PyDespike is a program to graphically process (ie. despike) Raman and other spectroscopic data. It reduces the tedium involved in removing spikes in data due to artificial background fluctuations.

PyMOL is a molecular graphics system with an embedded Python interpreter designed for real-time visualization and rapid generation of high-quality molecular graphics images and animations. It can also perform many other valuable tasks (such as editing PDB files) to assist you in your research.

PyQuante is an open source suite of programs for developing quantum chemistry methods, written in the Python programming language, but with many rate-determining modules written in C for speed. The resulting code is easy to understand and modify, providing a well-engineered set of tools so that scientists can construct their own quantum chemistry programs without going through the tedium of having to write every low-level routine.

PyVib2 is a program for analyzing vibrational motion and vibrational spectra, written in pure Python. PyVib2 permits the automatic correlation of vibrational motions of molecules thereby allowing an understanding of Raman, Raman optical activity (ROA), infrared vibrational absorption (IR), and vibrational circular dichroism (VCD) spectra. Features include a Versatile representation of vibrational motions, visualization of Raman/ROA and IR/VCD generation in molecules and the production of publication quality spectra. It currently supports DALTON and Gaussian output files.

Q-Chem is a modern ab initio quantum chemistry software package capable of analyzing large structures in practical amounts of time without compromising accuracy.

QikProp provides rapid predictions for physically-significant descriptors and pharmaceutically-relevant properties of neutral organic molecules. Accurate predictions are made for free energies of solvation in hexadecane, octanol, and water, octanol/water partition coefficient (log P), aqueous solubility (log S), and Caco-2 cell permeabilty. Results for libraries of compounds are output in a format ready for facile incorporation into spreadsheet and QSAR programs.

QMForge is a program to analyze the results of quantum chemistry (DFT) calculations: Gaussian 98/03, ADF, GAMESS (US), GAMESS (UK), and PC-GAMESS files are supported. The following analyses are available for user-defined molecular fragments: Mulliken, C-squared and Overlap Population analyses, Fragment and Charge Decomposition Analyses.

qmol is a simple molecular weight calculator, available for Linux and Windows. You can enter a formula, (e.g. CH3(CH2)2OH) and get its molecular weight (60.0959 g/mol) and its elemental composition (C3H8O: C 59.96; H 13.42; O 26.62 %).

QSite is a mixed mode QM/MM program for energy calculations of protein-ligand interactions in the active site.

QTree is a program for generating CPK, Ball and Stick and worms pictures of molecules using the quad-tree algorithm. This is a relatively fast method of generating near-photographic quality images though it does not generate shadows. A sense of depth is provided by darkening atoms farther away from the viewer.