refactor acpype

utils/acpype-plugin/ict.yml → utils/molecular-dynamics/amber/acpype-tool/ict.yml

@@ -1,12 +1,12 @@
 specVersion: "0.1.0"
 name: acpype
 version: 0.1.0
-container: acpype-plugin
+container: acpype-tool
 entrypoint:
 title: acpype
 description: This class is a wrapper of Acpype tool for generation of topologies for GROMACS.
-author: Data Scientist
-contact: [email protected]
+author: Brandon Walker, Nazanin Donyapour
+contact: [email protected], [email protected]
 repository:
 documentation:
 citation:

utils/acpype-plugin/pyproject.toml → utils/molecular-dynamics/amber/acpype-tool/pyproject.toml

@@ -8,8 +8,7 @@ readme = "README.md"
 [tool.poetry.dependencies]
 python = ">=3.9,<3.12"
 typer = "^0.7.0"
-cwl-utils = "0.33"
-cwltool = "3.1.20240404144621"
+sophios = "0.1.1"
 
 [tool.poetry.group.dev.dependencies]
 bump2version = "^1.0.1"

utils/molecular-dynamics/amber/acpype-tool/tests/test_acpype.py

@@ -0,0 +1,38 @@
+"""Tests for acpype."""
+from pathlib import Path
+
+from sophios.api.pythonapi import Step
+from sophios.api.pythonapi import Workflow
+
+
+def test_acpype() -> None:
+    """Test acpype CWL."""
+    # Define paths and input properties
+    input_path = Path(__file__).resolve().parent / Path("5umx_ligand.sdf")
+    cwl_file_str = "acpype.cwl"
+    cwl_file = Path(__file__).resolve().parent.parent / Path(cwl_file_str)
+
+    # Create the CWL step
+    acpype_step = Step(clt_path=cwl_file)
+    acpype_step.input_path = str(input_path)
+    acpype_step.output_gro_path = "system.gro"
+    acpype_step.output_itp_path = "system.itp"
+    acpype_step.output_top_path = "system.top"
+    acpype_step.base_name = "ligand"
+    acpype_step.charge_method = "bcc"
+    acpype_step.output_pdb_path = "system.pdb"
+
+    # Create the workflow and run it
+    steps = [acpype_step]
+    filename = "acpype_workflow"
+    workflow = Workflow(steps, filename)
+    workflow.run()
+
+    # Define the output directory and pattern
+    outdir = Path("outdir")  # Output directory
+    output_files = list(outdir.rglob("ligand_GMX.gro"))
+
+    # Check if the expected output file exists
+    assert (
+        output_files
+    ), f"No file matching pattern 'ligand_GMX.gro' found in '{outdir}'."