chem: collection of mostly python code for molecular visualization, QM/MM, FEP, etc
chem: collection of mostly python code for molecular visualization, QM/MM, FEP, etc. Very long-term goal is something like enzyme design. Intended for interactive use from standard python prompt.
Major features:
- 3D visualization of molecular geometry, orbitals, ESP, etc.
- fast OpenGL volume and isosurface rendering
- oriented toward analysis and debugging of calculations rather than presentation
- QM/MM driver supporting electrostatic embedding with various charge shifting schemes
- DLC/HDLC/Redundant internal coordinates
- transition state search (Dimer method, Lanczos method), reaction path optimization (NEB)
- read/write .pdb, TINKER, GAMESS and NWChem files
- model creation and setup: build polypeptides, add hydrogens and bonds, mutate residues, solvate
How to use this code:
- If an example in projects/ or test/ looks promising, try using that as a starting point … all the examples are outdated or work-in-progress currently. Open