Calculate NPR values & Generate Heatmap: Difference between revisions

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=== Run NPR calculation ===
=== Run NPR calculation ===
Your smiles file should be format like this
Your smiles file should be in this format with no header: <smiles> <cid>
 
'''<smiles> <cid>'''
  (npr-py3)$ python extra_newprops.py {smiles_file}
  (npr-py3)$ python extra_newprops.py {smiles_file}
Notes:
- Failed and success molecules are output from this script
- The calculation maybe slow. It is recommend that you chunk the file and run it on parallel.


== Make Heatmap ==
== Make Heatmap ==

Revision as of 06:53, 5 November 2020

Calculate NPR

Setup Python environment

- Download Anaconda3 installer and install follow the instruction (https://www.anaconda.com/products/individual) - Create anaconda env and install packages

(base)$ conda create -c rdkit --name npr-py3 rdkit
(base)$ conda activate npr-py3
# Install jupyter notebook 
(npr-py3)$ conda install -c conda-forge notebook
# Install vaex - dataframe library for huge libraries
(npr-py3)$ conda install -c conda-forge vaex 

Run NPR calculation

Your smiles file should be in this format with no header: <smiles> <cid>

(npr-py3)$ python extra_newprops.py {smiles_file}

Notes: - Failed and success molecules are output from this script - The calculation maybe slow. It is recommend that you chunk the file and run it on parallel.

Make Heatmap