Only use names if the user specifies names.

molssi-seamm · Nov 9, 2023 · 4674dd9 · 4674dd9
1 parent b51dab6
commit 4674dd9
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diff --git a/HISTORY.rst b/HISTORY.rst
@@ -2,6 +2,11 @@
 History
 =======
 
+2023.11.9.1 -- Removed using structure names when perceiving type
+    * Using structure names is too dangerous to use by perceiving if text is a name of
+      SMILES and there is no easy test for valid SMILES. So change to only using names
+      if the user specifies names.
+
 2023.11.9 -- Improved structure handling, added from names
     * Switched to standard structure handling, which adds more options
     * Added getting structures from Pubchem using the chemical name.

diff --git a/from_smiles_step/from_smiles.py b/from_smiles_step/from_smiles.py
@@ -121,28 +121,9 @@ def run(self):
                 notation = "InChI"
             else:
                 notation = "SMILES"
-                # Some characters are not valid in SMILES
-                # fmt: off
-                for c in (
-                    "d", "f", "g", "h", "i", "j", "k", "l", "m",
-                    "q", "r", "t", "u", "v", "w", "x", "y", "z"
-                ):
-                    # fmt: on
-                    if c in text:
-                        notation = "name"
-                        break
 
         if notation == "SMILES":
-            if P["notation"] == "perceive":
-                try:
-                    # See if it is a name...
-                    configuration.PC_from_identifier(text, namespace="name")
-                except Exception as e:
-                    print(f"PubCHem exception {e}")
-                    # SMILES?
-                    configuration.from_smiles(text, rdkit=True)
-            else:
-                configuration.from_smiles(text)
+            configuration.from_smiles(text)
         elif notation == "InChI":
             configuration.from_inchi(text)
         elif notation == "InChIKey":