smolscripts

Internal: processing scripts for creating metabolomics/small molecule BMRB entries from NMR facility data.

Some of this code is of more general use:

• create BMRB entry from (carefully crafted) JSON,
• create NMR-STAR molecule sections from SDF/MOL,
• create molecule images from SFD/MOL. incl. WSGI web insterface for that.

require:

• pymol
• rdkit
• obabel

files

Dockerfile builds a container for use @ NMRFAM

• conda install of uwsgi, python 3.6, werkzeug (flask), rdkit, and openbabel
• runs wsgi.py in uwsgi on port 9090
• WSGI interface creates molecule images and atom list from MOL/SDF, docker exec the shell to get to everything else.

assign_bmseid.py and bmrbids[.*].sql|sqlt3 - table (sqlite3) of BMSE IDs and associated InChI strings, and a script to look up/append new one

__main__.py and bmrbmb.properties - command line wrapper for creating an NMR-STAR file from files prepared at NMRFAM and its config file

release.py and release.conf - makes "release" version of the BMRB entry file. Requires BMRB validator package with all its dependencies (single .egg).