Find Missing Structure

This program is designed specifically for Open Enventory to fix issue with molecules missing structures (could not be extracted through "Read data from supplier")

GitHub - khoivan88/oe_find_structure: for Open Enventory using python to automatically update sql queries in 'molecule' table with mol filesGitHub

DETAILS

This programs does:

1. Connect into mysql database and find molecule in 'molecule' table

   of specific database and find those molecule with missing structure (smiles)

2. folder "missing_mol_files" needs to be created inside /var/lib/mysql

   with 'mysql' as ownner (chown mysql:mysql)

3. Try to download mol files from various sources into a folder in

   /var/lib/mysql/missing_mol_files

4. Update those sql entries with new downloaded mol_files

REQUIREMENTS

• root access to the server hosting Open Enventory

• Python 3+

• This file is made for Linux environment, you should be able

  to used it on other OS with changing the location of the "download_path"

USAGE

After cloning this repo onto the Open Enventory server:

1. Change into directory of the new file:

   cd update_sql_mol

2. (Optional): create virtual environment for python to install dependency:

   # you can change "update_sql_mol_venv" to other name too
   python3 -m venv update_sql_mol_venv   # Create virtual environment
   source update_sql_mol_venv/bin/activate    # Activate the virtual environment

3. Install python dependencies:

   pip install -r requirements.txt

4. Run the program:

   python3 update_sql_mol_v6/update_sql_mol.py    # Replace "update_sql_mol_v6" with latest version

   • Answer questions for:

     • confirming running under root

     • mySQL root password (typing password will not be shown on screen)

     • the name of the database you want to update (twice to confirm)

     • url path for your Open Enventory server (including 'http/https' and no trailing '/')

VERSIONS

Version 4:

• Using simple download bar with bar=wget.bar_thermometer in wget.download

• Added handling database connection error (wrong password, wrong database)

• Added confirmation for database

Version 5

• Change to https (from http) for ChemicalBook site

Version 6 (2020-01-18):

• Remove this extra step of going into Open Enventory manual by the user using a web browser and doing Batch Processing.

  Why: for versions 5 and before:

  after running this program, YOU STILL NEED TO LOGIN INTO OPEN ENVENTORY ON A WEB BROWSER AS ROOT, GO TO "SETTINGS/BATCH PROCESSING". CHOOSE DATABASE THAT YOU WANT TO UPDATE AND THEN CHOOSE "MOLECULE", "EMPIRICAL FORMULA", "MW", "DEG. OF UNSAT." , "STRUCTURE", "SMILES" AND "FINGERPRINT" AND THEN SUBMIT TO UPDATE THE SQL QUERY. ONLY AFTER THIS, THE STRUCTURE WILL SHOW UP