OpenChemVault

This project is a framework which can be used to setup a data repository of computational chemistry format log files and deploy a (public) server providing REST API and web interface to browse and view the documents in the repository, search/filter using parsed attributes available, add new files to the database, download a document’s data and instantly parse a log file with cclib just by uploading the file in browser.

Setup

With Docker

Install docker and docker-compose on your machine

Clone this repository

git clone https://github.com/nitish6174/openchemvault

Setup the docker environment file
```
cp .env.example .env
```
- Set SETUP_DB as 1 to seed database with parsed files else set 0
- DATA_FOLDER_PATH is the local path to the directory of log files which will be parsed and inserted in dockerized image's database if SETUP_DB is 1
- Setting PRODUCTION to 0 runs flaskapp in debug mode

Build the Docker setup and run it

sudo docker-compose build
sudo docker-compose up

The flask application can now be accessed in browser at localhost:5000

Using python virtual environment

Note : Use Python 3. OpenBabel setup is not added in the below steps.

Below instructions are given for ubuntu

Install python pip and virtualenv

sudo apt-get install python3 python3-pip
pip3 install virtualenv

Install MongoDB and start MongoDB server

sudo apt-get install mongo
sudo service mongodb start

Clone repository and setup virtualenv for project

git clone https://github.com/nitish6174/openchemvault.git
cd openchemvault
virtualenv -p python3 venv_py3

Download cclib repository inside the openchemvault folder:
```
git clone https://github.com/cclib/cclib.git
```

Install pip dependencies and build cclib inside virtual environment

source venv_py3/bin/activate
pip3 install -r requirements.txt
cd cclib
python3 setup.py build
python3 setup.py install

Set configuration
```
cp config.py.example config.py
```
Change the variable values in config.py as suitable
Running :
- Go to openchemvault directory (root of repo) and make sure virtualenv is activated.
  (Run source venv_py3/bin/activate to enter virtual environment)
- Run python run.py <SETUP_DB> <PRODUCTION> <DATA_FOLDER_PATH> with suitable arguments:
- SETUP_DB : Set as 1 to seed database with files in specified folder (Default: 0 )
- PRODUCTION : Setting to 0 runs flaskapp in debug mode (Default: 1 )
- DATA_FOLDER_PATH : Path to the directory containing log files which will be parsed and inserted in host's MongoDB database (provided SETUP_DB is 1) (Default value taken from config.py)
Note : All the 3 arguments are optional
- Then, flask server will start on the machine at port 5000.
- The application can now be accessed in browser at localhost:5000
- Stop flask server with Ctrl-C and deactivate virtualenv using deactivate command

Project structure

This project is a framework having 3 modules :

Script which processes computational chemistry output files in specified folder and builds a MongoDB database (planned schema given below).
API for browsing & searching documents in data repository.
Web-interface based on above API allowing document browsing, searching, adding new files to data repository etc.

Available functionality

Details can be found in the TODO list

Here are the features available in web front-end as of now:

Any computational chemistry log file (of format supported by cclib) can be uploaded on the webpage to view the parsed data from it
A 3D rendering of the molecule if atom coordinates information is available
Browse menu listing the various molecular formulas for which documents are available in the deployed instance's data repository
Listing of documents corresponding to a molecular formula
Search page supporting filtering with various attributes of logfiles
Displaying details of a document selected from browsing menu or search results
Download data of a particular document
Page to upload and add a log file to the data repository

MongoDB schema

The current schema design has 3 collections:

parsed_file : Documents containing the parsed data from each of the logfile. Contains parsed attributes and molecular formula.
molecule : List of unique molecular formulas of the various parsed_files. Each document contains a list of ObjectIDs of the parsed_file documents corresponding to that molecular formula.
attr_stats : Contains a single document containing min and max value for some parsed attributes (used for setting range in searching/filtering).

nitish6174 / openchemvault