ChemBDDB Python Module Tutorial¶

The setup, insert, and delete modules of chembddb can also be called using python code, making it easier to use and simple.

Step 1: import the chembddb module and initialize variables for mysql credentials¶

import chembddb
host = '127.0.0.1'
username = 'root'
password = 'yourpassword'

Step 2: call the setup module¶

# uncomment the following line if you want to know more about the setup module
# print(help(chembddb.setup))

chembddb.setup(host=host, user=username, pw=password, db='abc')

Step 3.1: call the insert module and use the path to the configuration and data files¶

# uncomment the following line if you want to know more about the setup module
# print(help(chembddb.insert))

chembddb.insert(host=host, user=username, pw=password, db='abc',smi_col='smiles',mol_identifier='name',conf_file='../test-files/config_hsp.csv',data_file='../test-files/benzene.csv')

Step 3.2: call the insert module and use pandas dataframes for the configuration and data files¶

import pandas as pd
conf = pd.read_csv('../test-files/config_hsp.csv')
data = pd.read_csv('../test-files/benzene.csv')

# uncomment the following line if you want to know more about the setup module
# print(help(chembddb.insert))

chembddb.insert(host=host, user=username, pw=password, db='abc',smi_col='smiles',mol_identifier='name',conf_file=conf,data_file=data)

Step 4: call the delete module¶

# uncomment the following line if you want to know more about the setup module
# print(help(chembddb.delete))

chembddb.delete(host=host,user=username,pw=password,db='abc')