Python uses Open Babel to process molecular structure and chemical data

Python uses Open Babel to process molecular structure and chemical data Open Babel is an open source toolkit for chemical computing. It provides a series of functions and algorithms used to process molecular structure and chemical data.This article will introduce how to use Open Babel in Python to process molecular structure and chemical data. First, we need to install Open Babel in Python.You can install Open Babel by running the following commands: pip install openbabel After the installation is completed, we can import the Open Babel library: python import openbabel as ob Next, we can use Open Babel to read the molecular structure file.Open Babel can read a variety of different chemical file formats, including common SMILES, MOL, SDF, etc.Below is an example of reading the molecular structure of Smiles format: python obConversion = ob.OBConversion() obConversion.SetInAndOutFormats("smi", "mol") mol = ob.OBMol() obConversion.ReadString(mol, "CC(=O)O") In the above example, we use the Obconversion class to set the input and output molecular structure file format.Then, we created an OBMOL object and read the molecular structure from the SMILES string with the ReadString function. Next, we can handle some of the molecular structure.Open Babel provides many functions and algorithms to process molecular structures, such as calculating molecular weight, computing chemical bonds, and computing molecular topology.Here are some commonly used examples: python # Calculating molecular weight mol_weight = mol.GetMolWeight() # num_bonds = mol.NumBonds() # mol.AddHydrogens() mol.PerceiveBondOrders() # Output molecular information mol_name = mol.GetTitle() Print ("molecular name:", mol_name) Print ("molecular weight:", mol_weight) Print ("Number of chemical bonds:", num_bonds) The above example demonstrates how to calculate the amount of molecular weight, the number of chemical bonds, and how to add hydrogen atoms and the sequential chemical bond to the molecule.You can also use other Open Babel functions and algorithms according to your needs. Finally, we can write the molecular structure into the file with Open Babel.You can use the following code to write the molecular structure in the mol format: python obConversion.SetInAndOutFormats("mol", "mol") obConversion.WriteString(mol, "output.mol") The above code will create a file called output.mol, and write the molecular structure in MOL format. In this article, we introduced the basic methods of processing molecular structure and chemical data with Python and Open Babel.By using the functions and algorithms provided by Open Babel, we can read, processes and write into the molecular structure, and perform other operations related to chemical data.