RDKit usage memo

Preparation

The environment and things that should be installed

environment

Installation

Create a virtual environment for RDKit with conda

$ conda create -c rdkit -n (Virtual environment name) rdkit

If you try using import rdkit as it is, it is said that there is no library of ○○, so download it ( libxrender1 in my case)

$ sudo apt install libxrender1

Others Install matplotlib and scikit-learn with $ conda install XXXX (And tabulate for article creation)

Try out

Display of molecules

from rdkit import Chem
from rdkit.Chem import Draw

#Changed the molecule written in SMILES notation to a format called mol file
molecule_1 = Chem.MolFromSmiles('Cc1ccccc1')

#Convert mol format file to image(display)
Draw.MolToImage(molecule_1)

[Output result] 001_DrawTest.png

Creating a fingerprint

Obtain data on SMILES and solubility of compounds by referring to the following articles. Introduction to Chemical Informatics with RDKit and Scikit-learn

smile XXXX logS
0 O=C(C)N 60-35-5 1.58
1 NNC 60-34-4 1.34
2 O=C(C)O 64-19-7 1.22
3 N1CCCC1 123-75-1 1.15
4 O=C(N)NO 127-07-1 1.12

Converts what is saved in SMILE format to MOL format. Then get a fingerprint. --radius: Radius. How many atoms ahead should be considered from the atom of interest?

smiles = df['smile']
molecules = [Chem.MolFromSmiles(smile) for smile in smiles]

#Create only one fingerprint as a trial
from rdkit.Chem import AllChem
molecule_1 = molecules[0]

fingerprint = AllChem.GetMorganFingerprintAsBitVect(mol=molecule_1, radius=2, nBits=2048)
# -> rdkit.DataStructs.cDataStructs.Data of class called ExplicitBitVect is created

fingerprint.ToBitString()
# ->Changed to something like 000000000000000100000000000000100
# ->After that, you can use this and plunge into the machine learning model as you like.


Recommended Posts

RDKit usage memo
deap usage memo (OneMax)
virtualenv Basic command usage memo
Easy usage memo of Anaconda (conda)
gzip memo
Raspberry-pi memo
Pandas memo
HackerRank memo
Python memo
python memo
graphene memo
Flask memo
pyenv memo
Matplotlib memo
pytest memo
sed memo
Python memo
Install Memo
BeautifulSoup4 memo
networkx memo
python memo
command memo
Generator memo.
psycopg2 memo
Python memo
SSH memo
Command memo
Memo: rtl8812
pandas memo
Shell memo
Python memo
BESS Development Memo # 01: BESS Installation and Basic Usage
Pycharm memo
Python memo