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

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

• root access to the server hosting Open Enventory
• Python 3+
• conda (Optional)
  • conda is used to install rdkit and molvs to clean mol files (e.g. convert explicit hydrogens to implicit hydrogens, etc.)
  • If you don't already have conda, you can install it using the following link. If you are not sure what to install, I suggest you install miniconda3 and NOT anaconda3 for much smaller package footprint.
• This file is made for Linux environment, you should be able to used it on other OS by changing the location of the "download_path"

1. Clone this repository:

   git clone https://github.com/khoivan88/oe_find_structure.git    #if you have git
   # if you don't have git, you can download the zip file then unzip

2. Change into the directory of the program:

   cd oe_find_structure

Skip ahead to this if you have conda installed.

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

   # you can change "update_sql_mol_venv" to other name too
   python3 -m venv oe_find_structure_venv   # Create virtual environment
   source oe_find_structure_venv/bin/activate    # Activate the virtual environment on Linux
   # oe_find_structure_venv\Scripts\activate    # Activate the virtual environment on Windows

4. Install python dependencies:

   pip install -r requirements.txt   # Install all dependencies (without rdkit and molvs)

Instead of step 3 AND step 4 above, if you have conda installed, you can do this instead:

conda env create --prefix oe_find_structure_conda-env --file ./environment.yml    # Create virtual  environment with conda and install all dependancies
conda activate ./oe_find_structure_conda-env    # Activate the virtual environment

5. Run the program:

   python oe_find_structure/find_structure.py

   • Answer questions for:
     • 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 '/')

   You can enable debug mode (more error printing during structure search) by adding '-d' :

   python oe_find_structure/find_structure.py -d    # Enable debug mode