refactor pose_cluster_filter

utils/docking/diffdock/.gitattributes

@@ -0,0 +1,5 @@
+*.pdb filter=lfs diff=lfs merge=lfs -text
+*.pdbqt filter=lfs diff=lfs merge=lfs -text
+*.mol2 filter=lfs diff=lfs merge=lfs -text
+*.xlsx filter=lfs diff=lfs merge=lfs -text
+*.sdf filter=lfs diff=lfs merge=lfs -text

utils/pose-cluster-filter-plugin/Dockerfile → utils/docking/diffdock/pose-cluster-filter-tool/Dockerfile

@@ -1,5 +1,5 @@
 
-# docker build -f Dockerfile -t mrbrandonwalker/pose_cluster_filter_tool .
+# docker build -f Dockerfile -t polusai/pose-cluster-filter-tool .
 FROM condaforge/mambaforge
 
 ENV EXEC_DIR="/opt/executables"

utils/docking/diffdock/pose-cluster-filter-tool/build-docker.sh

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

utils/pose-cluster-filter-plugin/ict.yml → utils/docking/diffdock/pose-cluster-filter-tool/ict.yml

@@ -1,12 +1,12 @@
 specVersion: "0.1.0"
 name: pose_cluster_filter
 version: 0.1.0
-container: pose-cluster-filter-plugin
+container: pose-cluster-filter-tool
 entrypoint:
 title: pose_cluster_filter
 description: Cluster poses in protein and take max confident pose for each cluster
-author: Data Scientist
-contact: [email protected]
+author: Brandon Walker, Nazanin Donyapour
+contact: [email protected], [email protected]
 repository:
 documentation:
 citation:

utils/pose-cluster-filter-plugin/pose_cluster_filter.cwl → utils/docking/diffdock/pose-cluster-filter-tool/pose_cluster_filter_0.1.0.cwl

@@ -12,7 +12,7 @@ baseCommand: ["conda", "run", "-n", "project_env", "python", "-m", "polus.mm.uti
 
 hints:
   DockerRequirement:
-    dockerPull: mrbrandonwalker/pose_cluster_filter_tool
+    dockerPull: polusai/pose-cluster-filter-tool@sha256:f994fc02360bb22515b324600628b286f9daa7ddf91876fa1e44bc11728f6e9a
 
 requirements:
   InlineJavascriptRequirement: {}

utils/pose-cluster-filter-plugin/tests/test_pose_cluster_filter.py → utils/docking/diffdock/pose-cluster-filter-tool/tests/test_pose_cluster_filter.py

@@ -35,7 +35,7 @@ def test_pose_cluster_filter() -> None:
 
 def test_pose_cluster_filter_cwl() -> None:
     """Test the pose_cluster_filter CWL."""
-    cwl_file = Path("pose_cluster_filter.cwl")
+    cwl_file = Path("pose_cluster_filter_0.1.0.cwl")
     input_to_props = parse_cwl_arguments(cwl_file)
     predicted_poses = [
         "rank2_confidence0.35.sdf",
@@ -50,7 +50,7 @@ def test_pose_cluster_filter_cwl() -> None:
         file_dict_current["path"] = path_pose
         input_to_props["predicted_poses"].append(file_dict_current)
 
-    input_yaml_path = Path("pose_cluster_filter.yml")
+    input_yaml_path = Path("pose_cluster_filter_0.1.0.yml")
     create_input_yaml(input_to_props, input_yaml_path)
     stdout, stderr = call_cwltool(cwl_file, input_yaml_path)
     assert "success" in stderr