What’s new

Version 0.4

  • Added a full-fledged molecular viewer. But it will be gone in favor of the notebook based chemview.
  • Added cclib integration
  • New module with functions for the IPython notebook. Requires chemview.
  • Example module for quantum chemistry calculation. Please file an issue on GitHub if you want to maintain it.

Version 0.3

  • New bond handling with the Molecule.bonds and System.bonds attributes
  • Possibility to add charges
  • Post Processing Effects:
    • FXAA – Fast Approximate Antialiasing
    • Gamma Correction
    • Glow
    • Outline
    • SSAO – Screen Space Ambient Occlusion
  • Renderers:
    • Implemented toon shading for different shapes.
    • CylinderImpostorRenderer – a really fast way to draw cylinders
  • Offline Rendering at any resolution supported by the video card.

  • Started some work on user interaction for a full molecular viewer.


  • New Databases:
    • RCSB for protein structures
    • ToxNetDB for properties
    • ChemspiderDB

Version 0.2


  • Serialization through json with from_json and tojson for Atom, System and Molecule;
  • Removing atoms and molecules from System. System.remove_atoms, System.remove_molecules;
  • Experimental support for customized Atom/Molecule/System types.
  • Some indexing routines: System.atom_to_molecules_indices and System.mol_to_atom_indices;
  • Custom sorting of systems throught System.reorder_molecules;
  • Support for bonds in molecules and experimental support for bonds in Systems throught Molecule.bonds and System.get_bonds_array
  • System.merge_systems has a better overlap handling.
  • Removed boxsize attribute, now you have to always specify box_vectors.
  • Implemented random_lattice_box to do random solvent boxes.


  • New Renderers: - BallAndStickRenderer - BondRenderer - WireframeRenderer
  • Implemented Camera.autozoom for autoscaling
  • Reimplemented BondRenderer in cython.


  • New Handlers:
    • MDL molfile (.mol extension)
    • Chemical Markup Language (.cml extension)


  • New package to handle databases
  • CirDB to retrieve molecules from chemical identifier resolver
  • ChemlabDB to retrieve built-in data
  • LocalDB to make personal databases


  • Preliminary ipython notebook integration. It can display Molecule and System instances by using out-of-screen rendering.


  • Implemented some (periodic/non-periodic) distance finding routines.