stjames 0.0.65__tar.gz → 0.0.67__tar.gz

{stjames-0.0.65/stjames.egg-info → stjames-0.0.67}/PKG-INFO

@@ -1,6 +1,6 @@
-Metadata-Version: 2.2
+Metadata-Version: 2.4
 Name: stjames
-Version: 0.0.65
+Version: 0.0.67
 Summary: standardized JSON atom/molecule encoding scheme
 Author-email: Corin Wagen <corin@rowansci.com>
 Project-URL: Homepage, https://github.com/rowansci/stjames
@@ -12,6 +12,7 @@ Requires-Dist: pydantic>=2.4
 Requires-Dist: numpy
 Requires-Dist: requests
 Requires-Dist: rdkit
+Dynamic: license-file
 
 # stjames
 

{stjames-0.0.65 → stjames-0.0.67}/pyproject.toml

@@ -1,6 +1,6 @@
 [project]
 name = "stjames"
-version = "0.0.65"
+version = "0.0.67"
 description = "standardized JSON atom/molecule encoding scheme"
 readme = "README.md"
 requires-python = ">=3.11"

{stjames-0.0.65 → stjames-0.0.67}/stjames/molecule.py

@@ -1,6 +1,6 @@
 import re
 from pathlib import Path
-from typing import Annotated, Iterable, Optional, Self, TypeAlias
+from typing import Annotated, Any, Iterable, Optional, Self, Sequence, TypeAlias, TypedDict, TypeVar
 
 import pydantic
 from pydantic import AfterValidator, NonNegativeInt, PositiveInt, ValidationError
@@ -9,6 +9,7 @@ from rdkit.Chem import AllChem
 
 from .atom import Atom
 from .base import Base, round_float, round_optional_float
+from .data import SYMBOL_ELEMENT
 from .periodic_cell import PeriodicCell
 from .types import (
     FloatPerAtom,
@@ -246,28 +247,102 @@ class Molecule(Base):
         return cls.from_extxyz_lines(extxyz.strip().splitlines(), charge=charge, multiplicity=multiplicity)
 
     @classmethod
-    def from_extxyz_lines(cls: type[Self], lines: Iterable[str], charge: int = 0, multiplicity: PositiveInt = 1) -> Self:
-        # ensure first line is number of atoms
-        lines = list(lines)
+    def from_extxyz_lines(
+        cls: type[Self],
+        lines: Iterable[str],
+        charge: int | None = None,
+        multiplicity: PositiveInt | None = None,
+        cell: PeriodicCell | None = None,
+    ) -> Self:
+        """
+        Parses an EXTXYZ file, extracting atom positions, forces (if present), and metadata.
+
+        Supports:
+        - Lattice vectors (cell information)
+        - Properties field (species, positions, forces, etc.)
+        - Other metadata like charge, multiplicity, energy, etc.
+
+        :param lines: Iterable of lines from an EXTXYZ file
+        :param charge: total charge of the molecule (default: 0 if not found)
+        :param multiplicity: spin multiplicity of the molecule (default: 1 if not found)
+        :param cell: PeriodicCell containing lattice vectors
+        :return: Molecule
+        :raises MoleculeReadError: if the file is not in the correct format
+        """
+        if not isinstance(lines, Sequence):
+            lines = list(lines)
+
+        # Ensure first line contains number of atoms
         if len(lines[0].split()) == 1:
             natoms = lines[0].strip()
-            if not natoms.isdigit() or (int(lines[0]) != len(lines) - 2):
-                raise MoleculeReadError(f"First line of EXTXYZ file should be the number of atoms, got: {lines[0]} != {len(lines) - 2}")
-            lines = lines[1:]
+            if not natoms.isdigit() or (int(natoms) != len(lines) - 2):
+                raise MoleculeReadError(f"First line should be number of atoms, got: {lines[0]} != {len(lines) - 2}")
+            data_line, *lines = lines[1:]
         else:
-            raise MoleculeReadError(f"First line of EXTXYZ should be only an int denoting number of atoms. Got {lines[0].split()}")
+            raise MoleculeReadError(f"First line should be an integer denoting atom count. Got {lines[0].split()}")
 
-        # ensure second line contains key-value pairs
-        if "=" not in lines[0]:
-            raise MoleculeReadError(f"Invalid property line, got {lines[0]}")
+        metadata = parse_extxyz_comment_line(data_line)
 
-        cell = parse_comment_line(lines[0])
-        lines = lines[1:]
+        T = TypeVar("T")
 
-        try:
-            return cls(atoms=[Atom.from_xyz(line) for line in lines], cell=cell, charge=charge, multiplicity=multiplicity)
-        except (ValueError, ValidationError) as e:
-            raise MoleculeReadError("Error reading molecule from extxyz") from e
+        def metadata_optional_get(key: str, value: T | None, default: T) -> T:
+            """Set key to default if not found in metadata"""
+            if value is None:
+                return metadata.get(key, default)  # type: ignore [return-value]
+
+            return value
+
+        charge = metadata_optional_get("total_charge", charge, 0)
+        multiplicity = metadata_optional_get("multiplicity", multiplicity, 1)
+        cell = cell or metadata.get("cell")
+        energy = metadata.get("energy", None)
+
+        force_idx = None
+        if properties := metadata.get("properties", "").split(":"):
+            if properties[0].lower() != "species":
+                raise MoleculeReadError(f"Invalid or missing 'Properties' field in EXTXYZ, got: {properties}")
+
+            # Identify column indices for position and force data
+            pos_idx = None
+            current_idx = 0  # Start after 'species:S'
+
+            while current_idx < len(properties):
+                if properties[current_idx].lower() == "pos" and properties[current_idx + 1].lower() == "r" and properties[current_idx + 2] == "3":
+                    pos_idx = current_idx
+                elif properties[current_idx].lower() == "forces" and properties[current_idx + 1].lower() == "r" and properties[current_idx + 2] == "3":
+                    force_idx = current_idx
+                current_idx += 3
+
+            if pos_idx is None:
+                raise MoleculeReadError("No position data ('pos:R:3') found in Properties field.")
+
+        def parse_line_atoms(line: str) -> Atom:
+            symbol, sx, sy, sz, *_ = line.split()
+            atomic_number = SYMBOL_ELEMENT[symbol.title()]
+            x, y, z = map(float, (sx, sy, sz))
+
+            return Atom(atomic_number=atomic_number, position=(x, y, z))
+
+        def parse_line_with_grad(line: str) -> tuple[Atom, Vector3D]:
+            symbol, sx, sy, sz, sgx, sgy, sgz, *_ = line.split()
+            atomic_number = SYMBOL_ELEMENT[symbol.title()]
+            x, y, z = map(float, (sx, sy, sz))
+            gx, gy, gz = map(float, (sgx, sgy, sgz))
+
+            return (
+                Atom(atomic_number=atomic_number, position=(x, y, z)),
+                (-gx, -gy, -gz),
+            )
+
+        atoms: list[Atom]
+        gradients: list[Vector3D] | None
+        if force_idx is not None:
+            atoms, gradients = zip(*map(parse_line_with_grad, lines), strict=True)  # type: ignore [assignment]
+        else:
+            atoms = [parse_line_atoms(line) for line in lines]
+            gradients = None
+
+        return cls(atoms=atoms, cell=cell, charge=charge, multiplicity=multiplicity, energy=energy, gradient=gradients)
 
     @classmethod
     def from_rdkit(cls: type[Self], rdkm: RdkitMol, cid: int = 0) -> Self:
@@ -313,43 +388,62 @@ def _embed_rdkit_mol(rdkm: RdkitMol) -> RdkitMol:
     return rdkm
 
 
-def parse_comment_line(line: str) -> PeriodicCell:
-    """
-    currently only supporting lattice and porperites fields from comment line
-    modify in future to support other fields from comment from_xyz_lines
-    ex: name, mulitplicity, charge, etc.
+class EXTXYZMetadata(TypedDict, total=False):
+    properties: Any
+    total_charge: int
+    multiplicity: int
+    energy: float
+    cell: PeriodicCell
+
+
+def parse_extxyz_comment_line(line: str) -> EXTXYZMetadata:
     """
-    cell = None
+    Parse the comment line of an EXTXYZ file, extracting lattice, properties, and metadata.
+
+    Supports:
+    - Lattice vectors (cell information)
+    - Properties field (species, positions, forces, etc.)
+    - Other metadata fields like charge, multiplicity, energy, etc.
+
+    :param line: comment line from an EXTXYZ file
+    :return: parsed properties
+
+    >>> parse_extxyz_comment_line('Lattice="6.0 0.0 0.0 6.0 0.0 0.0 6.0 0.0 0.0"Properties=species:S:1:pos:R:3')
+    {'cell': PeriodicCell(lattice_vectors=((6.0, 0.0, 0.0), (6.0, 0.0, 0.0), (6.0, 0.0, 0.0)), is_periodic=(True, True, True), volume=0.0), 'properties': 'species:S:1:pos:R:3'}
+    """  # noqa: E501
+
     # Regular expression to match key="value", key='value', or key=value
     pattern = r"(\S+?=(?:\".*?\"|\'.*?\'|\S+))"
     pairs = re.findall(pattern, line)
 
-    prop_dict = {}
+    prop_dict: EXTXYZMetadata = {}
     for pair in pairs:
         key, value = pair.split("=", 1)
-        if key.lower() == "lattice":
-            value = value.strip("'\"").split()
-            if len(value) != 9:
-                raise MoleculeReadError(f"Lattice should have 9 entries got {len(value)}")
+        key = key.lower().strip()
+        value = value.strip("'\"")
+
+        if key == "lattice":
+            lattice_values = value.split()
+            if len(lattice_values) != 9:
+                raise MoleculeReadError(f"Lattice should have 9 entries, got {len(lattice_values)}")
 
-            # Convert the value to a 3x3 tuple of tuples of floats
             try:
-                cell = tuple(tuple(map(float, value[i : i + 3])) for i in range(0, 9, 3))
+                cell = tuple(tuple(map(float, lattice_values[i : i + 3])) for i in range(0, 9, 3))
             except ValueError:
-                raise MoleculeReadError(f"Lattice should be floats, got {value}")
+                raise MoleculeReadError(f"Lattice should be floats, got {lattice_values}")
 
-            prop_dict[key] = value
+            prop_dict["cell"] = PeriodicCell(lattice_vectors=cell)
 
-        elif key.lower() == "properties":
-            if value.lower() != "species:s:1:pos:r:3":
-                raise MoleculeReadError(f"Only accepting properties of form species:S:1:pos:R:3, got {value}")
-            prop_dict[key] = value
-        else:
-            raise MoleculeReadError(f"Currently only accepting lattice and propery keys. Got {key}")
+        elif key == "properties":
+            prop_dict["properties"] = value
 
-    if cell is None:
-        raise MoleculeReadError("Lattice field is required but missing.")
+        elif key == "total_charge":
+            prop_dict["total_charge"] = int(value)
+        elif key == "multiplicity":
+            prop_dict["multiplicity"] = int(value)
+        elif key == "energy":
+            prop_dict["energy"] = float(value)
+        else:
+            prop_dict[key] = value  # type: ignore [literal-required]
 
-    if "properties" not in [key.lower() for key in prop_dict.keys()]:
-        raise MoleculeReadError(f"Property field is required, got keys {prop_dict.keys()}")
-    return PeriodicCell(lattice_vectors=cell)
+    return prop_dict

{stjames-0.0.65 → stjames-0.0.67}/stjames/pdb.py

@@ -1,3 +1,4 @@
+import re
 from datetime import date, datetime
 from pathlib import Path
 from typing import Any, Literal
@@ -276,7 +277,7 @@ def pdb_object_to_pdb_filestring(
                         atom=atom,
                         chain_id=this_chain_id,
                         res_name=residue.name,
-                        res_num=int(_residue_id[2:]),
+                        res_num=_residue_id[2:],
                         alt_loc=atom.alt_loc or "",
                     )
                     pdb_lines.append(line)
@@ -286,12 +287,12 @@ def pdb_object_to_pdb_filestring(
                             atom=atom,
                             chain_id=this_chain_id,
                             res_name=residue.name,
-                            res_num=int(_residue_id[2:]),
+                            res_num=_residue_id[2:],
                             alt_loc=atom.alt_loc or "",
                         )
                         pdb_lines.append(line)
 
-            pdb_lines.append(f"TER   {_atom_id + 1:>5}      {residue.name:>3} {this_chain_id}{int(_residue_id[2:]):>4}")
+            pdb_lines.append(f"TER   {_atom_id + 1:>5}      {residue.name:>3} {this_chain_id}{_residue_id[2:]:>4}")
 
         # === 2) Non-polymers (e.g. ligands, ions) ===
         for _np_id, nonpoly in model.non_polymer.items():
@@ -308,7 +309,7 @@ def pdb_object_to_pdb_filestring(
                     atom=atom,
                     chain_id=chain_id_for_np,
                     res_name=nonpoly.name,
-                    res_num=int(_np_id[2:]),
+                    res_num=_np_id[2:],
                 )
                 pdb_lines.append(line)
                 if atom.anisotropy and atom.anisotropy != [0, 0, 0, 0, 0, 0]:
@@ -317,7 +318,7 @@ def pdb_object_to_pdb_filestring(
                         atom=atom,
                         chain_id=chain_id_for_np,
                         res_name=nonpoly.name,
-                        res_num=int(_np_id[2:]),
+                        res_num=_np_id[2:],
                     )
                     pdb_lines.append(line)
 
@@ -330,7 +331,7 @@ def pdb_object_to_pdb_filestring(
                     atom=atom,
                     chain_id=_w_id[0],  # Or you can use water.polymer if set
                     res_name="HOH",
-                    res_num=int(_w_id[2:]),  # or an incrementing value
+                    res_num=_w_id[2:],  # or an incrementing value
                 )
                 pdb_lines.append(line)
                 if atom.anisotropy and atom.anisotropy != [0, 0, 0, 0, 0, 0]:
@@ -339,7 +340,7 @@ def pdb_object_to_pdb_filestring(
                         atom=atom,
                         chain_id=_w_id[0],
                         res_name="HOH",
-                        res_num=int(_w_id[2:]),
+                        res_num=_w_id[2:],
                     )
                     pdb_lines.append(line)
 
@@ -357,7 +358,7 @@ def pdb_object_to_pdb_filestring(
                         atom=atom,
                         chain_id="B",
                         res_name="BRN",  # or branched_obj.get("name", "BRN")
-                        res_num=1,
+                        res_num="1",
                     )
                     pdb_lines.append(line)
                     if atom.anisotropy and atom.anisotropy != [0, 0, 0, 0, 0, 0]:
@@ -366,7 +367,7 @@ def pdb_object_to_pdb_filestring(
                             atom=atom,
                             chain_id="B",
                             res_name="BRN",
-                            res_num=1,
+                            res_num="1",
                         )
                         pdb_lines.append(line)
 
@@ -407,7 +408,7 @@ def _format_atom_line(
     atom: PDBAtom,
     chain_id: str,
     res_name: str,
-    res_num: int | None,
+    res_num: str | None,
     alt_loc: str = "",
 ) -> str:
     """
@@ -423,7 +424,15 @@ def _format_atom_line(
     alt_loc_char = alt_loc if alt_loc else " "
     residue_name = (res_name or "UNK")[:3]  # limit to 3 chars
     chain_char = (chain_id or "A")[:1]  # PDB chain ID is 1 char
-    residue_num = res_num if res_num is not None else 1
+    residue_num_str = "1"
+    insertion_code = " "
+    if res_num:
+        match = re.match(r"(\d+)([a-zA-Z]*)", res_num)
+        if match:
+            residue_num_str, insertion_code = match.groups()
+            insertion_code = insertion_code if insertion_code != "" else " "
+
+    residue_num = int(residue_num_str)
 
     # Format charge: PDB uses e.g. " 2-", " 1+" in columns 79-80
     # If your model stores charges differently, adapt as needed.
@@ -451,7 +460,8 @@ def _format_atom_line(
         f"{residue_name:>3}"  # residue name (columns 18-20)
         f" {chain_char}"  # chain ID (column 22)
         f"{residue_num:4d}"  # residue sequence number (columns 23-26)
-        f"    "  # columns 27-30 (insertion code plus spacing)
+        f"{insertion_code}"
+        f"   "  # columns 27-30 (spacing)
         f"{atom.x:8.3f}"  # x (columns 31-38)
         f"{atom.y:8.3f}"  # y (columns 39-46)
         f"{atom.z:8.3f}"  # z (columns 47-54)
@@ -469,7 +479,7 @@ def _format_anisou_line(
     atom: PDBAtom,
     chain_id: str,
     res_name: str,
-    res_num: int | None,
+    res_num: str | None,
     alt_loc: str = "",
 ) -> str:
     """
@@ -485,7 +495,15 @@ def _format_anisou_line(
     alt_loc_char = alt_loc if alt_loc else " "
     residue_name = (res_name or "UNK")[:3]  # limit to 3 chars
     chain_char = (chain_id or "A")[:1]  # PDB chain ID is 1 char
-    residue_num = res_num if res_num is not None else 1
+    residue_num_str = "1"
+    insertion_code = " "
+    if res_num:
+        match = re.match(r"(\d+)([a-zA-Z]*)", res_num)
+        if match:
+            residue_num_str, insertion_code = match.groups()
+            insertion_code = insertion_code if insertion_code != "" else " "
+
+    residue_num = int(residue_num_str)
 
     chg = ""
     if atom.charge and abs(atom.charge) > 0:
@@ -528,7 +546,8 @@ def _format_anisou_line(
         f"{residue_name:>3}"  # residue name (columns 18-20)
         f" {chain_char}"  # chain ID (column 22)
         f"{residue_num:4d}"  # residue sequence number (columns 23-26)
-        f"  "  # columns 27-28 (insertion code plus spacing)
+        f"{insertion_code}"
+        f" "  # columns 27-28 (plus spacing)
         f"{aniso_lines}"
         f"      "  # columns 70-76 (padding)
         f"{atom.element:>2}"  # element (columns 77-78)

{stjames-0.0.65 → stjames-0.0.67/stjames.egg-info}/PKG-INFO

@@ -1,6 +1,6 @@
-Metadata-Version: 2.2
+Metadata-Version: 2.4
 Name: stjames
-Version: 0.0.65
+Version: 0.0.67
 Summary: standardized JSON atom/molecule encoding scheme
 Author-email: Corin Wagen <corin@rowansci.com>
 Project-URL: Homepage, https://github.com/rowansci/stjames
@@ -12,6 +12,7 @@ Requires-Dist: pydantic>=2.4
 Requires-Dist: numpy
 Requires-Dist: requests
 Requires-Dist: rdkit
+Dynamic: license-file
 
 # stjames
 

stjames-0.0.67/tests/test_from_extxyz.py

@@ -0,0 +1,322 @@
+from pytest import mark, raises
+
+from stjames import Atom, Molecule, MoleculeReadError, PeriodicCell
+
+# Valid EXTXYZ without forces (only positions)
+valid_extxyz = """
+5
+Lattice="6.0 0.0 0.0 0.0 6.0 0.0 0.0 0.0 6.0" Properties=species:S:1:pos:R:3
+C        0.0        0.0        0.0
+H        0.0        0.0        1.0
+H        1.0        0.0        0.0
+H        0.0        1.0        0.0
+H        1.0        1.0        1.0
+"""
+
+# Valid EXTXYZ with forces: forces are provided after positions.
+# For each atom, the forces are given and the molecule's gradient should be -forces.
+valid_extxyz_with_forces_and_energy = """
+22
+Properties=species:S:1:pos:R:3:forces:R:3:MACE_forces:R:3 smiles="[H:13][C:5]([H:14])([H:15])[C:7]([H:18])([H:19])[C:6]([H:16])([H:17])[S:2][C:4]([H:11])([H:12])[S:1][C:3]([H:8])([H:9])[H:10].[H:21][O:20][H:22]" total_charge=0 energy=-29139.55729148458 config_type="DES370K Dimers" MACE_energy=-29139.53445598132 pbc="F F F"
+S        2.75637007       2.70758009       4.82925987       1.55959951      -0.22801913      -0.54136018       1.57411973      -0.23083920      -0.56575688
+S        2.84554004       0.22606000       3.09241009      -0.21334177      -1.76227773       0.33161567      -0.21053821      -1.76733183       0.31476973
+C        1.01258004       2.49340009       4.93010997      -1.31854381      -0.37388875      -0.24927582      -1.32686027      -0.41468579      -0.24419847
+C        3.17725992       1.94638002       3.18563008      -0.09910375       1.52775439      -0.55371287      -0.09844947       1.52902410      -0.49063227
+C        0.00000000       0.00000000       0.00000000       0.54047842      -1.02932160      -0.37462899       0.55420524      -1.04859973      -0.38165141
+C        2.22169995      -0.06399999       1.41622007      -0.74959058       0.13849016      -0.66947629      -0.74189889       0.14272211      -0.65926828
+C        0.72196996       0.27478000       1.31911993      -0.88825228       1.14448169       0.10462363      -0.88035930       1.15971257       0.11942591
+H        0.73436999       1.43289995       4.80946970       0.11871475       0.45471041       0.08255662       0.12983545       0.47803891       0.09119142
+H        0.46778000       3.08784985       4.17749977       0.24911941      -0.20360289       0.32966949       0.24533754      -0.20850576       0.33744960
+H        0.70124000       2.82674027       5.93438053       0.20534666      -0.13940533      -0.46775994       0.20706729      -0.12047003      -0.47116810
+H        2.59819007       2.49752998       2.41988992       0.29845053      -0.31965051       0.34195845       0.29323885      -0.33151445       0.32609726
+H        4.25116014       2.06114006       2.94268989      -0.62592601       0.53239934       0.63500463      -0.63988801       0.53433737       0.61779540
+H        0.01781000      -1.10166001      -0.05143000      -0.31652062       0.33261293      -0.62734778      -0.32052002       0.33247610      -0.62978105
+H        0.50296998       0.40217999      -0.89547998      -0.14484048      -0.10780390       0.42454441      -0.15022920      -0.10846825       0.42265847
+H       -1.05070996       0.33554000      -0.00612000       0.55084403      -0.10031390       0.18450139       0.55970312      -0.09816881       0.19243150
+H        2.77840995       0.53621000       0.67106002      -0.14551747      -0.35971650       0.43068238      -0.14826788      -0.34813759       0.42951233
+H        2.39210987      -1.13260996       1.18280005       0.04825265       0.56114332       0.26057253       0.04712810       0.55862479       0.26730085
+H        0.59988999       1.35992002       1.50082004       0.18014249      -0.45468505       0.36480505       0.17898520      -0.45518615       0.36105601
+H        0.10381000      -0.26278001       2.06366992       0.77321355       0.35561432       0.04327458       0.76235138       0.36555290       0.03043141
+O        5.42839002       0.27989000       7.42625999      -0.71867266       0.97644353       0.67783188      -0.72326306       0.98088507       0.67544292
+H        4.56538010       0.65290999       7.13586997       1.00844588      -0.37843304       0.30550308       0.99937753      -0.37383106       0.29632339
+H        5.64198017       0.76508999       8.25524997      -0.31126251      -0.56856677      -1.03720163      -0.31107513      -0.57563526      -1.03942973
+"""  # noqa: E501
+
+# Other invalid cases (these remain unchanged)
+incorrect_num_atoms = """
+6
+Lattice="6.0 0.0 0.0 0.0 6.0 0.0 0.0 0.0 6.0" Properties=species:S:1:pos:R:3
+C        0.0        0.0        0.0
+H        0.0        0.0        1.0
+H        1.0        0.0        0.0
+H        0.0        1.0        0.0
+H        1.0        1.0        1.0
+"""
+
+not_digit_num_atoms = """
+v
+Lattice="6.0 0.0 0.0 0.0 6.0 0.0 0.0 0.0 6.0" Properties=species:S:1:pos:R:3
+C        0.0        0.0        0.0
+H        0.0        0.0        1.0
+H        1.0        0.0        0.0
+H        0.0        1.0        0.0
+H        1.0        1.0        1.0
+"""
+
+many_num_atoms = """
+6 9
+Lattice="6.0 0.0 0.0 0.0 6.0 0.0 0.0 0.0 6.0" Properties=species:S:1:pos:R:3
+C        0.0        0.0        0.0
+H        0.0        0.0        1.0
+H        1.0        0.0        0.0
+H        0.0        1.0        0.0
+H        1.0        1.0        1.0
+"""
+
+no_num_atoms = """
+Lattice="6.0 0.0 0.0 0.0 6.0 0.0 0.0 0.0 6.0" Properties=species:S:1:pos:R:3
+C        0.0        0.0        0.0
+H        0.0        0.0        1.0
+H        1.0        0.0        0.0
+H        0.0        1.0        0.0
+H        1.0        1.0        1.0
+"""
+
+xyz_style = """
+5
+Comment
+C        0.0        0.0        0.0
+H        0.0        0.0        1.0
+H        1.0        0.0        0.0
+H        0.0        1.0        0.0
+H        1.0        1.0        1.0
+"""
+
+missing_properties = """
+5
+Lattice="6.0 0.0 0.0 0.0 6.0 0.0 0.0 0.0 6.0"
+C        0.0        0.0        0.0
+H        0.0        0.0        1.0
+H        1.0        0.0        0.0
+H        0.0        1.0        0.0
+H        1.0        1.0        1.0
+"""
+
+incorrect_properites = """
+5
+Lattice="6.0 0.0 0.0 0.0 6.0 0.0 0.0 0.0 6.0" Properties=species:S:1:pos:R:3foo:1
+C        0.0        0.0        0.0
+H        0.0        0.0        1.0
+H        1.0        0.0        0.0
+H        0.0        1.0        0.0
+H        1.0        1.0        1.0
+"""
+
+incorrect_lattice_extra = """
+5
+Lattice="6.0 0.0 0.0 0.0 6.0 0.0 0.0 0.0 6.0 3.14" Properties=species:S:1:pos:R:3
+C        0.0        0.0        0.0
+H        0.0        0.0        1.0
+H        1.0        0.0        0.0
+H        0.0        1.0        0.0
+H        1.0        1.0        1.0
+"""
+
+incorrect_lattice_equals = """
+5
+Lattice="6.0 0.0 =0.0 0.0 6.0 0.0 0.0 0.0 6.0" Properties=species:S:1:pos:R:3
+C        0.0        0.0        0.0
+H        0.0        0.0        1.0
+H        1.0        0.0        0.0
+H        0.0        1.0        0.0
+H        1.0        1.0        1.0
+"""
+
+incorrect_lattice_str = """
+5
+Lattice="6.0 0.0 0.0 hi 6.0 0.0 0.0 0.0 6.0" Properties=species:S:1:pos:R:3
+C        0.0        0.0        0.0
+H        0.0        0.0        1.0
+H        1.0        0.0        0.0
+H        0.0        1.0        0.0
+H        1.0        1.0        1.0
+"""
+
+incorrect_lattice_extra_string = """
+5
+Lattice="6.0 0.0 0.0 0.0 sup 6.0 0.0 0.0 0.0 6.0" Properties=species:S:1:pos:R:3
+C        0.0        0.0        0.0
+H        0.0        0.0        1.0
+H        1.0        0.0        0.0
+H        0.0        1.0        0.0
+H        1.0        1.0        1.0
+"""
+
+incorrect_lattice_single_quote = """
+5
+Lattice="6.0 0.0 0.0 0.0 6.0 '0.0 0.0 0.0 6.0" Properties=species:S:1:pos:R:3
+C        0.0        0.0        0.0
+H        0.0        0.0        1.0
+H        1.0        0.0        0.0
+H        0.0        1.0        0.0
+H        1.0        1.0        1.0
+"""
+
+incorrect_lattice_double_quote = """
+5
+Lattice="6.0 0.0 0.0 0.0 "6.0 0.0 0.0 0.0 6.0" Properties=species:S:1:pos:R:3
+C        0.0        0.0        0.0
+H        0.0        0.0        1.0
+H        1.0        0.0        0.0
+H        0.0        1.0        0.0
+H        1.0        1.0        1.0
+"""
+
+incorrect_lattice_double_single_quote = """
+5
+Lattice="6.0 0.0 0.0 0.0 '6.0 0.0 0.0 '0.0 6.0" Properties=species:S:1:pos:R:3
+C        0.0        0.0        0.0
+H        0.0        0.0        1.0
+H        1.0        0.0        0.0
+H        0.0        1.0        0.0
+H        1.0        1.0        1.0
+"""
+
+incorrect_lattice_double_double_quote = """
+5
+Lattice="6.0 0.0 "0.0 0.0 6.0 0.0 0.0 "0.0 6.0" Properties=species:S:1:pos:R:3
+C        0.0        0.0        0.0
+H        0.0        0.0        1.0
+H        1.0        0.0        0.0
+H        0.0        1.0        0.0
+H        1.0        1.0        1.0
+"""
+
+expected_cell = (
+    (6.0, 0.0, 0.0),
+    (0.0, 6.0, 0.0),
+    (0.0, 0.0, 6.0),
+)
+
+expected_atoms = [
+    Atom(atomic_number=6, position=(0.0, 0.0, 0.0)),  # C
+    Atom(atomic_number=1, position=(0.0, 0.0, 1.0)),  # H
+    Atom(atomic_number=1, position=(1.0, 0.0, 0.0)),  # H
+    Atom(atomic_number=1, position=(0.0, 1.0, 0.0)),  # H
+    Atom(atomic_number=1, position=(1.0, 1.0, 1.0)),  # H
+]
+
+expected_atoms_force_energy = [
+    Atom(atomic_number=16, position=(2.75637007, 2.70758009, 4.82925987)),  # S
+    Atom(atomic_number=16, position=(2.84554004, 0.22606000, 3.09241009)),  # S
+    Atom(atomic_number=6, position=(1.01258004, 2.49340009, 4.93010997)),  # C
+    Atom(atomic_number=6, position=(3.17725992, 1.94638002, 3.18563008)),  # C
+    Atom(atomic_number=6, position=(0.00000000, 0.00000000, 0.00000000)),  # C
+    Atom(atomic_number=6, position=(2.22169995, -0.06399999, 1.41622007)),  # C
+    Atom(atomic_number=6, position=(0.72196996, 0.27478000, 1.31911993)),  # C
+    Atom(atomic_number=1, position=(0.73436999, 1.43289995, 4.80946970)),  # H
+    Atom(atomic_number=1, position=(0.46778000, 3.08784985, 4.17749977)),  # H
+    Atom(atomic_number=1, position=(0.70124000, 2.82674027, 5.93438053)),  # H
+    Atom(atomic_number=1, position=(2.59819007, 2.49752998, 2.41988992)),  # H
+    Atom(atomic_number=1, position=(4.25116014, 2.06114006, 2.94268989)),  # H
+    Atom(atomic_number=1, position=(0.01781000, -1.10166001, -0.05143000)),  # H
+    Atom(atomic_number=1, position=(0.50296998, 0.40217999, -0.89547998)),  # H
+    Atom(atomic_number=1, position=(-1.05070996, 0.33554000, -0.00612000)),  # H
+    Atom(atomic_number=1, position=(2.77840995, 0.53621000, 0.67106002)),  # H
+    Atom(atomic_number=1, position=(2.39210987, -1.13260996, 1.18280005)),  # H
+    Atom(atomic_number=1, position=(0.59988999, 1.35992002, 1.50082004)),  # H
+    Atom(atomic_number=1, position=(0.10381000, -0.26278001, 2.06366992)),  # H
+    Atom(atomic_number=8, position=(5.42839002, 0.27989000, 7.42625999)),  # O
+    Atom(atomic_number=1, position=(4.56538010, 0.65290999, 7.13586997)),  # H
+    Atom(atomic_number=1, position=(5.64198017, 0.76508999, 8.25524997)),  # H
+]
+
+expected_gradient = [
+    (-1.55959951, 0.22801913, 0.54136018),
+    (0.21334177, 1.76227773, -0.33161567),
+    (1.31854381, 0.37388875, 0.24927582),
+    (0.09910375, -1.52775439, 0.55371287),
+    (-0.54047842, 1.02932160, 0.37462899),
+    (0.74959058, -0.13849016, 0.66947629),
+    (0.88825228, -1.14448169, -0.10462363),
+    (-0.11871475, -0.45471041, -0.08255662),
+    (-0.24911941, 0.20360289, -0.32966949),
+    (-0.20534666, 0.13940533, 0.46775994),
+    (-0.29845053, 0.31965051, -0.34195845),
+    (0.62592601, -0.53239934, -0.63500463),
+    (0.31652062, -0.33261293, 0.62734778),
+    (0.14484048, 0.10780390, -0.42454441),
+    (-0.55084403, 0.10031390, -0.18450139),
+    (0.14551747, 0.35971650, -0.43068238),
+    (-0.04825265, -0.56114332, -0.26057253),
+    (-0.18014249, 0.45468505, -0.36480505),
+    (-0.77321355, -0.35561432, -0.04327458),
+    (0.71867266, -0.97644353, -0.67783188),
+    (-1.00844588, 0.37843304, -0.30550308),
+    (0.31126251, 0.56856677, 1.03720163),
+]
+
+
+expected_molecule = Molecule(
+    charge=0,
+    multiplicity=1,
+    atoms=expected_atoms,
+    cell=PeriodicCell(lattice_vectors=expected_cell),
+    gradient=None,
+)
+
+expected_molecule_with_forces_and_energy = Molecule(
+    charge=0,
+    multiplicity=1,
+    atoms=expected_atoms_force_energy,
+    cell=None,
+    gradient=expected_gradient,
+    energy=-29139.55729148458,
+)
+
+
+def test_molecule_from_extxyz_valid() -> None:
+    """
+    Test a valid extxyz string (without forces).
+    """
+    molecule = Molecule.from_extxyz(valid_extxyz)
+    assert molecule == expected_molecule, f"Valid case failed:\nGot {molecule}\nExpected {expected_molecule}"
+
+
+def test_molecule_from_extxyz_valid_with_forces() -> None:
+    """
+    Test a valid extxyz string that includes forces.
+    The forces should be converted to gradients (as the negative of forces).
+    """
+    molecule = Molecule.from_extxyz(valid_extxyz_with_forces_and_energy)
+    assert molecule == expected_molecule_with_forces_and_energy, (
+        f"Valid forces case failed:\nGot {molecule}\nExpected {expected_molecule_with_forces_and_energy}"
+    )
+
+
+@mark.parametrize(
+    "invalid_extxyz",
+    [
+        incorrect_num_atoms,
+        no_num_atoms,
+        not_digit_num_atoms,
+        many_num_atoms,
+        xyz_style,
+        missing_properties,
+        incorrect_properites,
+        incorrect_lattice_extra,
+        incorrect_lattice_equals,
+        incorrect_lattice_str,
+        incorrect_lattice_extra_string,
+        incorrect_lattice_single_quote,
+        incorrect_lattice_double_quote,
+        incorrect_lattice_double_single_quote,
+        incorrect_lattice_double_double_quote,
+    ],
+)
+def test_molecule_from_extxyz_invalid(invalid_extxyz: str) -> None:
+    """
+    Test that invalid extxyz strings raise MoleculeReadError.
+    """
+    with raises(MoleculeReadError):
+        Molecule.from_extxyz(invalid_extxyz)

{stjames-0.0.65 → stjames-0.0.67}/tests/test_pdb.py

@@ -96,6 +96,21 @@ def test_from_pdb_to_pdb_1ema() -> None:
 
     assert pdb == pdb2
 
+def test_from_pdb_to_pdb_2hu4() -> None:
+    with open("tests/data/2HU4.pdb") as f:
+        data = f.read()
+    pdb = pdb_from_pdb_filestring(data)
+    filestring = pdb_object_to_pdb_filestring(pdb, header=True, source=True, keyword=True, crystallography=True)
+
+    pdb2 = pdb_from_pdb_filestring(filestring)
+
+    assert pdb.description == pdb2.description
+    assert pdb.experiment == pdb2.experiment
+    # not true but doesn't matter
+    print(pdb.geometry == pdb2.geometry)
+    assert pdb.models == pdb2.models
+    assert pdb.quality == pdb2.quality
+
 def mmcif_author_format_to_pdb_format(authors: list[str]) -> list[str]:
     return [f"{last.upper()}{first.upper()}" for first, last in
             (author.split(", ") for author in authors)]

stjames-0.0.65/tests/test_from_extxyz.py

@@ -1,231 +0,0 @@
-import pytest
-
-from stjames import Atom, Molecule, MoleculeReadError, PeriodicCell
-
-valid_extxyz = """
-5
-Lattice="6.0 0.0 0.0 0.0 6.0 0.0 0.0 0.0 6.0" Properties=species:S:1:pos:R:3
-C        0.0        0.0        0.0
-H        0.0        0.0        1.0
-H        1.0        0.0        0.0
-H        0.0        1.0        0.0
-H        1.0        1.0        1.0
-"""
-
-incorrect_num_atoms = """
-6
-Lattice="6.0 0.0 0.0 0.0 6.0 0.0 0.0 0.0 6.0" Properties=species:S:1:pos:R:3
-C        0.0        0.0        0.0
-H        0.0        0.0        1.0
-H        1.0        0.0        0.0
-H        0.0        1.0        0.0
-H        1.0        1.0        1.0
-"""
-
-not_digit_num_atoms = """
-v
-Lattice="6.0 0.0 0.0 0.0 6.0 0.0 0.0 0.0 6.0" Properties=species:S:1:pos:R:3
-C        0.0        0.0        0.0
-H        0.0        0.0        1.0
-H        1.0        0.0        0.0
-H        0.0        1.0        0.0
-H        1.0        1.0        1.0
-"""
-
-many_num_atoms = """
-6 9
-Lattice="6.0 0.0 0.0 0.0 6.0 0.0 0.0 0.0 6.0" Properties=species:S:1:pos:R:3
-C        0.0        0.0        0.0
-H        0.0        0.0        1.0
-H        1.0        0.0        0.0
-H        0.0        1.0        0.0
-H        1.0        1.0        1.0
-"""
-no_num_atoms = """
-Lattice="6.0 0.0 0.0 0.0 6.0 0.0 0.0 0.0 6.0" Properties=species:S:1:pos:R:3
-C        0.0        0.0        0.0
-H        0.0        0.0        1.0
-H        1.0        0.0        0.0
-H        0.0        1.0        0.0
-H        1.0        1.0        1.0
-"""
-
-xyz_style = """
-5
-Comment
-C        0.0        0.0        0.0
-H        0.0        0.0        1.0
-H        1.0        0.0        0.0
-H        0.0        1.0        0.0
-H        1.0        1.0        1.0
-"""
-
-missing_lattice = """
-5
-Properties=species:S:1:pos:R:3
-C        0.0        0.0        0.0
-H        0.0        0.0        1.0
-H        1.0        0.0        0.0
-H        0.0        1.0        0.0
-H        1.0        1.0        1.0
-"""
-
-missing_properties = """
-5
-Lattice="6.0 0.0 0.0 0.0 6.0 0.0 0.0 0.0 6.0"
-C        0.0        0.0        0.0
-H        0.0        0.0        1.0
-H        1.0        0.0        0.0
-H        0.0        1.0        0.0
-H        1.0        1.0        1.0
-"""
-
-incorrect_properites = """
-5
-Lattice="6.0 0.0 0.0 0.0 6.0 0.0 0.0 0.0 6.0" Properties=species:S:1:pos:R:3foo:1
-C        0.0        0.0        0.0
-H        0.0        0.0        1.0
-H        1.0        0.0        0.0
-H        0.0        1.0        0.0
-H        1.0        1.0        1.0
-"""
-
-incorrect_lattice_extra = """
-5
-Lattice="6.0 0.0 0.0 0.0 6.0 0.0 0.0 0.0 6.0 3.14" Properties=species:S:1:pos:R:3
-C        0.0        0.0        0.0
-H        0.0        0.0        1.0
-H        1.0        0.0        0.0
-H        0.0        1.0        0.0
-H        1.0        1.0        1.0
-"""
-
-incorrect_lattice_equals = """
-5
-Lattice="6.0 0.0 =0.0 0.0 6.0 0.0 0.0 0.0 6.0" Properties=species:S:1:pos:R:3
-C        0.0        0.0        0.0
-H        0.0        0.0        1.0
-H        1.0        0.0        0.0
-H        0.0        1.0        0.0
-H        1.0        1.0        1.0
-"""
-
-incorrect_lattice_str = """
-5
-Lattice="6.0 0.0 0.0 hi 6.0 0.0 0.0 0.0 6.0" Properties=species:S:1:pos:R:3
-C        0.0        0.0        0.0
-H        0.0        0.0        1.0
-H        1.0        0.0        0.0
-H        0.0        1.0        0.0
-H        1.0        1.0        1.0
-"""
-
-incorrect_lattice_extra_string = """
-5
-Lattice="6.0 0.0 0.0 0.0 sup 6.0 0.0 0.0 0.0 6.0" Properties=species:S:1:pos:R:3
-C        0.0        0.0        0.0
-H        0.0        0.0        1.0
-H        1.0        0.0        0.0
-H        0.0        1.0        0.0
-H        1.0        1.0        1.0
-"""
-
-
-incorrect_lattice_single_quote = """
-5
-Lattice="6.0 0.0 0.0 0.0 6.0 '0.0 0.0 0.0 6.0" Properties=species:S:1:pos:R:3
-C        0.0        0.0        0.0
-H        0.0        0.0        1.0
-H        1.0        0.0        0.0
-H        0.0        1.0        0.0
-H        1.0        1.0        1.0
-"""
-
-incorrect_lattice_double_quote = """
-5
-Lattice="6.0 0.0 0.0 0.0 "6.0 0.0 0.0 0.0 6.0" Properties=species:S:1:pos:R:3
-C        0.0        0.0        0.0
-H        0.0        0.0        1.0
-H        1.0        0.0        0.0
-H        0.0        1.0        0.0
-H        1.0        1.0        1.0
-"""
-
-incorrect_lattice_double_single_quote = """
-5
-Lattice="6.0 0.0 0.0 0.0 '6.0 0.0 0.0 '0.0 6.0" Properties=species:S:1:pos:R:3
-C        0.0        0.0        0.0
-H        0.0        0.0        1.0
-H        1.0        0.0        0.0
-H        0.0        1.0        0.0
-H        1.0        1.0        1.0
-"""
-
-incorrect_lattice_double_double_quote = """
-5
-Lattice="6.0 0.0 "0.0 0.0 6.0 0.0 0.0 "0.0 6.0" Properties=species:S:1:pos:R:3
-C        0.0        0.0        0.0
-H        0.0        0.0        1.0
-H        1.0        0.0        0.0
-H        0.0        1.0        0.0
-H        1.0        1.0        1.0
-"""
-
-
-expected_cell = (
-    (6.0, 0.0, 0.0),
-    (0.0, 6.0, 0.0),
-    (0.0, 0.0, 6.0),
-)
-
-expected_atoms = [
-    Atom(atomic_number=6, position=(0.0, 0.0, 0.0)),  # C
-    Atom(atomic_number=1, position=(0.0, 0.0, 1.0)),  # H
-    Atom(atomic_number=1, position=(1.0, 0.0, 0.0)),  # H
-    Atom(atomic_number=1, position=(0.0, 1.0, 0.0)),  # H
-    Atom(atomic_number=1, position=(1.0, 1.0, 1.0)),  # H
-]
-
-expected_molecule = Molecule(
-    charge=0,
-    multiplicity=1,
-    atoms=expected_atoms,
-    cell=PeriodicCell(lattice_vectors=expected_cell),
-)
-
-
-def test_molecule_from_extxyz_valid() -> None:
-    """
-    Test case for valid extxyz string.
-    """
-    molecule = Molecule.from_extxyz(valid_extxyz)
-    assert molecule == expected_molecule, f"Valid case failed: got {molecule}, expected {expected_molecule}"
-
-
-@pytest.mark.parametrize(
-    "invalid_extxyz",
-    [
-        incorrect_num_atoms,
-        no_num_atoms,
-        not_digit_num_atoms,
-        many_num_atoms,
-        xyz_style,
-        missing_lattice,
-        missing_properties,
-        incorrect_properites,
-        incorrect_lattice_extra,
-        incorrect_lattice_equals,
-        incorrect_lattice_str,
-        incorrect_lattice_extra_string,
-        incorrect_lattice_single_quote,
-        incorrect_lattice_double_quote,
-        incorrect_lattice_double_single_quote,
-        incorrect_lattice_double_double_quote,
-    ],
-)
-def test_molecule_from_extxyz_invalid(invalid_extxyz: str) -> None:
-    """
-    Test case for invalid extxyz strings, ensuring they raise MoleculeReadError.
-    """
-    with pytest.raises(MoleculeReadError):
-        Molecule.from_extxyz(invalid_extxyz)