stjames 0.0.75__tar.gz → 0.0.77__tar.gz

{stjames-0.0.75/stjames.egg-info → stjames-0.0.77}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: stjames
-Version: 0.0.75
+Version: 0.0.77
 Summary: standardized JSON atom/molecule encoding scheme
 Author-email: Corin Wagen <corin@rowansci.com>
 Project-URL: Homepage, https://github.com/rowansci/stjames

{stjames-0.0.75 → stjames-0.0.77}/pyproject.toml

@@ -1,6 +1,6 @@
 [project]
 name = "stjames"
-version = "0.0.75"
+version = "0.0.77"
 description = "standardized JSON atom/molecule encoding scheme"
 readme = "README.md"
 requires-python = ">=3.11"

{stjames-0.0.75 → stjames-0.0.77}/stjames/atomium_stjames/pdb.py

@@ -526,6 +526,25 @@ def add_atom_to_non_polymer(line: str, model: dict[Any, Any], res_id: str, aniso
         }
 
 
+def guess_element_from_name(atom_name: str) -> str | None:
+    atom_name = atom_name.strip()
+    if not atom_name:
+        return None
+
+    # Case 1: Atom name starts with a digit (e.g. '1HG1') → element is second character
+    if atom_name[0].isdigit() and len(atom_name) > 1:
+        return atom_name[1].upper()
+
+    # # Case 2: Atom name starts with a letter
+    # if len(atom_name) >= 2 and atom_name[:2].isalpha():
+    #     possible = atom_name[:2].strip().capitalize()
+    #     # Check for common two-letter elements
+    #     if possible in {"Cl", "Br", "Fe", "Mg", "Zn", "Ca", "Na", "Cu", "Mn", "Co", "Ni"}:
+    #         return possible
+    # Fallback to first letter
+    return atom_name[0].upper()
+
+
 def atom_line_to_dict(line: str, aniso_dict: dict[Any, Any]) -> dict[str, Any]:
     """Converts an ATOM or HETATM record to an atom dictionary.
 
@@ -545,6 +564,8 @@ def atom_line_to_dict(line: str, aniso_dict: dict[Any, Any]) -> dict[str, Any]:
     if line[60:66].strip():
         a["bvalue"] = float(line[60:66].strip())
     a["element"] = line[76:78].strip() or None
+    if not a["element"]:
+        a["element"] = guess_element_from_name(a["name"])
     if line[78:80].strip():
         try:
             a["charge"] = int(line[78:80].strip())

{stjames-0.0.75 → stjames-0.0.77}/stjames/method.py

@@ -35,6 +35,7 @@ class Method(LowercaseStrEnum):
     MACE_MP_0B2_L = "mace_mp_0b2_l"
     OCP24_S = "ocp24_s"
     OCP24_L = "ocp24_l"
+    OMOL25_CONSERVING_S = "omol25_conserving_s"
     ORB_V2 = "orb_v2"
     ORB_V3_CONSERVATIVE_INF_OMAT = "orb_v3_conservative_inf_omat"
 
@@ -56,13 +57,22 @@ class Method(LowercaseStrEnum):
 
 
 PrepackagedNNPMethod = Literal[
-    Method.AIMNET2_WB97MD3, Method.OCP24_S, Method.OCP24_L, Method.RM1, Method.ORB_V3_CONSERVATIVE_INF_OMAT, Method.EGRET_1, Method.EGRET_1E, Method.EGRET_1T
+    Method.AIMNET2_WB97MD3,
+    Method.OCP24_S,
+    Method.OCP24_L,
+    Method.OMOL25_CONSERVING_S,
+    Method.RM1,
+    Method.ORB_V3_CONSERVATIVE_INF_OMAT,
+    Method.EGRET_1,
+    Method.EGRET_1E,
+    Method.EGRET_1T,
 ]
 
 PREPACKAGED_NNP_METHODS = [
     Method.AIMNET2_WB97MD3,
     Method.OCP24_S,
     Method.OCP24_L,
+    Method.OMOL25_CONSERVING_S,
     Method.RM1,
     Method.ORB_V3_CONSERVATIVE_INF_OMAT,
     Method.EGRET_1,

{stjames-0.0.75 → stjames-0.0.77}/stjames/molecule.py

@@ -2,6 +2,7 @@ import re
 from pathlib import Path
 from typing import Annotated, Any, Iterable, Optional, Self, Sequence, TypeAlias, TypedDict, TypeVar
 
+import numpy as np
 import pydantic
 from pydantic import AfterValidator, NonNegativeInt, PositiveInt, ValidationError
 from rdkit import Chem
@@ -75,15 +76,34 @@ class Molecule(Base):
     def __len__(self) -> int:
         return len(self.atoms)
 
-    def distance(self, atom1: PositiveInt, atom2: PositiveInt) -> float:
+    def distance(self, i: PositiveInt, j: PositiveInt) -> float:
         r"""
-        Get the distance between atoms.
+        Calculate the distance between atoms.
 
         >>> mol = Molecule.from_xyz("H 0 1 0\nH 0 0 1")
         >>> mol.distance(1, 2)
         1.4142135623730951
         """
-        return sum((q2 - q1) ** 2 for q1, q2 in zip(self.atoms[atom1 - 1].position, self.atoms[atom2 - 1].position)) ** 0.5  # type: ignore [no-any-return,unused-ignore]
+        return sum((q2 - q1) ** 2 for q1, q2 in zip(self.atoms[i - 1].position, self.atoms[j - 1].position)) ** 0.5  # type: ignore [no-any-return,unused-ignore]
+
+    def angle(self, i: PositiveInt, j: PositiveInt, k: PositiveInt, degrees: bool = True) -> float:
+        r"""
+        Calculate the angle between three atoms.
+
+        >>> Molecule.from_xyz("H 0 0 0\nO 0 0 1\nH 0 1 1").angle(0, 1, 2)
+        90.0
+        """
+
+        return angle(self.coordinates[i], self.coordinates[j], self.coordinates[k], degrees=degrees)
+
+    def dihedral(self, i: int, j: int, k: int, l: int, degrees: bool = True, positive_domain: bool = True) -> float:
+        r"""
+        Calculate the dihedral angle between four atoms.
+
+        >>> Molecule.from_xyz("H 0 0 0\nO 0 0 1\nO 0 1 1\nH 1 1 1").dihedral(0, 1, 2, 3)
+        270.0
+        """
+        return dihedral(self.coordinates[i], self.coordinates[j], self.coordinates[k], self.coordinates[l], degrees=degrees, positive_domain=positive_domain)
 
     @property
     def coordinates(self) -> Vector3DPerAtom:
@@ -447,3 +467,67 @@ def parse_extxyz_comment_line(line: str) -> EXTXYZMetadata:
             prop_dict[key] = value  # type: ignore [literal-required]
 
     return prop_dict
+
+
+def angle(p0: Sequence[float], p1: Sequence[float], p2: Sequence[float], degrees: bool = True) -> float:
+    """
+    Angle between three points.
+
+    :param i, j, k: positions of points
+    :param degrees: whether to return in degrees
+    :return: angle in radians or degrees
+    """
+    a0, a1, a2 = map(np.asarray, (p0, p1, p2))
+    u = a1 - a0
+    v = a1 - a2
+
+    nu = np.linalg.norm(u)
+    nv = np.linalg.norm(v)
+    cos_theta = np.dot(u, v) / (nu * nv)
+    cos_theta = np.clip(cos_theta, -1.0, 1.0)
+
+    ang = np.arccos(cos_theta)
+    if degrees:
+        return float(np.degrees(ang))
+    return float(ang)
+
+
+def dihedral(p0: Sequence[float], p1: Sequence[float], p2: Sequence[float], p3: Sequence[float], degrees: bool = True, positive_domain: bool = True) -> float:
+    """
+    Dihedral angle between four points.
+
+    :param p0, p1, p2, p3: points
+    :param degrees: whether to return in degrees
+    :param positive_domain: (0, 360] if True else (-180, 180]
+    :return: angle in degrees or radians (or nan if collinearities detected)
+
+    >>> a = [0, 0, 0]
+    >>> b = [0, 0, 1]
+    >>> c = [0, 1, 1]
+    >>> d1 = [0, 1, 2]
+    >>> d2 = [0.5, 1, 1.5]
+    >>> dihedral(a, b, c, d1)
+    180.0
+    >>> dihedral(a, b, c, d2, positive_domain=False)
+    -135.0
+    """
+    a0, a1, a2, a3 = map(np.asarray, (p0, p1, p2, p3))
+    b0 = a1 - a0
+    b1 = a2 - a1
+    b2 = a3 - a2
+
+    b1 = b1 / np.linalg.norm(b1)
+
+    v = b1 * np.dot(b0, b1) - b0
+    w = b2 - b1 * np.dot(b2, b1)
+
+    x = np.dot(v, w)
+    y = np.dot(np.cross(b1, v), w)
+    ang = np.arctan2(y, x)
+
+    if positive_domain and ang < 0:
+        ang += 2 * np.pi
+
+    if degrees:
+        return float(np.degrees(ang))
+    return float(ang)

{stjames-0.0.75 → stjames-0.0.77/stjames.egg-info}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: stjames
-Version: 0.0.75
+Version: 0.0.77
 Summary: standardized JSON atom/molecule encoding scheme
 Author-email: Corin Wagen <corin@rowansci.com>
 Project-URL: Homepage, https://github.com/rowansci/stjames