def analyse_mols(mols, target, specified_site=False, site_description=None):
"""Analyse a list of molecules for a given target
:param mols: the Django molecules to analyse
:param target: the Django target
:param specified_site:
:param site_description:
:return: None
"""
rd_mols = [Chem.MolFromMolBlock(x.sdf_info) for x in mols]
if not specified_site:
cluster_mols(rd_mols, mols, target)
else:
centre = process_site(rd_mols)
# look for molgroup with same target and description
mol_group = search_for_molgroup_by_description(
target=target.title, description=site_description)
if not mol_group:
mol_group = MolGroup()
mol_group.group_type = "MC"
mol_group.target_id = target
mol_group.x_com = centre[0]
mol_group.y_com = centre[1]
mol_group.z_com = centre[2]
mol_group.description = site_description
mol_group.save()
ids = [m.id for m in mols]
print([a['id'] for a in mol_group.mol_id.values()])
for mol_id in ids:
if mol_id not in [a['id'] for a in mol_group.mol_id.values()]:
print(mol_id)
this_mol = Molecule.objects.get(id=mol_id)
mol_group.mol_id.add(this_mol)
get_vectors(mols)
def cluster_mols(rd_mols, mols, target):
"""
Cluster a series of 3D molecules
:param rd_mols: the RDKit molecules to cluster
:param mols: the Django moleculs they refer to
:param target: the Django target it refers to
:return: None
"""
id_mols = [x.pk for x in mols]
out_data = run_lig_cluster(rd_mols, id_mols)
for clust_type in out_data:
for cluster in out_data[clust_type]:
# look for molgroup with same coords - need to implement tolerance?
mol_group = search_for_molgroup_by_coords(coords=[out_data[clust_type][cluster]["centre_of_mass"][0],
out_data[clust_type][cluster]["centre_of_mass"][1],
out_data[clust_type][cluster]["centre_of_mass"][2]],
target=target.title)
if not mol_group:
mol_group = MolGroup()
if clust_type != "c_of_m":
mol_group.group_type = "PC"
else:
mol_group.group_type = "MC"
mol_group.target_id = target
mol_group.x_com = out_data[clust_type][cluster]["centre_of_mass"][0]
mol_group.y_com = out_data[clust_type][cluster]["centre_of_mass"][1]
mol_group.z_com = out_data[clust_type][cluster]["centre_of_mass"][2]
mol_group.description = clust_type
mol_group.save()
for mol_id in out_data[clust_type][cluster]["mol_ids"]:
if mol_id not in [a['id'] for a in mol_group.mol_id.values()]:
this_mol = Molecule.objects.get(id=mol_id)
mol_group.mol_id.add(this_mol)