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
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)
Built Distribution
Close
Hashes for tessellate-0.3.3-py2.py3-none-any.whl
Algorithm | Hash digest | |
---|---|---|
SHA256 | b82849b9acfe4b858b0e69fb4b585c252138c15d05ecac8f9ecdac556176a5f5 |
|
MD5 | 4bd87c09298110305f6f1c6983a7ae68 |
|
BLAKE2b-256 | 473012a847887686910d0a438b8a248ca19228d183482f28b294aaccf3a01ed8 |