mantelijo / bmol2d Goto Github PK

Currently, secondary structures cannot be generated completely in browser because in order to calculate secondary structure coordinates, a dot-braket string for given structure is needed. This dot-braket string is then provided to WASM naview algorithm wrapper which generates the coordinates of secondary structure.

In order to generate dot-braket string wasm/secondary_structure.py python script must be running locally. For this, forgi v1.0 library along with MC-Annotate executable are used. MC-Annotate must be present on user's system as it is called by forgi library.

Or dot-braket can be provided by the user.

It would be ideal if the application could generate the dot-braket string automatically entirely in the browser. For this, solutions to two issues are needed:

1. Porting MC-Annotate to WASM via Emscripten. This should be relatively straight forward.
2. Rewriting parts of forgi library that are used to generate the dot-braket string from python to JS/WASM. This might be a more involved step, since forgi uses few external packages such as Biopython for PDB file parsing.