pdb_fixer clean up

utils/pdbfixer-plugin/Dockerfile → utils/pre-process/structure-changes/pdbfixer-tool/Dockerfile

@@ -1,4 +1,4 @@
-# docker build -f Dockerfile -t mrbrandonwalker/pdbfixer .
+# docker build -f Dockerfile -t polusai/pdbfixer-tool:0.1.0 .
 
 FROM condaforge/mambaforge
 # pdbfixer not installable with poetry

utils/pre-process/structure-changes/pdbfixer-tool/build-docker.sh

@@ -0,0 +1,4 @@
+#!/bin/bash
+
+version=$(<VERSION)
+docker build . -t polusai/pdbfixer-tool:${version}

utils/pdbfixer-plugin/environment.yml → utils/pre-process/structure-changes/pdbfixer-tool/environment.yml

@@ -7,5 +7,6 @@ dependencies:
   - pdbfixer==1.9
   - ruamel.yaml==0.17.21
   - pytest==8.1.1
-  - cwltool==3.1.20240404144621
-  - cwl-utils==0.33
+  - pip
+  - pip:
+    - sophios=0.1.1

utils/pdbfixer-plugin/ict.yml → utils/pre-process/structure-changes/pdbfixer-tool/ict.yml

@@ -1,11 +1,12 @@
 specVersion: 0.1.0
 name: labshare/pdbfixer
 version: 0.1.0
-container: polusai/pdbfixer-plugin:0.1.0
+container: polusai/pdbfixer-tool:0.1.0
 entrypoint: ""
 title: pdbfixer
 description: Fix pdbfiles.
-author: Data Scientist ([email protected])
+author: Brandon Walker, Nazanin Donyapour
+contact: [email protected], [email protected]
 repository: https://github.com/labshare/mmtools
 documentation: https://ncats.nih.gov/preclinical/core/informatics
 citation:

utils/pdbfixer-plugin/pdb_fixer.cwl → utils/pre-process/structure-changes/pdbfixer-tool/pdb_fixer_0@1@0.cwl

@@ -12,7 +12,7 @@ baseCommand: ["python", "-m", "polus.mm.utils.pdbfixer"]
 
 hints:
   DockerRequirement:
-    dockerPull: mrbrandonwalker/pdbfixer
+    dockerPull: polusai/pdbfixer-tool@sha256:a44142a9b23b60950bdc2cb7d6c760f4216cc7f59dad0468f92ff87a976f3ab2
 
 inputs:
   input_pdb_path:

utils/pre-process/structure-changes/pdbfixer-tool/tests/test_pdbfixer.py

@@ -0,0 +1,71 @@
+"""Tests for pdbfixer."""
+from pathlib import Path
+
+from polus.mm.utils.pdbfixer.pdbfixer import runpdbfixer
+from sophios.api.pythonapi import Step
+from sophios.api.pythonapi import Workflow
+
+
+def test_pdbfixer() -> None:
+    """Test pdbfixer."""
+    add_atoms = "all"
+    add_residues = True
+    pdbid = ""
+    url = ""
+    replace_nonstandard = True
+    keep_heterogens = "all"
+    input_pdb_path = "1msn_protein.pdb"
+    input_helper_pdb_path = "1msn_protein.pdb"
+    input_pdb_path = str(Path(__file__).resolve().parent / Path(input_pdb_path))
+    input_helper_pdb_path = str(
+        Path(__file__).resolve().parent / Path(input_helper_pdb_path),
+    )
+    output_pdb_path = "test.pdb"
+    output_pdb_path = str(Path(__file__).resolve().parent / Path(output_pdb_path))
+
+    runpdbfixer(
+        input_pdb_path,
+        input_helper_pdb_path,
+        output_pdb_path,
+        add_atoms,
+        add_residues,
+        pdbid,
+        url,
+        replace_nonstandard,
+        keep_heterogens,
+    )
+
+    assert Path(output_pdb_path).exists()
+
+
+def test_cwl_pdb_fixer() -> None:
+    """Test the pdbfixer function in cwltool."""
+    cwl_file = Path("pdb_fixer_0@[email protected]")
+
+    # Create a Step instance
+    pdb_fixer_step = Step(clt_path=cwl_file)
+
+    # Define input paths and parameters
+    input_pdb_path = str(Path(__file__).resolve().parent / "1msn_protein.pdb")
+    input_helper_pdb_path = str(Path(__file__).resolve().parent / "1msn_protein.pdb")
+    output_pdb_path = "output.pdb"
+
+    # Assign inputs to the step
+    pdb_fixer_step.input_pdb_path = input_pdb_path
+    pdb_fixer_step.input_helper_pdb_path = input_helper_pdb_path
+    pdb_fixer_step.output_pdb_path = output_pdb_path
+
+    # Create a Workflow instance
+    steps = [pdb_fixer_step]
+    viz = Workflow(steps, "pdb_fixer")
+
+    # Run the workflow
+    viz.run()
+
+    # Check if the expected output file exists
+    outdir = Path("outdir")
+    files = list(outdir.rglob(output_pdb_path))
+
+    assert (
+        files
+    ), f"The file '{output_pdb_path}' does not exist in any subdirectory of '{outdir}'."