MolecularAnalysis

MolecularAnalysis is a Python library with valuable tools designed to facilitate molecular analysis tasks in the field of chemistry and bioinformatics. This library provides a wide range of tools and functions for handling molecular data.

It consists of 2 main classes:

• mol.Mol: This class can upload molecules in different formats (rdkit mol, smile, pdb, etc.).
• moldb.MolDB: This class can upload databases of molecules in different formats (rdkit mol list, sdf, smi, etc.).

It also contains multiple modules:

• analysis.plot: To plot molecular databases using dimensional reduction approaches (UMAP, TSNE, ...)
• analysis.sts: To perform multiple statistical analyses such as ROC plots or confusion plots
• fragments.fragmentation: to fragmentize molecules
• utils.protstruct: This module allows the manipulation of proteins, such as extracting the protein and ligands from the PDB complex, to superimpose the structures to a fixed target, prepare the proteins using Protein Preparation Wizard, etc.
• utils.interactions: This module allows the calculation of interaction fingerprints and subsequent analysis given a target pdb and a sdf of docked molecules. It has a single class, InteractionFingerprints, which can retrieve a DataFrame of interactions as well as a barcode to visualize and a cluster map to cluster it.

Note: Some functions in utils.pdb need a Schrödinger licence.