Updated naming of get_atomic_number

valence-labs · Sep 25, 2023 · bd2e008 · bd2e008
1 parent 56834ee
commit bd2e008
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Showing 5 changed files with 9 additions and 9 deletions.
diff --git a/src/openqdc/datasets/geom.py b/src/openqdc/datasets/geom.py
@@ -6,7 +6,7 @@
 from openqdc.datasets.base import BaseDataset
 from openqdc.utils import load_json, load_pkl
 from openqdc.utils.constants import MAX_ATOMIC_NUMBER
-from openqdc.utils.molecule import get_atomic_numuber_and_charge
+from openqdc.utils.molecule import get_atomic_number_and_charge
 
 
 def read_mol(mol_id, mol_dict, base_path, partition):
@@ -34,7 +34,7 @@ def read_mol(mol_id, mol_dict, base_path, partition):
     try:
         d = load_pkl(p_join(base_path, mol_dict["pickle_path"]), False)
         confs = d["conformers"]
-        x = get_atomic_numuber_and_charge(confs[0]["rd_mol"])
+        x = get_atomic_number_and_charge(confs[0]["rd_mol"])
         positions = np.array([cf["rd_mol"].GetConformer().GetPositions() for cf in confs])
         n_confs = positions.shape[0]
 

diff --git a/src/openqdc/datasets/molecule3d.py b/src/openqdc/datasets/molecule3d.py
@@ -9,13 +9,13 @@
 
 from openqdc.datasets.base import BaseDataset
 from openqdc.utils.constants import BOHR2ANG, MAX_ATOMIC_NUMBER
-from openqdc.utils.molecule import get_atomic_numuber_and_charge
+from openqdc.utils.molecule import get_atomic_number_and_charge
 
 
 def read_mol(mol, energy):
     smiles = dm.to_smiles(mol, explicit_hs=False)
     # subset = dm.to_smiles(dm.to_scaffold_murcko(mol, make_generic=True), explicit_hs=False)
-    x = get_atomic_numuber_and_charge(mol)
+    x = get_atomic_number_and_charge(mol)
     positions = mol.GetConformer().GetPositions() * BOHR2ANG
 
     res = dict(

diff --git a/src/openqdc/datasets/qmugs.py b/src/openqdc/datasets/qmugs.py
@@ -7,7 +7,7 @@
 
 from openqdc.datasets.base import BaseDataset
 from openqdc.utils.constants import MAX_ATOMIC_NUMBER
-from openqdc.utils.molecule import get_atomic_numuber_and_charge
+from openqdc.utils.molecule import get_atomic_number_and_charge
 
 
 def read_mol(mol_dir):
@@ -19,7 +19,7 @@ def read_mol(mol_dir):
         return None
 
     smiles = dm.to_smiles(mols[0], explicit_hs=False)
-    x = get_atomic_numuber_and_charge(mols[0])[None, ...].repeat(n_confs, axis=0)
+    x = get_atomic_number_and_charge(mols[0])[None, ...].repeat(n_confs, axis=0)
     positions = np.array([mol.GetConformer().GetPositions() for mol in mols])
     props = [mol.GetPropsAsDict() for mol in mols]
     targets = np.array([[p[el] for el in QMugs.energy_target_names] for p in props])

diff --git a/src/openqdc/datasets/spice.py b/src/openqdc/datasets/spice.py
@@ -7,14 +7,14 @@
 from openqdc.datasets.base import BaseDataset
 from openqdc.utils import load_hdf5_file
 from openqdc.utils.constants import BOHR2ANG, MAX_ATOMIC_NUMBER
-from openqdc.utils.molecule import get_atomic_numuber_and_charge
+from openqdc.utils.molecule import get_atomic_number_and_charge
 
 
 def read_record(r):
     smiles = r["smiles"].asstr()[0]
     subset = r["subset"][0].decode("utf-8")
     n_confs = r["conformations"].shape[0]
-    x = get_atomic_numuber_and_charge(dm.to_mol(smiles, add_hs=True))
+    x = get_atomic_number_and_charge(dm.to_mol(smiles, add_hs=True))
     positions = r["conformations"][:] * BOHR2ANG
 
     res = dict(

diff --git a/src/openqdc/utils/molecule.py b/src/openqdc/utils/molecule.py
@@ -14,6 +14,6 @@ def get_atomic_charge(mol: Chem.Mol):
     return np.array([atom.GetFormalCharge() for atom in mol.GetAtoms()])
 
 
-def get_atomic_numuber_and_charge(mol: Chem.Mol):
+def get_atomic_number_and_charge(mol: Chem.Mol):
     """Returns atoms number and charge for rdkit molecule"""
     return np.array([[atom.GetAtomicNum(), atom.GetFormalCharge()] for atom in mol.GetAtoms()])