Patch covalent radii for elements past Cm

.vscode/settings.json

@@ -0,0 +1,4 @@
+{
+    "python-envs.defaultEnvManager": "ms-python.python:conda",
+    "python-envs.defaultPackageManager": "ms-python.python:conda"
+}

pysipfenn/misc/conveniences.py

@@ -1,22 +1,143 @@
-from importlib.resources import files
+import ast
+import inspect
 import json
+from importlib.resources import files
+from importlib import import_module
+import pkgutil
+
+def _find_pymatgen_class(class_name: str):
+    """Locate a class anywhere in pymatgen, robust to module reorganization."""
+    import pymatgen
+    for _, modname, _ in pkgutil.walk_packages(pymatgen.__path__, prefix="pymatgen."):
+        try:
+            mod = import_module(modname)
+        except Exception:
+            continue
+        obj = getattr(mod, class_name, None)
+        if isinstance(obj, type) and obj.__module__.startswith("pymatgen"):
+            return obj
+    return None
+
+def patchCovalentRadiiForExoticElements() -> None:
+    """
+    """
+    patchRadii = {
+        "Bk": 1.68,
+        "Cf": 1.68,
+        "Es": 1.65,
+        "Fm": 1.67,
+        "Md": 1.73,
+        "No": 1.76,
+        "Lr": 1.61,
+        "Rf": 1.57,
+        "Db": 1.49,
+        "Sg": 1.43,
+        "Bh": 1.41,
+        "Hs": 1.34,
+        "Mt": 1.29,
+        "Ds": 1.28,
+        "Rg": 1.21,
+        "Cn": 1.22,
+        "Nh": 1.36,
+        "Fl": 1.43,
+        "Mc": 1.62,
+        "Lv": 1.75,
+        "Ts": 1.65,
+        "Og": 1.57,
+    }
+
+
+    CovalentRadius = _find_pymatgen_class("CovalentRadius")
+    if CovalentRadius is None:
+        raise RuntimeError(
+            "Could not locate `CovalentRadius` class in pymatgen; "
+            "pymatgen's layout may have changed and this patch needs updating."
+        )
+    source_file = inspect.getsourcefile(CovalentRadius)
+    with open(source_file, "r") as f:
+        src = f.read()
+
+    dict_node = None
+    for cls in ast.walk(ast.parse(src)):
+        if not (isinstance(cls, ast.ClassDef) and cls.name == "CovalentRadius"):
+            continue
+        for stmt in cls.body:
+            if isinstance(stmt, ast.AnnAssign) and isinstance(stmt.target, ast.Name):
+                target, value = stmt.target.id, stmt.value
+            elif (isinstance(stmt, ast.Assign)
+                    and len(stmt.targets) == 1
+                    and isinstance(stmt.targets[0], ast.Name)):
+                target, value = stmt.targets[0].id, stmt.value
+            else:
+                continue
+            if target == "radius" and isinstance(value, ast.Dict):
+                dict_node = value
+                break
+        break
+
+    if dict_node is None:
+        raise RuntimeError(
+            f"Could not locate `CovalentRadius.radius` dict in {source_file}; "
+            "pymatgen's layout may have changed and this patch needs updating."
+        )
+
+    existing = ast.literal_eval(dict_node)
+    # Skip writing if the file is already up to date with our patch values.
+    if any(existing.get(el) is None for el in patchRadii):
+        merged = {**patchRadii, **existing}
+
+        # Match pymatgen's existing indentation by reading it from the source
+        # rather than hardcoding spaces, so the patch survives style changes.
+        src_lines = src.splitlines(keepends=True)
+        first_key = dict_node.keys[0]
+        entry_indent = src_lines[first_key.lineno - 1][:first_key.col_offset]
+        close_indent = src_lines[dict_node.end_lineno - 1][:dict_node.end_col_offset - 1]
+
+        new_literal = "{\n" + "".join(
+            f'{entry_indent}"{el}": {v},\n' for el, v in merged.items()
+        ) + close_indent + "}"
+
+        # Convert (line, col) bounds to byte offsets and splice.
+        line_starts = [0]
+        for line in src.splitlines(keepends=True):
+            line_starts.append(line_starts[-1] + len(line))
+        start = line_starts[dict_node.lineno - 1] + dict_node.col_offset
+        end = line_starts[dict_node.end_lineno - 1] + dict_node.end_col_offset
+
+        src = src[:start] + new_literal + src[end:]
+        with open(source_file, "w") as f:
+            f.write(src)
 
 def patchPymatgenForExoticElements(
         x: bool = True,
-        iupacOrder: bool = True
+        iupacOrder: bool = True,
+        radii: bool = True,
 ) -> None:
-    """Patches pymatgen's ``core/periodic_table.json`` with (selectable) electronegativities and IUPAC ordering values
-    needed to correctly handle some exotic chemical elements. The IUPAC rules are followed exactly per Table VI in the 
-    same reference. The electronegativity values are `not` Pauling ones but based on Oganov 2021 and are meant to be 
+    """
+    Patch pymatgen's installed element data for elements whose properties are
+    missing or incomplete in the default pymatgen data files.
+
+    This function directly edits files inside the installed pymatgen package:
+
+    1. Patches pymatgen's ``core/periodic_table.json`` with (selectable) electronegativities and IUPAC ordering values
+    needed to correctly handle some exotic chemical elements. The IUPAC rules are followed exactly per Table VI in the
+    same reference. The electronegativity values are `not` Pauling ones but based on Oganov 2021 and are meant to be
     used primarily for providing trend information for ML model deployment (has to be included in training).
 
+    2. CovalentRadius.radius
+    Adds missing covalent radii for elements Bk through Og using `ast` to locate the dictionary definition in
+    pymatgen's source code, merge in the missing values, and write the updated literal back to disk. Radii reference
+    values from Pekka Pyykkö, The Journal of Physical Chemistry A 2015 119 (11), 2326-2337,
+    DOI: 10.1021/jp5065819
+
     Args:
         x: Patch electronegativities.
         iupacOrder: Patch IUPAC ordering of elements in chemical formulas so that they can be handled at all.
+        radii: Patch ``CovalentRadius.radius`` with covalent radii for elements past Cm.
 
     Returns:
-        None. The ``core/periodic_table.json`` file in local install of ``pymatgen`` is patched. Reinstall or upgrade 
-        of ``pymatgen`` reverses the changes.
+        None. The ``core/periodic_table.json`` files and the python file containing the ``CovalentRadius`` in the
+        local install of ``pymatgen`` are patched. Reinstall or upgrade ``pymatgen`` to reverse the changes.
     """
 
     patchIUPAC = {
@@ -66,7 +187,12 @@ def patchPymatgenForExoticElements(
         if x:
             for el in patchX:
                 pt[el]["X"] = patchX[el]
-        if iupacOrder:        
+        if iupacOrder:
             for el in patchIUPAC:
                 pt[el]["IUPAC ordering"] = patchIUPAC[el]
-        json.dump(pt, f)
+        json.dump(pt, f)
+
+    # Patch covalent radii on disk. 
+    # We locate the dict with `ast` and splice a merged literal back in.
+    if radii:
+        patchCovalentRadiiForExoticElements()