smolscripts's Introduction

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).

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smolscripts's Issues

Some assembly tags not present in a loop section

Hey Dimitri,

In the assembly saveframe of the output JSON data, the following three tags are at the saveframe level, but seem like they should be in a loop. Here is an excerpt from the assembly section of lovastatin.json:

{
      "sf_category": "assembly",
      "name": "assembly_1",
      ...
      "conformational_isomer": "no",
      "chemical_exchange_state": "no",
      "physical_state": "native",
}

but the three tags I've shown here are actually part of the assembly loop _Entity_assembly, so it seems it should be:

{
      "sf_category": "assembly",
      "name": "assembly_1",
      ...
      "entity_assembly": 
      [{
      "conformational_isomer": "no",
      "chemical_exchange_state": "no",
      "physical_state": "native",
      }]
}

Is this an easy fix or am I misinterpreting the JSON file? Thanks!

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bmrb-io / smolscripts Goto Github PK

smolscripts's Introduction

smolscripts

require:

files

smolscripts's People

Contributors

Stargazers

Watchers

smolscripts's Issues

Some assembly tags not present in a loop section

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