Macs in Chemistry

Insanely Great Science

Python and compchem

 

Python seems to becoming the lingua franca for scientific scripting/progamming and it is perhaps not surprising that we now see increasing support for computational chemistry.

Chemtools is a set of modules that is intended to help with more advanced computations using common electronic structure methods/ programs. Currently the is some limited support for Gamess-US and MolPro program packages but other codes can be easily interfaced. It requires:

  • Python works with Python 2.7.x and 3.x
  • numba
  • numpy
  • mendeleev
  • scipy
  • setuptools

Chemtools is NOT hosted on pypi yet but in can be installed by pip from the bibbucket repository with:

pip install https://bitbucket.org/lukaszmentel/chemtools/get/tip.tar.gz

Pygamess is a GAMESS wrapper for Python, it requires:

  • Python 2.6 or later (not support 3.x)
  • RDKit
  • GAMESS

It can be installed using pip

pip install pygamess

Usage

single point calculation with RDKit

from pygamess import Gamess
from rdkit import Chem
from rdkit.Chem import AllChem
m = Chem.MolFromSmiles("CC")
m = Chem.AddHs(m)
AllChem.EmbedMolecule(m)
0
AllChem.UFFOptimizeMolecule(m,maxIters=200)
0
g = Gamess()
nm = g.run(m)
nm.GetProp("total_energy")
'-78.302511990200003'

PyQuante: Python Quantum Chemistry, an open-source suite of programs for developing quantum chemistry methods, it currently supports

  • Hartree-Fock: Restricted closed-shell HF and unrestricted open-shell HF;
  • DFT: LDA (SVWN, Xalpha) and GGA (BLYP) functionals;
  • Optimized-effective potential DFT;
  • Two electron integrals computed using Huzinaga, Rys, or Head-Gordon/Pople techniques; C and Python interfaces to all of these programs;
  • MINDO/3 semiempirical energies and forces;
  • CI-Singles excited states;
  • DIIS convergence acceleration;
  • Second-order Moller-Plesset (MP2) perturbation theory.

cclib is an open source library, written in Python, for parsing and interpreting the results of computational chemistry packages. The goals of cclib are centered around the reuse of data obtained from these programs and contained in output files, specifically

  • ADF (versions 2007 and 2013)
  • DALTON (versions 2013 and 2015)
  • Firefly, formerly known as PC GAMESS (version 8.0)
  • GAMESS (US) (version 2012)
  • GAMESS-UK (version 7.0)
  • Gaussian (versions 03 and 09)
  • Jaguar (versions 7.0 and 8.3)
  • Molpro (versions 2006 and 2012)
  • NWChem (versions 6.0 and 6.5)
  • ORCA (versions 2.9 and 3.0)
  • Psi (versions 3.4 and 4.0)
  • Q-Chem (version 4.2)

FragBuilder a tool to create, setup and analyse QM calculations on peptides. DOI.

Update

And of course there is OpenBabel that can be used create input files for a variety of computational chemistry packages.

If I've missed anything please feel free to let me know.


blog comments powered by Disqus