Commandline script to optimize molecules at the MMFF94 with openbabel, and print to screen.

mmff94opt.py

#!/usr/bin/env python2
# MIT LICENSE, Anders S. Christensen (c) 2018

import sys
import pybel
import openbabel

NAME = {
    1:  'H'  ,
    2:  'He' ,
    3:  'Li' ,
    4:  'Be' ,
    5:  'B'  ,
    6:  'C'  ,
    7:  'N'  ,
    8:  'O'  ,
    9:  'F'  ,
   10:  'Ne' ,
   11:  'Na' ,
   12:  'Mg' ,
   13:  'Al' ,
   14:  'Si' ,
   15:  'P'  ,
   16:  'S'  ,
   17:  'Cl' ,
   18:  'Ar' ,
   19:  'K'  ,
   20:  'Ca' ,
   21:  'Sc' ,
   22:  'Ti' ,
   23:  'V'  ,
   24:  'Cr' ,
   25:  'Mn' ,
   26:  'Fe' ,
   27:  'Co' ,
   28:  'Ni' ,
   29:  'Cu' ,
   30:  'Zn' ,
   31:  'Ga' ,
   32:  'Ge' ,
   33:  'As' ,
   34:  'Se' ,
   35:  'Br' ,
   36:  'Kr' ,
   37:  'Rb' ,
   38:  'Sr' ,
   39:  'Y'  ,
   40:  'Zr' ,
   41:  'Nb' ,
   42:  'Mo' ,
   43:  'Tc' ,
   44:  'Ru' ,
   45:  'Rh' ,
   46:  'Pd' ,
   47:  'Ag' ,
   48:  'Cd' ,
   49:  'In' ,
   50:  'Sn' ,
   51:  'Sb' ,
   52:  'Te' ,
   53:  'I'  ,
   54:  'Xe' ,
   55:  'Cs' ,
   56:  'Ba' ,
   57:  'La' ,
   58:  'Ce' ,
   59:  'Pr' ,
   60:  'Nd' ,
   61:  'Pm' ,
   62:  'Sm' ,
   63:  'Eu' ,
   64:  'Gd' ,
   65:  'Tb' ,
   66:  'Dy' ,
   67:  'Ho' ,
   68:  'Er' ,
   69:  'Tm' ,
   70:  'Yb' ,
   71:  'Lu' ,
   72:  'Hf' ,
   73:  'Ta' ,
   74:  'W'  ,
   75:  'Re' ,
   76:  'Os' ,
   77:  'Ir' ,
   78:  'Pt' ,
   79:  'Au' ,
   80:  'Hg' ,
   81:  'Tl' ,
   82:  'Pb' ,
   83:  'Bi' ,
   84:  'Po' ,
   85:  'At' ,
   86:  'Rn' ,
   87:  'Fr' ,
   88:  'Ra' ,
   89:  'Ac' ,
   90:  'Th' ,
   91:  'Pa' ,
   92:  'U'  ,
   93:  'Np' ,
   94:  'Pu' ,
   95:  'Am' ,
   96:  'Cm' ,
   97:  'Bk' ,
   98:  'Cf' ,
   99:  'Es' ,
  100:  'Fm' ,
  101:  'Md' ,
  102:  'No' ,
  103:  'Lr' ,
  104:  'Rf' ,
  105:  'Db' ,
  106:  'Sg' ,
  107:  'Bh' ,
  108:  'Hs' ,
  109:  'Mt' ,
  110:  'Ds' ,
  111:  'Rg' ,
  112:  'Cn' ,
  114:  'Uuq',
  116:  'Uuh'}


if __name__ == "__main__":

    forcefield = openbabel.OBForceField.FindForceField("MMFF94")

    filename = sys.argv[1]
    extension = filename[-3:]

    mol = pybel.readfile(extension, filename).next()
    mol.localopt()

    obmol = mol.OBMol
    forcefield.Setup(obmol)

    print len(mol.atoms)
    print forcefield.Energy(), "kcal/mol"
    for atom in mol:
        print NAME[atom.atomicnum], " %14.10f %14.10f %14.10f " % atom.coords