Manipulating Molecule Objects

  • import cctk is assumed

  • Assume a Molecule has been loaded as molecule.

  • cctk assumes molecular geometries are given in Angstroms

Measuring Distances and Angles

# the atomic numbers as a one-indexed array
atomic_numbers = molecule.atomic_numbers

# measure bond distance between atoms 1 and 2 in A
bond_distance = molecule.get_distance(1,2)

# measure bond angle between atoms 1, 2, and 3 in degrees
bond_angle = molecule.get_angle(1, 2, 3)

# measure dihedral angle between atoms 1, 2, 3, and 4 in degrees
dihedral_angle = molecule.get_dihedral(1, 2, 3, 4)

# alternately, all get_ or set_ methods will also take a list of atom numbers
dihedral_angle = molecule.get_dihedral(atoms=[1, 2, 3, 4])


# you can also get the volume!
vol = molecule.volume()

Setting Distances and Angles

  • Molecule objects are modified in-place.

  • When move is set to a group, rings are not allowed (see below).

# make a copy of the molecule if desired
molecule2 = copy.deepcopy(molecule)

# set bond distance between atoms 1 and 2 to 2.00 A
# move="group": all atoms connected to atom 2 will also be moved (this is the default)
#               if atom 2 is connected to any atom that is also connected to atom1,
#               there is a ring and an error will be thrown
# move="atom": only atom 2 will be moved
molecule2.set_distance(1, 2, 2.00, move="group")

# set the bond angle between atoms 1, 3, and 5 to 120 degrees
# move="group": all atoms connected to the third atom will also be moved (default, rings not allowed)
# move="atom": only the third atom will be moved
molecule2.set_angle(1, 3, 5, 120)

# set the dihedral angle between atoms 1, 7, 2, and 8 to 157 degrees
# move="atom": only the fourth atom will be moved
# move="group4": all atoms bonded to the fourth atom will be moved (rings not allowed)
# move="group34": all atoms bonded to the third and fourth atoms will be moved (default, rings not allowed)
molecule2.set_dihedral(1, 7, 2, 8, 157)

# use unpacking to pass in the atom numbers as a tuple or list
atom_tuple = (1, 7, 2, 8)
molecule2.set_dihedral(*atom_tuple, 157)
atom_list = [1, 7, 2, 8]
molecule2.set_dihedral(*atom_list, 157)

# or just pass the list directly!
molecule2.set_dihedral(atoms=atom_list)

Checking For Clashes

  • Checks for steric clashes based on covalent radii.

  • If two atoms are closer than the sum of their vdw radii + min_buffer, they are said to be clashing.

  • Returns True if there are no conflicts, or False if there are.

no_clashes_present = molecule.check_for_conflicts()

Generating Non-Ground States

  • The output of a frequency job can be used to generate molecules with realistic non-equilibrium geometries.

import cctk.quasiclassical as qc

# returns a new Molecule object and the energy above the ground state, sampled from the relevant Boltzmann distribution
perturbed_molecule, energy = qc.get_quasiclassical_perturbation(molecule, temperature=350)