Open Babel class library in Python: use guidelines and examples

The Open Babel class library in Python is an open source tool for chemical information and computing chemistry. It provides many functions for molecular chemistry and material science.This article will provide readers with the usage guidelines and examples of the Open Babel class library, and explain the complete programming code and related configuration when necessary. 1. Install the Open Babel class library To start using the Open Babel class library, you need to install it first.In Python, you can install the Open Babel library by using the PIP command.Run the following command in the command line to install: pip install openbabel 2. Introduce the Open Babel class library After the installation is complete, we need to import the OpenBabel module in the Python code.Use the following code to import the Open Babel module into the Python script: python import openbabel as ob 3. Read the molecular structure Open Babel can read many different molecular file formats, such as Smiles, PDB, XYZ, etc.The following example shows how to read the molecular structure from a Smiles string: python obConversion = ob.OBConversion() obConversion.SetInAndOutFormats("smi", "mol") mol = ob.OBMol() obConversion.ReadString(mol, "CCO") In the above example, we first created an Obconversion object to convert the input SMILES string to the intermediate format (mol format) of Open Babel.We then created an OBMOL object to store the molecular structure.Using the `ReadString` method, we read the SMILES string" CCO "into the MOL object. Fourth, molecular conversion and output Open Babel can perform many molecular conversion operations, such as calculating molecular descriptions, modifying molecular structures by adding or deleting atoms.The following example demonstrates how to calculate the descriptor of a molecule and output the result to the console: python descriptor = ob.OBDescriptor.FindType("logP") value = descriptor.Calculate(mol) print("logP value:", value) In the above example, we first use the `FindType` method of the` Obdescriptor` class to find the logp descriptor.We then call the `Calculating" method of the descriptor to calculate the logp value of the MOL object.Finally, we will output the calculation results to the console. Five, chemical reactions Open Babel also provides a chemical reaction function.The following example shows how to use the Open Babel class library for chemical reactions: python rxn = ob.OBReaction() rxn.SetComment("Reaction example") reactant1 = ob.OBMol() obConversion.ReadString(reactant1, "CCO") reactant2 = ob.OBMol() obConversion.ReadString(reactant2, "CC(=O)O") product = ob.OBMol() rxn.AddReactant(reactant1) rxn.AddReactant(reactant2) rxn.AddProduct(product) obConversion.WriteFile(rxn, "output.reaction") In the above example, we first created an Obreaction object to represent the chemical reaction.Then, we created two OBMOL objects to represent the reactant1 and reactant2, and read their structure from the Smiles string with the `ReadString` method.Then, we created an OBMOL object to represent the product.By calling the `adDReactant` method, we add the reaction to the reaction object.Finally, we use the `writeFile` method to write the reaction object into the file. The above is the guidelines and examples of the use of the Open Babel class library in Python.Through these examples, readers can understand how to install the Open Babel class library and use some of its basic functions, such as reading molecular structure, calculating molecular descriptors, and processing chemical reactions.According to specific needs, readers can learn and practice more in depth according to the Open Babel's documentation and example code.