rdworks 0.37.1__tar.gz → 0.38.1__tar.gz

{rdworks-0.37.1 → rdworks-0.38.1}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: rdworks
-Version: 0.37.1
+Version: 0.38.1
 Summary: Frequently used tasks built on RDKit and other tools
 Author-email: Sung-Hun Bae <sunghun.bae@gmail.com>
 Maintainer-email: Sung-Hun Bae <sunghun.bae@gmail.com>

{rdworks-0.37.1 → rdworks-0.38.1}/src/rdworks/__init__.py

@@ -1,4 +1,4 @@
-__version__ = '0.37.1'
+__version__ = '0.38.1'
 
 from rdworks.conf    import Conf
 from rdworks.mol     import Mol

{rdworks-0.37.1 → rdworks-0.38.1}/src/rdworks/conf.py

@@ -417,7 +417,7 @@ class Conf:
 
         Args:
             calculator (str | Callable): 'MMFF', 'UFF', or ASE calculator.
-            torsion_key (int | None): torsion index to calculate. Defaults to None (all).
+            torsion_key (int | None): key to the torsion indices to calculate. Defaults to None (all).
             simplify (bool, optional): whether to use fragment surrogate. Defaults to True.
             fmax (float, optional): fmax of ASE optimizer. Defaults to 0.05.
             interval (float, optional): interval of torsion angles in degree. Defaults to 15.0.

{rdworks-0.37.1 → rdworks-0.38.1}/src/rdworks/mol.py

@@ -33,7 +33,7 @@ from rdkit.ML.Cluster import Butina
 from PIL import Image
 
 from rdworks.conf import Conf
-from rdworks.std import desalt_smiles, standardize, clean_2d
+from rdworks.std import generate_inchi_key, desalt_smiles, standardize, clean_2d
 from rdworks.xml import list_predefined_xml, get_predefined_xml, parse_xml
 from rdworks.scaffold import rigid_fragment_indices
 from rdworks.descriptor import rd_descriptor, rd_descriptor_f
@@ -141,8 +141,7 @@ class Mol:
             self.name = 'untitled'
 
         self.rdmol.SetProp('_Name', self.name) # _Name can't be None
-        self.InChI = Chem.MolToInchi(self.rdmol)
-        self.InChIKey = inchi.InchiToInchiKey(self.InChI)
+        self.InChIKey = generate_inchi_key(self.rdmol)
         self.props.update({
             'aka' : [], # <-- to be set by MolLibr.unique()
             'atoms' : self.rdmol.GetNumAtoms(), # hydrogens not excluded?
@@ -1596,8 +1595,7 @@ class Mol:
         self.smiles = data['smiles'] # isomeric SMILES, no H
         self.rdmol = Chem.MolFromSmiles(data['smiles']) # for 2D depiction
         self.rdmol.SetProp('_Name', self.name)
-        self.InChI = Chem.MolToInchi(self.rdmol)
-        self.InChIKey = inchi.InchiToInchiKey(self.InChI)
+        self.InChIKey = generate_inchi_key(self.rdmol)
         self.props = data['props']
         self.confs = [Conf().deserialize(_) for _ in data['confs']] # for 3D conformers (iterable)
         

{rdworks-0.37.1 → rdworks-0.38.1}/src/rdworks/std.py

@@ -1,10 +1,32 @@
 import operator
 
 from rdkit import Chem
-from rdkit.Chem import rdDepictor
+from rdkit.Chem import rdDepictor, inchi
 from rdkit.Chem.MolStandardize import rdMolStandardize
 
 
+def generate_inchi_key(rdmol: Chem.Mol) -> str:
+    """Generate InChIKey.
+
+    Note:
+        - An InChIKey is a 27-character string consisting of three parts: 
+            - 14 characters: Derived from the connectivity layer of the InChI.
+            - Hyphen (-): Separates the first two blocks.
+            - 9 characters: Derived from the remaining InChI layers.
+            - A hyphen (-): Separates the second and third blocks.
+            - A final checksum character: Ensures the integrity of the key.
+
+    Args:
+        rdmol (Chem.Mol): input molecule
+
+    Returns:
+        str: 27-character InChIKey
+    """
+    InChI = Chem.MolToInchi(rdmol)
+    InChIKey = inchi.InchiToInchiKey(InChI)
+    
+    return InChIKey
+
 
 def desalt_smiles(smiles: str) -> tuple[str, Chem.Mol]:
     """Remove salt(s) from SMILES.

{rdworks-0.37.1 → rdworks-0.38.1}/src/rdworks.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: rdworks
-Version: 0.37.1
+Version: 0.38.1
 Summary: Frequently used tasks built on RDKit and other tools
 Author-email: Sung-Hun Bae <sunghun.bae@gmail.com>
 Maintainer-email: Sung-Hun Bae <sunghun.bae@gmail.com>

{rdworks-0.37.1 → rdworks-0.38.1}/tests/test_basics.py

@@ -475,7 +475,6 @@ def test_torsion_fragment():
     frag, frag_ijkl = create_torsion_fragment(mol.confs[0].rdmol, ta[6])
     assert frag_ijkl == (5, 6, 7, 12)
 
-
     mol2 = Mol(molecule='CC(=O)Nc1ccc(O)cc1', name='acetaminophen.3').make_confs(n=1)
     ta2 = mol2.torsion_atoms()
     # {0: (5, 4, 3, 1)}
@@ -486,12 +485,41 @@ def test_torsion_fragment():
     assert frag_ijkl == ta2[0]
 
 
+def test_torsion_fragment_from_conf():
+    from rdworks.torsion import create_torsion_fragment
+    mol = Mol(molecule="CC(C)C1=C(C(=C(N1CC[C@H](C[C@H](CC(=O)O)O)O)C2=CC=C(C=C2)F)C3=CC=CC=C3)C(=O)NC4=CC=CC=C4",
+              name="atorvastatin").make_confs(n=1)
+    ref_conf = mol.confs[0]
+    ta = ref_conf.torsion_atoms()
+    assert len(ta) == 12
+    # {0: (0, 1, 3, 7),  1: (3, 4, 32, 33),  2: (4, 5, 26, 27),  3: (7, 6, 19, 20),
+    # 4: (3, 7, 8, 9),  5: (7, 8, 9, 10),   6: (8, 9, 10, 18),   7: (18, 10, 11, 12),
+    # 8: (10, 11, 12, 17),  9: (17, 12, 13, 14),   10: (12, 13, 14, 15),   11: (36, 35, 34, 32)}
+    frag, frag_ijkl = create_torsion_fragment(ref_conf.rdmol, ta[6])
+    assert frag_ijkl == (5, 6, 7, 12)
+
+    ref_conf = ref_conf.torsion_energies(calculator='MMFF94', torsion_key=6, interval=15)
+
+    mol2 = Mol(molecule='CC(=O)Nc1ccc(O)cc1', name='acetaminophen.3').make_confs(n=1)
+    ref_conf2 = mol2.confs[0]
+    ta2 = ref_conf2.torsion_atoms()
+    # {0: (5, 4, 3, 1)}
+    assert len(ta2) == 1
+    frag, frag_ijkl = create_torsion_fragment(ref_conf2.rdmol, ta2[0])
+    # expects no fragmentation
+    assert frag == ref_conf2.rdmol
+    assert frag_ijkl == ta2[0]
+
+    ref_conf2 = ref_conf2.torsion_energies(calculator='MMFF94', interval=15)
+
+
 def test_torsion_energies():
     libr = MolLibr(torsion_dataset_smiles, torsion_dataset_names)
     with open(workdir / 'test_torsion_energies.html', 'w') as f:
         for mol in libr[:1]:
             mol = mol.make_confs().drop_confs(similar=True, similar_rmsd=0.3).sort_confs().rename()
-            mol = mol.optimize_confs(calculator='MMFF94').torsion_energies(calculator='MMFF94', interval=15)
+            mol = mol.optimize_confs(calculator='MMFF94').torsion_energies(calculator='MMFF94', 
+                                                                           interval=15)
             f.write(mol.to_html())
             print(mol.dumps('torsion', decimals=2))