data_curation

Data Curation Process of B3DB

Working environment setting up

All the calculations were performed in a Python 3.7.9 virtual environment created with Conda in CentOS Linux release 7.9.2009. The Conda environment includes the following Python packages,

• ChEMBL_Structure_Pipeline==1.0.0, https://github.com/chembl/ChEMBL_Structure_Pipeline/
• RDKit==2020.09.1, https://www.rdkit.org/
• openeye-toolkit==2020.2.0, https://docs.eyesopen.com/toolkits/python/index.html/
• mordred==1.1.2, https://github.com/mordred-descriptor/mordred/ (required networkx==2.3.0)
• numpy==1.19.2, https://numpy.org/
• pandas==1.2.1, https://pandas.pydata.org/
• pubchempy==1.0.4, https://github.com/mcs07/PubChemPy/
• PyTDC==0.1.5, https://github.com/mims-harvard/TDC/
• SciPy==1.10.0, https://www.scipy.org/
• tabula-py==2.2.0, https://pypi.org/project/tabula-py/

To creat a virtual environment named bbb_data with Python 3.7.9 to this specification, first,

conda create bbb_py37 python=3.7.9

Given that RDKit, ChEMBL_Structure_Pipeline are not available in PyPI and we will install them with conda,

# activate a virtual environment
conda activate bbb_py37

conda install -c rdkit rdkit=2020.09.1.0
conda install -c conda-forge chembl_structure_pipeline=1.0.0
# https://docs.eyesopen.com/toolkits/python/quickstart-python/linuxosx.html
conda install -c openeye openeye-toolkits=2020.2.0

Then we can install the requirements in requirements.txt with

pip install -r requirements.txt

An easier way is to run the follow script with bash,

#!/bin/bash

# create virtual environment
conda create bbb_py37 python=3.7.9
# activate virtual environment
conda activate bbb_py37

# install required packages
conda install -c rdkit rdkit=2020.09.1.0
conda install -c conda-forge chembl_structure_pipeline=1.0.0
# https://docs.eyesopen.com/toolkits/python/quickstart-python/linuxosx.html
conda install -c openeye openeye-toolkits=2020.2.0

pip install -r requirements.txt

ALOGPS version 2.1 can be accessed at http://www.vcclab.org/lab/alogps/.