Tessellate¶

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

Installing¶

Use Python3. For example, Anaconda Python https://www.anaconda.com/download/ https://repo.continuum.io/archive/Anaconda3-5.0.1-Linux-x86_64.sh
Use a virtual environment or conda environment.
Install with pip or compile the source code

# installing with pip
pip install tessellate

# Alternatively: compile from source
make install

Usecase 1 - timeseries data¶

tessellate  data/usecase-timeseries --input-format=builtin --output-format=json --output-dir=output-usecase-timeseries

This data is from an in vacuo ribose simulation stored in data/timeseries-from-VMD To recreate data use the run.sh script. This calls VMD and runs pucker-bigdcd.tcl.

Usecase 2 - RNA and DNA¶

tessellate  data/usecase-*DNA --input-format=pdblist --output-format=json --output-dir=output-usecase-rnadna

Usecase 3 - Alpha Cyclodextrin¶

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

Additional UseCases¶

Pandas Dataframes Supported with –output-format=pandas
Using Tessellate as a library

Viewing Data¶

Try out Montage to create reports for these datasets. For example:

Compare all outputs:

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

Features to include:¶

Improve testing and documentation. Port existing tests over.
Tables
include more RAD functionality

Uploading to PyPi¶

Use twine

Issues¶

Report Issues at https://github.com/scientificomputing/tessellate/issues Known issue - only relative paths supported

Read the Docs¶

Docs are here. RTD is authorised to access GitHub repos. The RTD service hook builds doc on push.

Pandas Dataframes¶

tessellate  data/usecase-timeseries --input-format=builtin --output-format=pandas --output-dir=output-usecase-timeseries

Using Tessellate as a library¶

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.