Reduce package size: installed size is 7.0Mb

[Barry Grant]

We should try to ensure that the package sources are not unnecessarily large. From the the following post

< http://r.789695.n4.nabble.com/CRAN-package-sizes-td3303606.html >

As a general rule, doc directories should not exceed 5Mb, and where data directories need to be 10Mb or more, consideration should be given to a separate package containing just the data. (Similarly for external data directories, large jar files and other libraries that need to be installed.)

Currently our data sub-directory is 5.6Mb - we should reduce this to 1Mb with trajectory compression and possibly moving some data online.

[Barry Grant]

Still aiming to reduce amount of example data.. * checking installed package size ... NOTE installed size is 7.0Mb sub-directories of 1Mb or more: data 5.6Mb

[Barry Grant]

Could reduce or replace example data file
"bio3d/data/kinesin.RData" 5.5M

However, its under 10Mb so this is not a pressing matter currently. Replacing would require painfully finding where it is used in all Rd files and vignettes...

[Barry Grant]

Suggest replacing all kinesin example data with a striped down example for transducin. This will consist of:

• a pdbs object (possibly with core fitted coordinates)
• an annotation object (that includes nucleotide classification and plot colors).
• Also include a small netcdf trajectory with cell information.

[Xinqiu Yao]

Transducin example data has been included, with following objects stored:

• pdbs, a pdbs object with original PDB coordinates (withouth core fitted)
• core, product of core.find(pdbs)
• pdbs.anno, product of pdb.annotate(pdbs$id)
• ligs, indicate nucleotide state of each structure in pdbs, and is constructed based on pdbs.anno

The file size is 248K, which substantially reduces package size if we replace all kinesin examples with transducin and remove kinesin.RData.

Trajectory file has not been included yet, in the case that we have the hiv simulation data which is probably enough for examples. Let's see what we really need during changing examples.

[Barry Grant]

Excellent!!!

[Xinqiu Yao]

File sizes substantially reduced!

du -h bio3d/data
# 556K