rdworks 0.37.1__py3-none-any.whl → 0.38.1__py3-none-any.whl

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/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/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/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.dist-info → rdworks-0.38.1.dist-info}/METADATA

@@ -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.dist-info → rdworks-0.38.1.dist-info}/RECORD

@@ -1,16 +1,16 @@
-rdworks/__init__.py,sha256=rItIwmmnZw067vfUbVTaDud0QrQtW2LkzfGjINiaQFA,1368
-rdworks/conf.py,sha256=1pmcEEEuEJwEaDhs8V2uq1ataA80Am5uYdWEv6yWvZE,28769
+rdworks/__init__.py,sha256=I7VqtqGi1BTUMH2KV5AU3UWjjteuPPjdB3td8SDB4sE,1368
+rdworks/conf.py,sha256=5j6KxncNn9eb3F-O3_S631azx-SK_KQ6oDAnf3Cke0A,28782
 rdworks/descriptor.py,sha256=34T_dQ6g8v3u-ym8TLKbQtxIIV5TEo-d3pdedq3o-cg,2106
 rdworks/display.py,sha256=JR0gR26UpH-JCxVOaqXZCUj2MiGZSrx9Me87FncspVI,13469
 rdworks/ionized.py,sha256=5oIjMRpkX792RIpEEE2Ir96icfFaN_h21mSihhfQPAw,6713
 rdworks/matchedseries.py,sha256=A3ON4CUpQV159mu9VqgNiJ8uoQ9ePOry9d3ra4NCAgc,10377
-rdworks/mol.py,sha256=UHgiPuo2ExBOMQbhsw-gjtoXZu4TpAyr1KNVZFmPJAo,67873
+rdworks/mol.py,sha256=R6ifd-KIquR9ayl1_HCOE9-tXm89vk9vkHPkQtHsRNU,67787
 rdworks/mollibr.py,sha256=X4UBO6Ga-QmNS7RwUiaDYAx0Q5hnWs71yTkEpH02Qb4,37696
 rdworks/pka.py,sha256=NVJVfpcNEMlX5QRyLBgUM7GIT7VMjO-llAR4LWc8J2c,1656
 rdworks/readin.py,sha256=0bnVcZcAmSLqc6zu1mYcv0LdBv2agQfOpKGwpSRL9VE,11742
 rdworks/rgroup.py,sha256=ivF2gzmRtt339rxEnkv2KfnCs0CUdBbnSje7Y54rtFI,57996
 rdworks/scaffold.py,sha256=60T5YacyxZsEpDo_J5Qxulm2YNQO4EQR8PcNUwjn1QU,22026
-rdworks/std.py,sha256=LX53gXNvAKHNEowoXzmdUH0mp_s0bSNSD07i8Nk-UrI,7186
+rdworks/std.py,sha256=qOVS_lGogueLKh4rsbrsYIMR0c7z_xh6BqLEzD4X9sE,7938
 rdworks/stereoisomers.py,sha256=g8hhPI-mbYX-MzbF1uAqo5fDZOCNiKYjxI-kLBGdGgg,4980
 rdworks/tautomers.py,sha256=gtZHZJ-aJbryhBdljHbfjx7xhVW3u_OzdYPtwPail54,610
 rdworks/torsion.py,sha256=qTRJWsxSktqprL8pUHWEOoV2dKEgoMozh3BB0eGNlZ8,18571
@@ -65,8 +65,8 @@ rdworks/predefined/misc/reactive-part-3.xml,sha256=LgWHSEbRTVmgBoIO45xbTo1xQJs0X
 rdworks/predefined/misc/reactive.xml,sha256=syedoQ6VYUfRLnxy99ObuDniJ_a_WhrWAJbTKFfJ6VY,11248
 rdworks/xtb/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 rdworks/xtb/wrapper.py,sha256=I0nW89vlJZ5Za5pCjIpjsEOFbTm7HpeNGiPgssheWn8,11350
-rdworks-0.37.1.dist-info/licenses/LICENSE,sha256=UOkJSBqYyQUvtCp7a-vdCANeEcLE2dnTie_eB1By5SY,1074
-rdworks-0.37.1.dist-info/METADATA,sha256=PmGou_FD-TsIQMhrJYvo847AZahu_ETfLPFvt3ktM08,1183
-rdworks-0.37.1.dist-info/WHEEL,sha256=_zCd3N1l69ArxyTb8rzEoP9TpbYXkqRFSNOD5OuxnTs,91
-rdworks-0.37.1.dist-info/top_level.txt,sha256=05C98HbvBK2axUBogC_hAT_CdpOeQYGnQ6vRAgawr8s,8
-rdworks-0.37.1.dist-info/RECORD,,
+rdworks-0.38.1.dist-info/licenses/LICENSE,sha256=UOkJSBqYyQUvtCp7a-vdCANeEcLE2dnTie_eB1By5SY,1074
+rdworks-0.38.1.dist-info/METADATA,sha256=_uZpCzy6HddNOJ1adyBo5oM0VX2-bhCBKz8P_7XHKbg,1183
+rdworks-0.38.1.dist-info/WHEEL,sha256=_zCd3N1l69ArxyTb8rzEoP9TpbYXkqRFSNOD5OuxnTs,91
+rdworks-0.38.1.dist-info/top_level.txt,sha256=05C98HbvBK2axUBogC_hAT_CdpOeQYGnQ6vRAgawr8s,8
+rdworks-0.38.1.dist-info/RECORD,,