Python 2 Python 3

Supported by

AWS AWS Cloud computing and Security Sponsor Datadog Datadog Monitoring Fastly Fastly CDN Google Google Download Analytics Microsoft Microsoft PSF Sponsor Pingdom Pingdom Monitoring Sentry Sentry Error logging StatusPage StatusPage Status page