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:

1. 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 all the examples are outdated or work-in-progress currently.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 an issue describing what you're interested in doing and I'll help with getting started.

• for example, see the "Preparation" section in projects/trypsin1.py; then from the folder containing 1MCT-trimI.pdb, at a Python prompt, run execfile(' /projects/trypsin1.py')
• add import pdb; pdb.set_trace() to step line by line
• see "Examples" in test/vis_test.py for standalone visualization examples or

2. Cut and paste what you need: code is kept as self-contained as possible

• opt/dlc.py: delocalized internal coordinates (DLC) and hybrid DLC; useful for geometry opt. w/ constraints
• opt/lbfgs.py: gradient-only BFGS and L-BFGS optimizers (i.e., no line search)
• opt/neb.py: nudged elastic band (reaction path optimization)
• opt/dimer.py: Dimer and Lanczos methods (transition state search)
• qmmm/resp.py: RESP/CHELPG charge fitting (only harmonic restraints currently)
• mm.py: slow but simple MM energy and gradient for AMBER-type force field (and Hessian for Coulomb and LJ)
• fep.py: simple FEP, BAR free energy calculations
• model/build.py: build polypeptides, add hydrogens and bonds, mutate residues

Requirements:

• Python 3 w/ scipy and numpy (should mostly still work with Python 2.7)
• OpenMM - molecular mechanics calculations
• PySCF - quantum chemistry calculations

See misc/chem-inst.sh for setup on Debian/Ubuntu

Optionally:

• openmmtools - free energy calculations
• TINKER - molecular mechanics calculations
• GAMESS (US) or NWChem - quantum chemistry calculations
• https://github.com/cclib/cclib - for reading GAMESS and NWChem output

Credit to chemlab (3D camera, some shaders) and speck (some shaders), among others.

License: Any published results obtained using this software should be accompanied by all code needed to replicate.

Screenshot: 1MCT.pdb shown with backbone ribbon, MM atoms as lines, QM atoms as sticks, and components of QM/MM force on each atom as yellow, cyan, magenta cylinders.