[Python for Organic/Medicinal Chemistry] How You Can Play with Molecular Structures of Drugs in Python I. Drawing & Converting File Format

In this post, I will show you how to convert drug names into molecular structure, save into Excel, read into Python, display the structure, and convert file format. The motivation was really to batch process a large number of organic molecules in a specific way to support drug discovery. In an effort to build high-throughput NMR (Nuclear Magnetic Resonance) capability, we are going to use either one of the two leading analytical data processing software programs from <a href="https://mestrelab.com/" rel="noopener ugc nofollow" target="_blank">MestReNova</a> or <a href="https://www.acdlabs.com/" rel="noopener ugc nofollow" target="_blank">ACD/Labs</a> for automated structure verification of small molecules using NMR & LC/MS data. This, of course, requires the input of molecular structure information, preferably in the <a href="https://en.wikipedia.org/wiki/Chemical_table_file" rel="noopener ugc nofollow" target="_blank">MDL Molfile (.mol)</a> format by vendors. Notably, there is another format for molecular structure information, namely <a href="https://en.wikipedia.org/wiki/Simplified_molecular-input_line-entry_system" rel="noopener ugc nofollow" target="_blank">Simplified Molecular-Input Line-Entry System (SMILES)</a>. Different from the MDL Molfile format which is two-dimensional, SMILES is a one-dimensional string. Thus it is much more convenient to store and communicate for a large number of molecules in the SMILES format. Let’s see <a href="https://en.wikipedia.org/wiki/Aspirin" rel="noopener ugc nofollow" target="_blank">Aspirin </a>as an example (you can easily understand why SMILES format is preferred for database storage, a single line!): <a href="https://ronghui-zhou.medium.com/python-or-organic-medicinal-chemistry-how-you-can-play-with-molecular-structure-in-python-i-fad10532fa06">Read More</a>