Marco Biasini

RFC: Jupyter/IPython Notebook Features

11

Hi All, I've pushed an initial version of an alternative Jupiter/IPython notebook module for PV to master. It's a little more powerful than the previous version and allows to load...

Add a DNA/RNA block representation mode as shown here: http://x3dna.org/articles/seeing-is-understanding-as-well-as-believing

When conectRecords : true is passed to io.pdb(), proper conectRecord semantics as outlined here should be used: http://wwpdb.org/documentation/format32/sect10.html

creating the vec3 instances has a non-zero cost during PDB parsing. Benchmarking has revealed that it would be faster to create an ArrayBuffer and create FloatArrayViews to the buffer afterwards.

The PDB parsing can already be started while the file is being downloaded which should make things faster.

The within selection code is rather slow an is unusable for large structures. Use a spatial partitioning to speed it up.