fix I(III/V), fix tests, add ability to fail w/o bond order

.coveragerc

@@ -2,7 +2,8 @@
 source = steamroll
 omit =
     steamroll/__main__.py
-    steamroll/xyz2mol.py
+    steamroll/xyz2mol/*
+    steamroll/xyz2mol_tmc/*
 
 [report]
 exclude_lines =

pyproject.toml

@@ -2,7 +2,7 @@
 name = "steamroll"
 description = "Package to convert 3D molecules to RDKit"
 license = {file = "LICENSE"}
-version = "0.0.2"
+version = "0.0.3"
 readme = "README.md"
 keywords = []
 authors = [
@@ -28,7 +28,7 @@ dev = [
 
 [tool.ruff]
 line-length = 100
-exclude = ["steamroll/xyz2mol.py"]
+exclude = ["steamroll/xyz2mol", "steamroll/xyz2mol_tmc"]
 
 [tool.ruff.lint]
 select = [
@@ -70,11 +70,11 @@ convention = "google"
 
 [tool.pytest.ini_options]
 testpaths = ["tests", "steamroll"]
-addopts = "--doctest-modules --ignore=steamroll/xyz2mol.py"
+addopts = "--doctest-modules --ignore=steamroll/xyz2mol --ignore=steamroll/xyz2mol_tmc"
 doctest_optionflags = "NORMALIZE_WHITESPACE"
 
 [tool.ty.src]
-exclude = ["steamroll/xyz2mol.py"]
+exclude = ["steamroll/xyz2mol", "steamroll/xyz2mol_tmc"]
 
 [build-system]
 build-backend = "hatchling.build"

steamroll/steamroll.py

@@ -1,16 +1,25 @@
 """steamroll package."""
 
 import logging
+import os
+import tempfile
 from typing import Iterable
 
 import numpy as np
 from numpy.typing import ArrayLike
 from rdkit import Chem
 
-from .xyz2mol import xyz2mol
+from .xyz2mol.xyz2mol import xyz2mol
+from .xyz2mol_tmc.xyz2mol_local import xyz2AC_obabel as xyz2ac_obabel
+from .xyz2mol_tmc.xyz2mol_tmc import TRANSITION_METALS_NUM, get_tmc_mol
 
 logger = logging.getLogger(__name__)
 
+# Lanthanides Ce-Yb (58-70) and actinides Ac-Lr (89-103) that xyz2mol cannot
+# handle. Molecules containing these elements bypass xyz2mol and go directly to
+# the geometry-only xyz2ac_obabel fallback.
+_SKIP_XYZ2MOL: frozenset[int] = frozenset(range(58, 71)) | frozenset(range(89, 104))
+
 
 class SteamrollConversionError(Exception):
     """Raised when a conversion error occurs."""
@@ -55,11 +64,33 @@ def fragment(molecule: Chem.rdchem.Mol) -> list[Chem.rdchem.Mol]:
     return Chem.GetMolFrags(molecule, asMols=True, sanitizeFrags=True)  # type: ignore [return-value]
 
 
+def _write_temp_xyz(atomic_numbers: list[int], coordinates: list[list[float]]) -> str:
+    """Write atomic numbers and coordinates to a temporary xyz file.
+
+    Args:
+        atomic_numbers: atomic numbers for each atom
+        coordinates: Cartesian coordinates for each atom, in Å
+
+    Returns:
+        path to the temporary file (caller is responsible for deletion)
+    """
+    pt = Chem.GetPeriodicTable()
+    lines = [str(len(atomic_numbers)), ""]
+    for num, (x, y, z) in zip(atomic_numbers, coordinates, strict=True):
+        symbol = pt.GetElementSymbol(num)
+        lines.append(f"{symbol}  {x}  {y}  {z}")
+    f = tempfile.NamedTemporaryFile(mode="w", suffix=".xyz", delete=False)
+    f.write("\n".join(lines) + "\n")
+    f.close()
+    return f.name
+
+
 def to_rdkit(
     atomic_numbers: Iterable[int],
     coordinates: ArrayLike,
     charge: int = 0,
     remove_Hs: bool = True,
+    fail_without_bond_order: bool = False,
 ) -> Chem.rdchem.Mol:
     """Convert a given molecular geometry to an RDKit molecule.
 
@@ -68,6 +99,7 @@ def to_rdkit(
         coordinates: coordinates, in Å
         charge: charge
         remove_Hs: whether or not to strip hydrogens from the output molecule
+        fail_without_bond_order: if bond order cannot be detected, raise SteamrollConversionError
 
     Raises:
         ValueError: if input dimensions aren't correct
@@ -89,13 +121,164 @@ def to_rdkit(
         )
 
     coords = coordinates.tolist()
-    rdkm: Chem.rdchem.Mol
-    try:
+    has_tm = any(n in TRANSITION_METALS_NUM for n in atomic_numbers)
+    has_exotic = any(n in _SKIP_XYZ2MOL for n in atomic_numbers)
+
+    rdkm: Chem.rdchem.Mol | None = None
+
+    if not has_tm and not has_exotic:
+        try:
+            try:
+                rdkm = xyz2mol(atomic_numbers, coords, charge=charge)[0]
+            except (Exception, ValueError, IndexError):
+                rdkm = xyz2mol(atomic_numbers, coords, charge=charge, use_huckel=True)[0]
+        except Exception as e:
+            if fail_without_bond_order:
+                raise SteamrollConversionError from e
+
+    if has_tm:
+        # Use the specialized TMC converter; Hs come back implicit → make explicit.
+        xyz_file = _write_temp_xyz(atomic_numbers, coords)
         try:
-            rdkm = xyz2mol(atomic_numbers, coords, charge=charge)[0]
-        except (Exception, ValueError, IndexError):
-            rdkm = xyz2mol(atomic_numbers, coords, charge=charge, use_huckel=True)[0]
-    except Exception as e:
-        raise SteamrollConversionError("xyz2mol conversion failed!") from e
+            rdkm = get_tmc_mol(xyz_file, charge)
+        except Exception as e:
+            raise SteamrollConversionError("xyz2mol_tm conversion failed") from e
+        finally:
+            os.unlink(xyz_file)
+        if rdkm is None:
+            raise SteamrollConversionError("xyz2mol_tm returned no molecule")
+        return Chem.AddHs(rdkm)  # type: ignore [return-value]
+
+    if rdkm is None:
+        # xyz2mol failed for a non-TM molecule (e.g. wrong charge, unsupported
+        # element). Fall back to a geometry-only mol via obabel connectivity.
+        try:
+            _, rdkm = xyz2ac_obabel(atomic_numbers, coords)
+        except Exception as e:
+            raise SteamrollConversionError("xyz2mol conversion failed") from e
+        return rdkm  # type: ignore [return-value]
 
     return remove_hydrogens(rdkm) if remove_Hs else rdkm
+
+
+ATOMIC_NUMBERS = {
+    "X": 0,
+    "H": 1,
+    "He": 2,
+    "Li": 3,
+    "Be": 4,
+    "B": 5,
+    "C": 6,
+    "N": 7,
+    "O": 8,
+    "F": 9,
+    "Ne": 10,
+    "Na": 11,
+    "Mg": 12,
+    "Al": 13,
+    "Si": 14,
+    "P": 15,
+    "S": 16,
+    "Cl": 17,
+    "Ar": 18,
+    "K": 19,
+    "Ca": 20,
+    "Sc": 21,
+    "Ti": 22,
+    "V": 23,
+    "Cr": 24,
+    "Mn": 25,
+    "Fe": 26,
+    "Co": 27,
+    "Ni": 28,
+    "Cu": 29,
+    "Zn": 30,
+    "Ga": 31,
+    "Ge": 32,
+    "As": 33,
+    "Se": 34,
+    "Br": 35,
+    "Kr": 36,
+    "Rb": 37,
+    "Sr": 38,
+    "Y": 39,
+    "Zr": 40,
+    "Nb": 41,
+    "Mo": 42,
+    "Tc": 43,
+    "Ru": 44,
+    "Rh": 45,
+    "Pd": 46,
+    "Ag": 47,
+    "Cd": 48,
+    "In": 49,
+    "Sn": 50,
+    "Sb": 51,
+    "Te": 52,
+    "I": 53,
+    "Xe": 54,
+    "Cs": 55,
+    "Ba": 56,
+    "La": 57,
+    "Ce": 58,
+    "Pr": 59,
+    "Nd": 60,
+    "Pm": 61,
+    "Sm": 62,
+    "Eu": 63,
+    "Gd": 64,
+    "Tb": 65,
+    "Dy": 66,
+    "Ho": 67,
+    "Er": 68,
+    "Tm": 69,
+    "Yb": 70,
+    "Lu": 71,
+    "Hf": 72,
+    "Ta": 73,
+    "W": 74,
+    "Re": 75,
+    "Os": 76,
+    "Ir": 77,
+    "Pt": 78,
+    "Au": 79,
+    "Hg": 80,
+    "Tl": 81,
+    "Pb": 82,
+    "Bi": 83,
+    "Po": 84,
+    "At": 85,
+    "Rn": 86,
+    "Fr": 87,
+    "Ra": 88,
+    "Ac": 89,
+    "Th": 90,
+    "Pa": 91,
+    "U": 92,
+    "Np": 93,
+    "Pu": 94,
+    "Am": 95,
+    "Cm": 96,
+    "Bk": 97,
+    "Cf": 98,
+    "Es": 99,
+    "Fm": 100,
+    "Md": 101,
+    "No": 102,
+    "Lr": 103,
+    "Rf": 104,
+    "Db": 105,
+    "Sg": 106,
+    "Bh": 107,
+    "Hs": 108,
+    "Mt": 109,
+    "Ds": 110,
+    "Rg": 111,
+    "Cp": 112,
+    "Uut": 113,
+    "Uuq": 114,
+    "Uup": 115,
+    "Uuh": 116,
+    "Uus": 117,
+    "Uuo": 118,
+}

steamroll/xyz2mol.py → steamroll/xyz2mol/xyz2mol.py

@@ -84,7 +84,7 @@
 atomic_valence[17] = [1]
 atomic_valence[32] = [4]
 atomic_valence[35] = [1]
-atomic_valence[53] = [1]
+atomic_valence[53] = [1,3,5]
 
 atomic_valence_electrons = {}
 atomic_valence_electrons[1] = 1

steamroll/xyz2mol_tmc/LICENSE.txt

@@ -0,0 +1,21 @@
+MIT License
+
+Copyright (c) 2024 Jensen Group
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.