Aligning Structures and Redundant Conformer Elimination

  • import cctk is assumed.

Calculating RMSD

  • We can calculate the root-mean-square deviation between two conformers.

  • Calculating the RMSD between two non-conformers is not supported (yet).

  • No alignment is performed; the two geometries are compared as-is.

# load molecule
path = "test/static/gaussian_file.out"
gaussian_file = cctk.GaussianFile.read_file(path)
ensemble = gaussian_file.ensemble
m1 = ensemble.molecules[0]
m2 = ensemble.molecules[-1]

# measure RMSD in Angstroms
RMSD = cctk.helper_functions.compute_RMSD(m1,m2)
RMSD == 0.0006419131435567976

Aligning Two Molecules

  • We can align all the conformers in an ensemble onto one of it members.

  • All conformers are translated to the origin. Then, a different rotation is applied to each conformer until the RMSD between the conformer and the template conformer is minimized.

  • A new ConformationalEnsemble is created and the original Molecule objects are not modified.

  • The Kabsch algorithm is used.

  • Alignment of non-conformers is not supported (yet).

# create a ConformationalEnsemble
path = "test/static/phenylpropane*.out"
conformational_ensemble = cctk.ConformationalEnsemble()
for filename in sorted(glob.glob(path)):
    gaussian_file = cctk.GaussianFile.read_file(filename)
    ensemble = gaussian_file.ensemble
    molecule = ensemble.molecules[-1]
    properties_dict = ensemble.get_properties_dict(molecule)

# define which atoms will be used for alignment
# alternatively, set comparison_atoms to "heavy" or "all"
comparison_atoms = [1,2,3,4,5,6]

# perform the alignment
# to_geometry is the template geometry (0-indexed)
# set compute_RMSD to True to calculate the RMSD before and after the aligment
aligned_ensemble, before_RMSD, after_RMSD = conformational_ensemble.align(to_geometry=np.int64(0), comparison_atoms=comparison_atoms, compute_RMSD=True)

# write out the result to a Gaussian input file
# open in GaussView and select "Single new molecule group for all files" in the "Open Files" dialog box under "Target"
# select geometries of interest of "select all" to compare the aligned molecules
cctk.GaussianFile.write_ensemble_to_file("test/static/phenylpropane_aligned.gjf", aligned_ensemble, "#p")

# alternatively, write all structures to a .mol2 file and open in Maestro or a similar program
# it be necessary to run molecule.assign_connectivity() on each member of the Ensemble first
# if the bond connectivity information is not available
cctk.MOL2File.write_ensemble_to_file("test/static/phenylpropane_aligned.mol2", aligned_ensemble)

Redundant Conformer Elimination

  • Useful for removing redundant conformers after conformational searches.

  • Every geometry is aligned and then a new ConformationalEnsemble is created that only contains unique conformations.

  • Whenever redundancies are found, the lowest energy conformer is kept.

  • The current ConformationalEnsemble is not modified.

# need a ConformationalEnsemble
assert isinstance(conformational_ensemble, ConformationalEnsemble)

# eliminate redundant conformers
# RMSD_cutoff is in Angstroms
# comparison_atoms is a list of atom numbers, "heavy" (default), or "all"
unique_conformers = conformational_ensemble.eliminate_redundant(RMSD_cutoff=0.5, comparison_atoms="heavy")

# how many conformers are left

# write out the entire ensemble
# alternatively, index the ensemble to retrieve a subset of the structures first
cctk.GaussianFile.write_ensemble_to_file("test/static/phenylpropane_aligned2.gjf", ensemble2, "#p")