Fix based on reviews

easydock/preparation_for_docking.py

@@ -142,6 +142,7 @@ def GetConformerRMSMatrixForSaturatedRingMolecule(mol: Chem.Mol, atomIds:list[li
  """
 
  cmat_list = []
+ total_ring_atoms = sum([len(atom_in_ring) for atom_in_ring in atomIds])
  for atom_id_in_ring in atomIds:
  # if necessary, align the conformers
  # Note: the reference conformer is always the first one
@@ -162,11 +163,10 @@ def GetConformerRMSMatrixForSaturatedRingMolecule(mol: Chem.Mol, atomIds:list[li
  for j in range(1, i):
  cmat_per_ring.append(GetConformerRMSFromAtomIds(mol, confIds[i], confIds[j], atomIds=atom_id_in_ring, prealigned=True))
 
- cmat_list.append(np.array(cmat_per_ring))
+ cmat_list.append(np.square(np.array(cmat_per_ring))*len(atom_id_in_ring))
 
  cmat_list_array = np.array(cmat_list)
-
- return list(np.mean(cmat_list_array, axis=0))
+ return list(np.sqrt(np.sum(cmat_list_array, axis=0)/total_ring_atoms))
 
 
 def mol_embedding_3d(mol: Chem.Mol, seed: int=43) -> Chem.Mol:
@@ -176,7 +176,7 @@ def find_saturated_ring(mol: Chem.Mol) -> list[list[int]]:
  saturated_ring_list = []
  for ring in ssr:
  is_atom_saturated_array = [mol.GetAtomWithIdx(atom_id).GetHybridization() == Chem.HybridizationType.SP3 for atom_id in ring]
- if all(is_atom_saturated_array):
+ if any(is_atom_saturated_array):
  saturated_ring_list.append(ring)
  return saturated_ring_list
 
@@ -236,21 +236,16 @@ def gen_ids(ids: int) -> Iterator[int]:
  if mol.GetNumConformers() == 1:
  return mol
 
- if keep_nconf:
- if mol.GetNumConformers() <= keep_nconf:
- return mol
-
- cids = [c.GetId() for c in mol.GetConformers()]
- arr = arr[np.ix_(cids, cids)]
-
+ if keep_nconf and mol.GetNumConformers() > keep_nconf:
+ arr = arr[np.ix_(keep_ids, keep_ids)]
  cl = AgglomerativeClustering(n_clusters=keep_nconf, linkage='complete', metric='precomputed').fit(arr)
 
- keep_ids = []
+ keep_ids_nconf_filter = []
  for i in set(cl.labels_):
  ids = np.where(cl.labels_ == i)[0]
  j = arr[np.ix_(ids, ids)].mean(axis=0).argmin()
- keep_ids.append(cids[j])
- remove_ids = set(cids) - set(keep_ids)
+ keep_ids_nconf_filter.append(cids[j])
+ remove_ids = set(keep_ids) - set(keep_ids_nconf_filter)
 
  for cid in sorted(remove_ids, reverse=True):
  mol.RemoveConformer(cid)