molify 0.2.4__tar.gz → 0.2.6__tar.gz

{molify-0.2.4 → molify-0.2.6}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: molify
-Version: 0.2.4
+Version: 0.2.6
 Summary: Molecular Structure Interface with RDKit, ASE, Packmol and NetworkX
 Project-URL: Repository, https://github.com/zincware/molify
 Project-URL: Releases, https://github.com/zincware/molify/releases
@@ -15,6 +15,7 @@ Requires-Dist: matplotlib>=3.10.1
 Requires-Dist: networkx>=3.4.2
 Requires-Dist: packmol>=21.1.2
 Requires-Dist: rdkit>=2024
+Requires-Dist: typer>=0.27.1
 Provides-Extra: vesin
 Requires-Dist: vesin>=0.3.7; extra == 'vesin'
 Description-Content-Type: text/markdown
@@ -58,6 +59,15 @@ print(atoms)
 >>> Atoms(symbols='OH2', pbc=False)
 ```
 
+## Command Line Interface
+
+Commands mirror the molify functions and write to standard output. `--format`
+takes any ASE format name or extension, defaulting to extxyz.
+
+```bash
+molify smiles2atoms CCO > etoh.xyz
+```
+
 ## Packmol Interface
 
 Given the molecular units, you can build periodic boxes with a given density

{molify-0.2.4 → molify-0.2.6}/README.md

@@ -37,6 +37,15 @@ print(atoms)
 >>> Atoms(symbols='OH2', pbc=False)
 ```
 
+## Command Line Interface
+
+Commands mirror the molify functions and write to standard output. `--format`
+takes any ASE format name or extension, defaulting to extxyz.
+
+```bash
+molify smiles2atoms CCO > etoh.xyz
+```
+
 ## Packmol Interface
 
 Given the molecular units, you can build periodic boxes with a given density

{molify-0.2.4 → molify-0.2.6}/docs/source/index.rst

@@ -100,6 +100,15 @@ The networkx.Graph representation can be obtained from either RDKit or ASE objec
    nh3_graph = molify.ase2networkx(nh3_atoms)
 
 
+**Command Line Interface**
+
+Commands mirror the molify functions and write to standard output. ``--format``
+takes any ASE format name or extension, defaulting to extxyz.
+
+.. code-block:: console
+
+   $ molify smiles2atoms CCO > etoh.xyz
+
 Advanced Features
 -----------------
 

{molify-0.2.4 → molify-0.2.6}/pyproject.toml

@@ -14,6 +14,7 @@ dependencies = [
     "networkx>=3.4.2",
     "packmol>=21.1.2",
     "rdkit>=2024",
+    "typer>=0.27.1",
 ]
 
 [dependency-groups]
@@ -32,6 +33,9 @@ docs = [
     "sphinxcontrib-mermaid>=1.0.0",
 ]
 
+[project.scripts]
+molify = "molify.cli:app"
+
 [project.optional-dependencies]
 
 vesin = [

molify-0.2.6/src/molify/__main__.py

@@ -0,0 +1,6 @@
+"""Entry point for ``python -m molify``."""
+
+from molify.cli import app
+
+if __name__ == "__main__":
+    app()

{molify-0.2.4 → molify-0.2.6}/src/molify/_version.py

@@ -18,7 +18,7 @@ version_tuple: tuple[int | str, ...]
 commit_id: str | None
 __commit_id__: str | None
 
-__version__ = version = '0.2.4'
-__version_tuple__ = version_tuple = (0, 2, 4)
+__version__ = version = '0.2.6'
+__version_tuple__ = version_tuple = (0, 2, 6)
 
 __commit_id__ = commit_id = None

molify-0.2.6/src/molify/cli.py

@@ -0,0 +1,97 @@
+"""Command line interface for molify."""
+
+import io
+import sys
+from typing import Annotated
+
+import ase.io
+import typer
+from ase.io.formats import extension2format
+
+from molify import __version__
+from molify import smiles2atoms as _smiles2atoms
+
+app = typer.Typer(
+    no_args_is_help=True,
+    add_completion=False,
+    pretty_exceptions_show_locals=False,
+)
+
+
+def _resolve_format(value: str) -> str:
+    """Map a format name or file extension onto an ASE format name.
+
+    Extensions resolve first, so ``XYZ`` selects ASE's ``extxyz`` writer, which
+    keeps the cell and the ``atoms.info`` payload such as the SMILES string and
+    the connectivity.
+
+    Parameters
+    ----------
+    value : str
+        Format name or file extension, in any capitalisation.
+
+    Returns
+    -------
+    str
+        The format name passed on to :func:`ase.io.write`.
+    """
+    key = value.strip().lower()
+    fmt = extension2format.get(key)
+    return fmt.name if fmt is not None else key
+
+
+def _version(value: bool) -> None:
+    """Print the molify version and exit."""
+    if value:
+        typer.echo(__version__)
+        raise typer.Exit
+
+
+@app.callback()
+def main(
+    version: Annotated[
+        bool,
+        typer.Option(
+            "--version",
+            callback=_version,
+            is_eager=True,
+            help="Show the molify version and exit.",
+        ),
+    ] = False,
+) -> None:
+    """Build molecular structures from the command line.
+
+    Each command mirrors the molify function of the same name and writes the
+    structure to standard output.
+    """
+
+
+@app.command()
+def smiles2atoms(
+    smiles: Annotated[
+        str, typer.Argument(help="SMILES string of the molecule, such as 'CCO'.")
+    ],
+    fmt: Annotated[
+        str,
+        typer.Option(
+            "--format",
+            "-f",
+            help=(
+                "Output format, given as an ASE format name or file extension."
+                " 'XYZ' selects extxyz, which keeps the SMILES string and the"
+                " connectivity."
+            ),
+        ),
+    ] = "extxyz",
+    seed: Annotated[
+        int, typer.Option(help="Random seed for conformer generation.")
+    ] = 42,
+) -> None:
+    """Convert a SMILES string into a single 3D structure on standard output.
+
+    Example: molify smiles2atoms CCO --format XYZ > etoh.xyz
+    """
+    atoms = _smiles2atoms(smiles, seed=seed)
+    with io.StringIO() as handle:
+        ase.io.write(handle, atoms, format=_resolve_format(fmt))
+        sys.stdout.write(handle.getvalue())

{molify-0.2.4 → molify-0.2.6}/src/molify/compress.py

@@ -18,7 +18,7 @@ def compress(
     atoms : ase.Atoms
         The Atoms object to compress.
     density : float
-        The target density in g/cm^3.
+        The target density in kg/m^3.
     freeze_molecules : bool
         If True, freeze the internal degrees of freedom of the molecules
         during compression, to prevent bond compression.

molify-0.2.6/tests/test_cli.py

@@ -0,0 +1,70 @@
+import io
+
+import ase.io
+import pytest
+from typer.testing import CliRunner
+
+from molify import __version__
+from molify.cli import app
+
+runner = CliRunner()
+
+
+def read_output(result) -> ase.Atoms:
+    """Read the structure the CLI wrote to standard output."""
+    return ase.io.read(io.StringIO(result.output), format="extxyz")
+
+
+def test_version():
+    result = runner.invoke(app, ["--version"])
+    assert result.exit_code == 0
+    assert result.output.strip() == __version__
+
+
+def test_no_args_shows_help():
+    result = runner.invoke(app, [])
+    assert "smiles2atoms" in result.output
+
+
+@pytest.mark.parametrize("fmt", ["XYZ", "xyz", "extxyz"])
+def test_smiles2atoms_format_aliases(fmt):
+    result = runner.invoke(app, ["smiles2atoms", "CCO", "--format", fmt])
+    assert result.exit_code == 0
+
+    lines = result.output.strip().split("\n")
+    assert lines[0] == "9"
+    assert "smiles=CCO" in lines[1]
+    assert "connectivity=" in lines[1]
+
+
+def test_smiles2atoms_defaults_to_extxyz():
+    result = runner.invoke(app, ["smiles2atoms", "CCO"])
+    assert result.exit_code == 0
+
+    atoms = read_output(result)
+    assert atoms.get_chemical_formula() == "C2H6O"
+    assert atoms.info["smiles"] == "CCO"
+    assert len(atoms.info["connectivity"]) == 8
+
+
+def test_smiles2atoms_pdb():
+    result = runner.invoke(app, ["smiles2atoms", "CCO", "-f", "pdb"])
+    assert result.exit_code == 0
+    assert result.output.startswith("MODEL")
+    assert ase.io.read(io.StringIO(result.output), format="proteindatabank")
+
+
+def test_smiles2atoms_seed_changes_positions():
+    positions = [
+        read_output(
+            runner.invoke(app, ["smiles2atoms", "CCO", "--seed", str(seed)])
+        ).get_positions()
+        for seed in (42, 1234)
+    ]
+    assert not (positions[0] == positions[1]).all()
+
+
+@pytest.mark.parametrize("fmt", ["zzz", "cif"])
+def test_smiles2atoms_ase_rejects_format(fmt):
+    result = runner.invoke(app, ["smiles2atoms", "CCO", "-f", fmt])
+    assert result.exit_code != 0

{molify-0.2.4 → molify-0.2.6}/uv.lock

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+]
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 [[package]]
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 source = { registry = "https://pypi.org/simple" }
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@@ -315,7 +324,7 @@ resolution-markers = [
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@@ -385,7 +394,7 @@ resolution-markers = [
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-    { name = "traitlets", marker = "python_full_version < '3.11'" },
-    { name = "typing-extensions", marker = "python_full_version < '3.11'" },
+    { name = "colorama", marker = "sys_platform == 'win32'" },
+    { name = "decorator" },
+    { name = "exceptiongroup" },
+    { name = "jedi" },
+    { name = "matplotlib-inline" },
+    { name = "pexpect", marker = "sys_platform != 'emscripten' and sys_platform != 'win32'" },
+    { name = "prompt-toolkit" },
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+    { name = "colorama", marker = "sys_platform == 'win32'" },
+    { name = "decorator" },
+    { name = "ipython-pygments-lexers" },
+    { name = "jedi" },
+    { name = "matplotlib-inline" },
+    { name = "pexpect", marker = "sys_platform != 'emscripten' and sys_platform != 'win32'" },
+    { name = "prompt-toolkit" },
+    { name = "pygments" },
+    { name = "stack-data" },
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@@ -1239,6 +1269,7 @@ dependencies = [
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     { name = "packmol" },
     { name = "rdkit" },
+    { name = "typer" },
 ]
 
 [package.optional-dependencies]
@@ -1270,6 +1301,7 @@ requires-dist = [
     { name = "networkx", specifier = ">=3.4.2" },
     { name = "packmol", specifier = ">=21.1.2" },
     { name = "rdkit", specifier = ">=2024" },
+    { name = "typer", specifier = ">=0.27.1" },
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