Cheminformatics

• Chemaxon: numerous tools for small molecules (standalone).
  

Chemical Formulas

• ChemFormula:
  
  
  

Coordinates

• chemcoord: # A python module for coordinates of molecules
  
  
  

Java

• CDK: toolkit for drug discovery, descriptors (standalone)
  
• OpenChemLib: Cheminformatics tool kit. Fully Automated Creation of Virtual Chemical Fragment Spaces Using the Open-Source Library OpenChemLib (standalone)
  
  

NMR

• nmrglue:
  
  
  

Other

• LillyMol: Eli Lilly set of cheminformatic tools (standalone)
  
  
• MayaChemTools: Cheminformatics tool kit. A growing collection of Perl and Python scripts, modules, and classes to support a variety of day-to-day computational discovery needs (standalone)
  

PDB

• PDBe CCDUtils: A small molecules chemistry toolkit using RDKit for the Protein Data Bank
  

Python

• CDPKit - CONFORT: High-Quality Conformer Generation (standalone).
  
  
  
• chemfunc:
  
  
• Chython: Library for processing molecules and reactions in python way.
  
  
• cinfony:
  
• ODDT: Open Drug Discovery Toolkit, toolkit for drug discovery (standalone)
  
  
  
• RDKit:
  
  
  
  
• rdkit-scripts: rdkit scripts making life easier (standalone)
  
  
• OpenBabel: toolkit for drug discovery, file format etc (standalone)
  
  

QM

• aqme: AQME, or Automated Quantum Mechanical Environments, facilitates transparent and reproducible quantum chemistry workflows, supporting tasks like conformer generation, QM input file creation, and descriptor generation.
  
  
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• psikit: Psikit is a Python library that serves as a wrapper for Psi4 and RDKit, designed for quick quantum chemical calculations and molecular manipulation.
  
  

Reaction Tools

• ChemPy:
  
  
  

Standalone

• DataWarrior: numerous tools (standalone).
  

Workflow Managers

• maize: a graph-based workflow manager for computational chemistry pipelines