def translate(mol: Chem.rdchem.Mol,
new_centroid: Union[np.ndarray, List[int]],
conf_id: int = -1):
"""Move a given conformer of a molecule to a new position. The transformation is performed
in place.
Args:
mol: the molecule.
new_centroid: the new position to move to of shape [x, y, z]
conf_id: id of the conformer.
"""
# Get conformer
conf = mol.GetConformer(conf_id)
# Compute the vector for translation
mol_center = rdMolTransforms.ComputeCentroid(conf)
mol_center = np.array([mol_center.x, mol_center.y, mol_center.z])
# Make the transformation matrix
T = np.eye(4)
T[:3, 3] = new_centroid - mol_center
# Transform
rdMolTransforms.TransformConformer(conf, T)
def get_coords(mol: Chem.rdchem.Mol, conf_id: int = -1):
"""Get the coordinate of a conformer of a molecule.
Args:
mol: a molecule.
conf_id: a conformer id.
"""
if mol.GetNumConformers() == 0:
raise ValueError("Molecule does not have any conformers.")
conf = mol.GetConformer(id=conf_id)
return conf.GetPositions()
def createRDKITconf(self, mol: Chem.rdchem.Mol, conversionFactor: float = 0.1):
"""creates a PyGromosTools CNF type from a rdkit molecule. If a conformation exists the first one will be used.
Parameters
----------
mol : Chem.rdchem.Mol
Molecule, possibly with a conformation
conversionFactor : float
the factor used to convert length from rdkit to Gromos
(default: angstrom -> nano meter = 0.1)
"""
inchi = Chem.MolToInchi(mol).split("/")
if len(inchi) >= 2:
name = inchi[1]
else:
name = "XXX"
self.__setattr__("TITLE", TITLE("\t" + name + " created from RDKit"))
# check if conformations exist else create a new one
if mol.GetNumConformers() < 1:
mol = Chem.AddHs(mol)
AllChem.EmbedMolecule(mol)
AllChem.UFFOptimizeMolecule(mol)
conf = mol.GetConformer(0)
# fill a list with atomP types from RDKit data
atomList = []
for i in range(mol.GetNumAtoms()):
x = conversionFactor * conf.GetAtomPosition(i).x
y = conversionFactor * conf.GetAtomPosition(i).y
z = conversionFactor * conf.GetAtomPosition(i).z
atomType = mol.GetAtomWithIdx(i).GetSymbol()
atomList.append(blocks.atomP(resID=1, resName=name, atomType=atomType, atomID=i + 1, xp=x, yp=y, zp=z))
# set POSITION attribute
self.__setattr__("POSITION", blocks.POSITION(atomList))
# Defaults set for GENBOX - for liquid sim adjust manually
self.__setattr__("GENBOX", blocks.GENBOX(pbc=1, length=[4, 4, 4], angles=[90, 90, 90]))
def return_centroids(
mol: Chem.rdchem.Mol,
conf_clusters: Sequence[Sequence[int]],
centroids: bool = True,
) -> Union[List[Chem.rdchem.Mol], Chem.rdchem.Mol]:
"""Given a list of cluster indices, return one single molecule
with only the centroid of the clusters of a list of molecules per cluster.
Args:
mol: a molecule.
conf_clusters: list of cluster indices.
centroids: If True, return one molecule with centroid conformers
only. If False return a list of molecules per cluster with all
the conformers of the cluster.
"""
if centroids:
# Collect centroid of each cluster (first element of the list)
centroid_list = [indices[0] for indices in conf_clusters]
# Keep only centroid conformers
mol_clone = copy.deepcopy(mol)
confs = [mol_clone.GetConformers()[i] for i in centroid_list]
mol.RemoveAllConformers()
[mol.AddConformer(conf, assignId=True) for conf in confs]
return mol
else:
# Create a new molecule for each cluster and add conformers to it.
mols = []
for cluster in conf_clusters:
m = copy.deepcopy(mol)
m.RemoveAllConformers()
[
m.AddConformer(mol.GetConformer(c), assignId=True)
for c in cluster
]
mols.append(m)
return mols
