Python - the scripting language of chemistry
Python is a cross-platform scripting language which is easy to learn, and encourages readability and elegant code. If you're a chemist, it's also the most widely-used scripting language out there:CheminformaticsOpenBabel (Pybel), RDKit, OEChem, Daylight (PyDaylight), Cambios Molecular Toolkit, Frowns, PyBabel and MolKit (both part of MGLTools)Computational chemistryOpenBabel, cclib, QMForge, Gauss
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Have your hamburger and eat it - Edit molecules in PDFs
Of OChRe, OSRA and OASA (but not OSCAR)
Faster block Tanimoto calculations
Five Open Tools for 2D Structure Layout (aka Structure Diagram Generation) | Depth-First
MadMol - Chemistry-aware code
http://www.cambioscomputing.com/users/chempython/
BMC Chemistry
Bosco K Ho's Emporium - match.py - calculating the RMSD of PDB structures
http://cheminfo.informatics.indiana.edu/~rguha/code/python/splitsdf.py
