def set_position(mol: rdkit.Mol, position, conformer=-1):
"""
Sets the centroid of the molecule to `position`.
Parameters
----------
position : :class:`numpy.array`
This array holds the position on which the centroid of the
molecule should be placed.
conformer : :class:`int`, optional
The id of the conformer to be used.
Returns
-------
:class:`rdkit.Chem.rdchem.Mol`
The ``rdkit`` molecule with the centroid placed at
`position`. This is the same instance as that in
:attr:`Molecule.mol`.
"""
conf_id = mol.GetConformer(conformer).GetId()
# Get the original centroid.
centroid = get_centroid(mol, conf_id)
# Find out how much it needs to shift to reach `position`.
shift = position - centroid
# Apply the shift and get the resulting rdkit conformer object.
new_conf = apply_shift(mol, shift, conf_id).GetConformer()
new_conf.SetId(conf_id)
# Replace the old rkdit conformer with one where the centroid
# is at `position`.
mol.RemoveConformer(conf_id)
mol.AddConformer(new_conf)
return mol
def prune_last_conformer(
mol: Chem.Mol, tfd_thresh: float,
energies: List[float]) -> Tuple[Chem.Mol, List[float]]:
"""Prunes the last conformer of the molecule.
If no conformers in `mol` have a TFD (Torsional Fingerprint Deviation) with the last conformer of less than `tfd_thresh`,
the last conformer is kept. Otherwise, the lowest energy conformer with TFD less than `tfd_thresh` is kept and all other conformers
are discarded.
Parameters
----------
mol : RDKit Mol
The molecule to be pruned. The conformers in the molecule should be ordered by ascending energy.
tfd_thresh : float
The minimum threshold for TFD between conformers.
energies : list of float
A list of all the energies of the conformers in `mol`.
Returns
-------
mol : RDKit Mol
The updated molecule after pruning, with conformers sorted by ascending energy.
energies : list of float
A list of all the energies of the conformers in `mol` after pruning and sorting by ascending energy.
"""
if tfd_thresh < 0 or mol.GetNumConformers() <= 1:
return mol, energies
idx = bisect.bisect(energies[:-1], energies[-1])
tfd = TorsionFingerprints.GetTFDBetweenConformers(
mol,
range(0,
mol.GetNumConformers() - 1), [mol.GetNumConformers() - 1],
useWeights=False)
tfd = np.array(tfd)
# if lower energy conformer is within threshold, drop new conf
if not np.all(tfd[:idx] >= tfd_thresh):
energies = energies[:-1]
mol.RemoveConformer(mol.GetNumConformers() - 1)
return mol, energies
else:
keep = list(range(0, idx))
keep.append(mol.GetNumConformers() - 1)
keep += [
x for x in range(idx,
mol.GetNumConformers() - 1)
if tfd[x] >= tfd_thresh
]
new = Chem.Mol(mol)
new.RemoveAllConformers()
for i in keep:
conf = mol.GetConformer(i)
new.AddConformer(conf, assignId=True)
return new, [energies[i] for i in keep]