Rosetta, the macromolecular software modeling suite (which I contribute to as a developer), is great at modeling proteins, but not always so great at dealing with non-protein chemistry, including small molecules.
I've worked on several projects that used Rosetta with the intent of designing a protein to bind a novel small molecule. At the beginning of the workflow, I usually download a two-dimensional representation of the small molecule that, when visualized, looks something like this:
Rosetta needs to be given a parameter file specifying the chemistry of a small molecule in order to score it. Recent design algorithms such as coupled moves [@@ollikainen_coupling_2015] also require input of "conformers", a set of low-energy, three-dimensional states that the molecule is likely to access. Appropriate conformer input, when visualized, looks like this:
Note that since acetyl-CoA is a large (small) molecule, the conformers I generated only access rotamer degrees of freedom at one end of the acetyl-CoA molecule. If I did not limit degrees of freedom in this way, the number of conformers to generate and then sample in Rosetta would be intractable. Additionally, if I were going to design a catalytic interaction between acetyl-CoA and a protein of interest, only the portion of the small molecule that is near the active site would need to be modeled as flexible in a coupled moves design simulation.
As my lab does not currently license any of the commercially available software (which can be quite expensive) commonly used to generate small molecule conformers, I needed to find free for academic use(and preferably open source) software to do the job. Fortunately, several good options exist, such as the Confab [@@oboyle_confab_2011] algorithm within the Open Babel [@@oboyle_open_2011] chemical toolbox. Even better, the performance of Confab has been compared with other open-source and paid software [@@ebejer_freely_2012], and it compares favorably, especially when used on flexible molecules (those with 10 or more rotatable bonds).
I then ran into a snag: I couldn't find an off-the-shelf way with Confab's command line interface to generate conformers/rotamers for only a subset of rotatable bonds in a small molecule. Fortunately, Open Babel has powerful bindings for scripting available, including in Python. I wrote a script that takes in a small molecule as input and an optional argument of atoms allowed to move in conformer generation. Rotatable bonds will only be sampled by Confab if they involve these specified "unfrozen" atoms.
You can view the script embedded below, at the gist page at Github with formatting and the ability to comment, or as a raw file ready to download. I hope it's useful! Improvements are welcome as well; I've licensed the script under the MIT license.
| # Copyright (c) 2016 Kyle Barlow | |
| # Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions: | |
| # The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software. | |
| # THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE. | |
| import sys | |
| import os | |
| import pybel # Not using this import, but available in case you want to use the alternate pybel interface into open babel | |
| import openbabel as ob | |
| """ | |
| A Python script that calls the Confab rotamer generator (within OpenBabel). | |
| The script allows for rotamers to be generated only for certain parts of the molecule | |
| if the user specifies atoms that should be "unfrozen" (allowed to move) during conformer generation. | |
| Script by: Kyle Barlow | |
| Confab software: | |
| O'Boyle NM, Vandermeersch T, Flynn CJ, Maguire AR, Hutchison GR. Confab - Systematic generation of diverse low-energy conformers. Journal of Cheminformatics. 2011;3:8. doi:10.1186/1758-2946-3-8. | |
| Open Babel: http://openbabel.org/ | |
| """ | |
| def read_molecules(filepath, single = False): | |
| in_format = filepath.strip().split( '.' )[-1] | |
| obconversion = ob.OBConversion() | |
| obconversion.SetInFormat( in_format ) | |
| obmol = ob.OBMol() | |
| molecules = [] | |
| notatend = obconversion.ReadFile( obmol, filepath ) | |
| while notatend: | |
| molecules.append( obmol ) | |
| obmol = ob.OBMol() | |
| notatend = obconversion.Read( obmol ) | |
| if single: | |
| assert( len(molecules) == 1 ) | |
| return molecules[0] | |
| else: | |
| return molecules | |
| def count_aromatic_bonds( mol ): | |
| aromatic_bond_count = 0 | |
| total_bond_count = 0 | |
| for bond in ob.OBMolBondIter( mol ): | |
| total_bond_count += 1 | |
| if bond.IsAromatic(): | |
| aromatic_bond_count += 1 | |
| print '%d bonds are aromatic (out of %d total)' % ( aromatic_bond_count, total_bond_count ) | |
| def generate_limited_rotamer_set( | |
| input_path, output_path, atoms_to_unfreeze, | |
| output_format = 'mol2', | |
| include_input_conformation_in_output = True, | |
| # Note: the Confab settings below (rmsd_cutoff, conf_cutoff, energy_cutoff, verbose) | |
| # are currently set to the default values from Confab. | |
| # You you might need to change these for your project. | |
| rmsd_cutoff = 0.5, | |
| conf_cutoff = 4000000, | |
| energy_cutoff = 50.0, | |
| confab_verbose = True | |
| ): | |
| assert( output_path.endswith(output_format) ) | |
| assert( os.path.isfile(input_path) ) | |
| mol = read_molecules( input_path, single = True ) | |
| pff = ob.OBForceField_FindType( "mmff94" ) | |
| assert( pff.Setup(mol) ) # Make sure setup works OK | |
| count_aromatic_bonds( mol ) | |
| print "Molecule " + mol.GetTitle() | |
| print "Number of rotatable bonds = " + str( mol.NumRotors() ) | |
| if len(atoms_to_unfreeze) > 0: | |
| print '%d atoms will be allowed to move; freezing others' % len( atoms_to_unfreeze ) | |
| constraints = ob.OBFFConstraints() | |
| for atom in ob.OBMolAtomIter(mol): | |
| atom_id = atom.GetIndex() + 1 | |
| if atom_id not in atoms_to_unfreeze: | |
| constraints.AddAtomConstraint(atom_id) | |
| pff.SetConstraints( constraints ) | |
| # Run Confab conformer generation | |
| pff.DiverseConfGen(rmsd_cutoff, conf_cutoff, energy_cutoff, confab_verbose) | |
| pff.GetConformers(mol); | |
| if include_input_conformation_in_output: | |
| confs_to_write = mol.NumConformers() | |
| else: | |
| confs_to_write = mol.NumConformers() - 1 | |
| print "Generated %d conformers total (%d will be written)" % (mol.NumConformers(), confs_to_write) | |
| obconversion = ob.OBConversion() | |
| obconversion.SetOutFormat(output_format) | |
| output_strings = [] | |
| for conf_num in xrange(confs_to_write): | |
| mol.SetConformer(conf_num); | |
| output_strings.append( obconversion.WriteString(mol) ) | |
| print 'Writing %d conformations to %s' % (len(output_strings), output_path) | |
| with open(output_path, 'w') as f: | |
| for output_string in output_strings: | |
| f.write(output_string) | |
| if __name__ == '__main__': | |
| # You can display atom numbers (IDs) in pymol with: | |
| # label all, " %s" % ID | |
| # This allows you to manually choose which atoms to "unfreeze" | |
| # Rotamers will only be generated if they involve only unfrozen atoms | |
| assert( len(sys.argv) >= 3 ) | |
| input_path = sys.argv[1] | |
| assert( os.path.isfile(input_path) ) | |
| output_path = sys.argv[2] | |
| output_format = output_path.strip().split('.')[-1] | |
| if len( sys.argv ) > 3: | |
| atoms_to_unfreeze = [int(x) for x in sys.argv[3:]] | |
| else: | |
| atoms_to_unfreeze = [] | |
| generate_limited_rotamer_set( input_path, output_path, atoms_to_unfreeze, output_format = output_format ) |