stjames 0.0.42__tar.gz → 0.0.43__tar.gz

{stjames-0.0.42/stjames.egg-info → stjames-0.0.43}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: stjames
-Version: 0.0.42
+Version: 0.0.43
 Summary: standardized JSON atom/molecule encoding scheme
 Author-email: Corin Wagen <corin@rowansci.com>
 Project-URL: Homepage, https://github.com/rowansci/stjames

{stjames-0.0.42 → stjames-0.0.43}/pyproject.toml

@@ -1,6 +1,6 @@
 [project]
 name = "stjames"
-version = "0.0.42"
+version = "0.0.43"
 description = "standardized JSON atom/molecule encoding scheme"
 readme = "README.md"
 requires-python = ">=3.11"

{stjames-0.0.42 → stjames-0.0.43}/stjames/atom.py

@@ -60,7 +60,7 @@ class Atom(Base):
         Atom(1, [0.00000, 0.00000, 0.00000])
         """
         name, *xyz = xyz_line.split()
-        symbol = int(name) if name.isdigit() else SYMBOL_ELEMENT[name]
+        symbol = int(name) if name.isdigit() else SYMBOL_ELEMENT[name.title()]
         if not len(xyz) == 3:
             raise ValueError("XYZ file should have 3 coordinates per atom")
         return cls(atomic_number=symbol, position=xyz)

{stjames-0.0.42 → stjames-0.0.43}/stjames/molecule.py

@@ -1,8 +1,9 @@
+import re
 from pathlib import Path
 from typing import Iterable, Optional, Self
 
 import pydantic
-from pydantic import NonNegativeInt, PositiveInt
+from pydantic import NonNegativeInt, PositiveInt, ValidationError
 
 from .atom import Atom
 from .base import Base
@@ -135,6 +136,8 @@ class Molecule(Base):
             match format:
                 case "xyz":
                     return cls.from_xyz_lines(f.readlines(), charge=charge, multiplicity=multiplicity)
+                case "extxyz":
+                    return cls.from_extxyz_lines(f.readlines(), charge=charge, multiplicity=multiplicity)
                 case _:
                     raise ValueError(f"Unsupported {format=}")
 
@@ -161,7 +164,7 @@ class Molecule(Base):
 
         try:
             return cls(atoms=[Atom.from_xyz(line) for line in lines], charge=charge, multiplicity=multiplicity)
-        except Exception as e:
+        except (ValueError, ValidationError) as e:
             raise MoleculeReadError("Error reading molecule from xyz") from e
 
     def to_xyz(self, comment: str = "", out_file: Path | str | None = None) -> str:
@@ -190,3 +193,85 @@ class Molecule(Base):
                 f.write(out)
 
         return out
+
+    @classmethod
+    def from_extxyz(cls: type[Self], extxyz: str, charge: int = 0, multiplicity: PositiveInt = 1) -> Self:
+        r"""
+        Generate a Molecule from a EXTXYZ string. Currently only supporting Lattice and Properties fields.
+
+        >>> Molecule.from_extxyz('''
+        ... 2
+        ... 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
+        ... H 0 0 0
+        ... H 0 0 1
+        ... ''').cell.lattice_vectors
+        ((6.0, 0.0, 0.0), (6.0, 0.0, 0.0), (6.0, 0.0, 0.0))
+        """
+
+        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)
+        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:]
+        else:
+            raise MoleculeReadError(f"First line of EXTXYZ should be only an int denoting number of atoms. 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]}")
+
+        cell = parse_comment_line(lines[0])
+        lines = lines[1:]
+
+        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 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.
+    """
+    cell = None
+    # Regular expression to match key="value", key='value', or key=value
+    pattern = r"(\S+?=(?:\".*?\"|\'.*?\'|\S+))"
+    pairs = re.findall(pattern, line)
+
+    prop_dict = {}
+    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)}")
+
+            # 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))
+            except ValueError:
+                raise MoleculeReadError(f"Lattice should be floats, got {value}")
+
+            prop_dict[key] = value
+
+        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}")
+
+    if cell is None:
+        raise MoleculeReadError("Lattice field is required but missing.")
+
+    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)

{stjames-0.0.42 → stjames-0.0.43/stjames.egg-info}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: stjames
-Version: 0.0.42
+Version: 0.0.43
 Summary: standardized JSON atom/molecule encoding scheme
 Author-email: Corin Wagen <corin@rowansci.com>
 Project-URL: Homepage, https://github.com/rowansci/stjames

{stjames-0.0.42 → stjames-0.0.43}/stjames.egg-info/SOURCES.txt

@@ -53,4 +53,5 @@ stjames/workflows/scan.py
 stjames/workflows/spin_states.py
 stjames/workflows/tautomer.py
 stjames/workflows/workflow.py
+tests/test_from_extxyz.py
 tests/test_molecule.py

stjames-0.0.43/tests/test_from_extxyz.py

@@ -0,0 +1,231 @@
+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)