Parsing and filtering 2d molecules' data
Python 3
Most of these are okay to install with pip. Install the necessary libraries for this project using this command
pip install -r requirements.txt
- Get the code.
$ git clonethe repo and install the Python dependencies - Load the data. I don't distribute the data in the Git repo, to get data from Pubchem database by FTP site run the command
from chem_dataset.data.ftp_download import load_data
load_data()- Parse/StandarDize the data. In this step (longest by duration) you can choose by which method are going to parse your data (close all your threads for maximum efficiency)
Alternative 1 : by using multiprocessing lib
from chem_dataset.data.parser_multi_pool import parse
parse()Alternative 2 : by using Ray framework
from chem_dataset.data.parser_ray_pubchem import parse_ray
parse_ray()- Remove the duplicates. Presence of duplicates can overestimate your results, so to remove them you should run the command
from chem_dataset.data.dup import delete_dup
delete_dup()You get the standardized and cleaned dataset
- Collecting statistics. Data collection by gathering and measuring information on targeted variables
from chem_dataset.features.build_features import stat
stat()- Visualize the statistics. This will visualize the statistics of dataset. By running following command you have to choose which statistic you have to visualize (by writing in a console). Then user have a choice to [show] the plot, set the boundaries (by command [edit]), [save] the resulting plot or terminate the program execution [exit]
from chem_dataset.visualization.visualize import vis
vis()Lastly, note that this is currently research code, so a lot of the documentation is inside individual Python files. If you wish to work with this code, you'll have to get familiar with it and be comfortable reading Python code.
The software is licensed under the MIT license (see LICENSE file), and is free and provided as-is.