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

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 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.