eagleplot 3.0.0__py3-none-any.whl

eagleplot/molecular/__init__.py

@@ -0,0 +1,21 @@
+"""Molecular data structures, parsers, and visualization helpers."""
+
+from .parsers import (
+    VibrationalMode,
+    VibrationalData,
+    parse_vibrations,
+    parse_gaussian_vibrations,
+    parse_orca_vibrations,
+    parse_molden_vibrations,
+    build_molecule_figure,
+)
+
+__all__ = [
+    "VibrationalMode",
+    "VibrationalData",
+    "parse_vibrations",
+    "parse_gaussian_vibrations",
+    "parse_orca_vibrations",
+    "parse_molden_vibrations",
+    "build_molecule_figure",
+]

eagleplot/molecular/atom_data.py

@@ -0,0 +1,287 @@
+"""Atomic property data for molecular visualization.
+
+Provides element colors (CPK scheme), symbols, van der Waals radii,
+and helper functions for element lookups by atomic number.
+"""
+
+BOHR_TO_ANGSTROM = 0.529177210903
+
+# CPK-style colors indexed by atomic number (index 0 = unknown/placeholder)
+_atom_colors_raw = [
+    "#000000",  # 0  unknown
+    "#FFFFFF",  # 1  H
+    "cyan",  # 2  He
+    "violet",  # 3  Li
+    "#B22222",  # 4  Be
+    "beige",  # 5  B
+    "#444444",  # 6  C
+    "blue",  # 7  N
+    "red",  # 8  O
+    "green",  # 9  F
+    "cyan",  # 10 Ne
+    "#FF1493",  # 11 Na
+    "#A52A2A",  # 12 Mg
+    "#800080",  # 13 Al
+    "#D2691E",  # 14 Si
+    "#228B22",  # 15 P
+    "yellow",  # 16 S
+    "green",  # 17 Cl
+    "cyan",  # 18 Ar
+    "#0000CD",  # 19 K
+    "#8B4513",  # 20 Ca
+    "#8FBC8F",  # 21 Sc
+    "#B8860B",  # 22 Ti
+    "#4682B4",  # 23 V
+    "#B22222",  # 24 Cr
+    "#2E8B57",  # 25 Mn
+    "#FFD700",  # 26 Fe
+    "#DAA520",  # 27 Co
+    "#A52A2A",  # 28 Ni
+    "#4169E1",  # 29 Cu
+    "#708090",  # 30 Zn
+    "#C0C0C0",  # 31 Ga
+    "#808000",  # 32 Ge
+    "#00FF00",  # 33 As
+    "#00CED1",  # 34 Se
+    "#0000FF",  # 35 Br
+    "cyan",  # 36 Kr
+    "#8A2BE2",  # 37 Rb
+    "#8B4513",  # 38 Sr
+    "#9400D3",  # 39 Y
+    "#FF4500",  # 40 Zr
+    "#4682B4",  # 41 Nb
+    "#B22222",  # 42 Mo
+    "#FFD700",  # 43 Tc
+    "#A52A2A",  # 44 Ru
+    "#228B22",  # 45 Rh
+    "#8B4513",  # 46 Pd
+    "#00CED1",  # 47 Ag
+    "#696969",  # 48 Cd
+    "#C0C0C0",  # 49 In
+    "#808000",  # 50 Sn
+    "#228B22",  # 51 Sb
+    "#D2691E",  # 52 Te
+    "#00FF00",  # 53 I
+    "cyan",  # 54 Xe
+    "#8A2BE2",  # 55 Cs
+    "#8B4513",  # 56 Ba
+    "#FF4500",  # 57 La
+]
+
+# Pad to 119 entries (elements up to Og, index 118)
+atom_colors: list[str] = _atom_colors_raw + ["#C0C0C0"] * (119 - len(_atom_colors_raw))
+
+# Element symbols indexed by atomic number (index 0 = unknown placeholder)
+atom_symbols: list[str] = [
+    "unk",
+    "H",
+    "He",
+    "Li",
+    "Be",
+    "B",
+    "C",
+    "N",
+    "O",
+    "F",
+    "Ne",
+    "Na",
+    "Mg",
+    "Al",
+    "Si",
+    "P",
+    "S",
+    "Cl",
+    "Ar",
+    "K",
+    "Ca",
+    "Sc",
+    "Ti",
+    "V",
+    "Cr",
+    "Mn",
+    "Fe",
+    "Co",
+    "Ni",
+    "Cu",
+    "Zn",
+    "Ga",
+    "Ge",
+    "As",
+    "Se",
+    "Br",
+    "Kr",
+    "Rb",
+    "Sr",
+    "Y",
+    "Zr",
+    "Nb",
+    "Mo",
+    "Tc",
+    "Ru",
+    "Rh",
+    "Pd",
+    "Ag",
+    "Cd",
+    "In",
+    "Sn",
+    "Sb",
+    "Te",
+    "I",
+    "Xe",
+    "Cs",
+    "Ba",
+    "La",
+    "Ce",
+    "Pr",
+    "Nd",
+    "Pm",
+    "Sm",
+    "Eu",
+    "Gd",
+    "Tb",
+    "Dy",
+    "Ho",
+    "Er",
+    "Tm",
+    "Yb",
+    "Lu",
+    "Hf",
+    "Ta",
+    "W",
+    "Re",
+    "Os",
+    "Ir",
+    "Pt",
+    "Au",
+    "Hg",
+    "Tl",
+    "Pb",
+    "Bi",
+    "Po",
+    "At",
+    "Rn",
+    "Fr",
+    "Ra",
+    "Ac",
+    "Th",
+    "Pa",
+    "U",
+    "Np",
+    "Pu",
+    "Am",
+    "Cm",
+    "Bk",
+    "Cf",
+    "Es",
+    "Fm",
+    "Md",
+    "No",
+    "Lr",
+    "Rf",
+    "Db",
+    "Sg",
+    "Bh",
+    "Hs",
+    "Mt",
+    "Ds",
+    "Rg",
+    "Cn",
+    "Nh",
+    "Fl",
+    "Mc",
+    "Lv",
+    "Ts",
+    "Og",
+]
+
+# Van der Waals radii in Angstroms indexed by atomic number (index 0 = fallback)
+_vdw_radii_raw = [
+    1.70,  # 0  unknown/fallback
+    1.20,  # 1  H
+    1.40,  # 2  He
+    1.82,  # 3  Li
+    1.53,  # 4  Be
+    1.92,  # 5  B
+    1.70,  # 6  C
+    1.55,  # 7  N
+    1.52,  # 8  O
+    1.47,  # 9  F
+    1.54,  # 10 Ne
+    2.27,  # 11 Na
+    1.73,  # 12 Mg
+    1.84,  # 13 Al
+    2.10,  # 14 Si
+    1.80,  # 15 P
+    1.80,  # 16 S
+    1.75,  # 17 Cl
+    1.88,  # 18 Ar
+    2.75,  # 19 K
+    2.31,  # 20 Ca
+    2.11,  # 21 Sc
+    2.00,  # 22 Ti
+    2.00,  # 23 V
+    2.00,  # 24 Cr
+    2.00,  # 25 Mn
+    2.00,  # 26 Fe
+    2.00,  # 27 Co
+    1.63,  # 28 Ni
+    1.40,  # 29 Cu
+    1.39,  # 30 Zn
+    1.87,  # 31 Ga
+    2.11,  # 32 Ge
+    1.85,  # 33 As
+    1.90,  # 34 Se
+    1.85,  # 35 Br
+    2.02,  # 36 Kr
+]
+
+# Pad to 119 entries with 2.00 Å as a reasonable default
+vdw_radii: list[float] = _vdw_radii_raw + [2.00] * (119 - len(_vdw_radii_raw))
+
+# Reverse lookup: element symbol → atomic number
+symbol_to_number: dict[str, int] = {sym: i for i, sym in enumerate(atom_symbols)}
+
+
+def get_atom_color(atomic_number: int) -> str:
+    """Return the CPK color string for an element.
+
+    Args:
+        atomic_number: Atomic number (1-based; 0 returns the unknown color).
+
+    Returns:
+        Hex color string or named color. Falls back to ``"#C0C0C0"`` (silver)
+        for out-of-range values.
+    """
+    if 0 <= atomic_number < len(atom_colors):
+        return atom_colors[atomic_number]
+    return "#C0C0C0"
+
+
+def get_atom_symbol(atomic_number: int) -> str:
+    """Return the element symbol for an atomic number.
+
+    Args:
+        atomic_number: Atomic number (1-based).
+
+    Returns:
+        Element symbol string (e.g. ``"C"``, ``"O"``).  Returns ``"?"``
+        for out-of-range values.
+    """
+    if 0 <= atomic_number < len(atom_symbols):
+        return atom_symbols[atomic_number]
+    return "?"
+
+
+def get_vdw_radius(atomic_number: int) -> float:
+    """Return the van der Waals radius (Å) for an element.
+
+    Args:
+        atomic_number: Atomic number (1-based).
+
+    Returns:
+        Van der Waals radius in Angstroms.  Returns ``1.70`` for
+        out-of-range values.
+    """
+    if 0 <= atomic_number < len(vdw_radii):
+        return vdw_radii[atomic_number]
+    return 1.70