Generating and depicting structures using the Open Babel API

aminoacids.py

def getAminoAcids(include_protonated=False):
  molecules = dict()
  molecules['GLY'] = 'NCC(=O)O'
  molecules['ALA'] = 'NC(C)C(=O)O'
  molecules['SER'] = 'NC(CO)C(=O)O'
  molecules['THR'] = 'NC(C(C)O)C(=O)O'
  molecules['CYS'] = 'NC(CS)C(=O)O'
  molecules['VAL'] = 'NC(C(C)C)C(=O)O'
  molecules['LEU'] = 'NC(CC(C)C)C(=O)O'
  molecules['ILE'] = 'NC(C(C)CC)C(=O)O'
  molecules['MET'] = 'NC(CCSC)C(=O)O'
  molecules['PRO'] = 'N1C(C(=O)O)CCC1'
  molecules['PHE'] = 'NC(Cc1ccccc1)C(=O)O'
  molecules['TYR'] = 'NC(Cc1cc(O)ccc1)C(=O)O'
  molecules['TRP'] = 'NC(Cc1c2ccccc2nc1)C(=O)O'
  molecules['ASP'] = 'NC(CC(=O)O)C(=O)O'
  molecules['GLU'] = 'NC(CCC(=O)O)C(=O)O'
  molecules['ASN'] = 'NC(CC(=O)N)C(=O)O'
  molecules['GLN'] = 'NC(CCC(=O)N)C(=O)O'
  molecules['HIS'] = 'NC(C(=O)O)Cc1cncn1'
  molecules['LYS'] = 'NC(CCCCN)C(=O)O'
  molecules['ARG'] = 'NC(CCCNC(=N)N)C(=O)O'

  if include_protonated is True:
    # add protonated versions of bases
    molecules['HISp'] = 'NC(C(=O)O)Cc1c[nH+]cn1'
    molecules['LYSp'] = 'NC(CCCC[NH3+])C(=O)O'
    molecules['ARGp'] = 'NC(CCCNC(=[H2+])N)C(=O)O'

    # add deprotonated versions of acids
    molecules['ASPd'] = 'NC(CC(=O)[O-])C(=O)O'
    molecules['GLUd'] = 'NC(CCC(=O)[O-])C(=O)O'

  return molecules

charge_molecule.py

#!/usr/bin/env python
"""
molecule_charge.py - Determine the charge of a molecule
"""
import sys

if( len(sys.argv) != 2 ):
  print "Usage: molecule_charge <in.pdb>"
  sys.exit()
file_in = sys.argv[1]

import openbabel
obConversion = openbabel.OBConversion()
obConversion.SetInFormat("pdb")

mol = openbabel.OBMol()
obConversion.ReadFile(mol, file_in)

# get the charges of the atoms
charge_model = openbabel.OBChargeModel.FindType("MMFF94")
charge_model.ComputeCharges(mol)
partial_charges = charge_model.GetPartialCharges()

print "%i" % int(sum(partial_charges))

generate_molecules.py

import openbabel

from obutil import OBStructureFromSmiles
from aminoacids import getAminoAcids

if __name__ == '__main__':

  # for now just default to amino acids from the amino acids library
  AA = getAminoAcids()
  for k in AA:
    OBStructureFromSmiles(AA[k], k)

obutil.py

def OBMolMinimize(mol):
  """Minimize a molecule
  """
  ff = openbabel.OBForceField.FindForceField("MMFF94")
  ff.Setup(mol)
  ff.ConjugateGradients(100, 1.0e-5)
  ff.GetCoordinates(mol)
  return mol

def OBStructureFromSmiles(smilesstring, filename=None):
  mol = openbabel.OBMol()
  obConversion = openbabel.OBConversion()
  obConversion.SetInAndOutFormats("smi", "pdb")
  obConversion.ReadString(mol, smilesstring)
  mol.AddHydrogens() #False, True, 7.4)
  builder = openbabel.OBBuilder()
  builder.Build(mol)
  mol = OBMolMinimize(mol)
  if filename is None: return mol
  # save structures in subfolder molecules
  obConversion.WriteFile(mol, "molecules/%s.pdb" % filename)