Code to calculate lddt

foldingdiff/lddt.py

@@ -0,0 +1,32 @@
+"""
+Code for computing lDDT scores.
+"""
+
+import os, sys
+from pathlib import Path
+import subprocess
+import tempfile
+import json
+
+IMAGE = "2d07309e7a56"  # Docker image from https://git.scicore.unibas.ch/schwede/openstructure/container_registry/
+
+DOCKER_OST = Path(os.path.realpath(__file__)).parent.parent / "scripts/run_docker_ost"
+assert DOCKER_OST.exists(), f"Cannot find docker wrapper script {DOCKER_OST}"
+
+
+def lddt(query: Path, ref: Path) -> float:
+    """Compute the lDDT between query and reference structures."""
+    with tempfile.NamedTemporaryFile(dir=os.getcwd()) as outfile:
+        cmd = f"{DOCKER_OST} {IMAGE} compare-structures -m {query} -r {ref} --lddt -o {os.path.basename(outfile.name)}"
+        subprocess.call(cmd, shell=True)
+
+        # outfile.seek(0)
+        data = json.loads(outfile.read().decode("utf-8"))
+
+    if "lddt" in data:
+        return data["lddt"]
+    return -1.0
+
+
+if __name__ == "__main__":
+    print(lddt(Path(sys.argv[1]), Path(sys.argv[2])))

scripts/run_docker_ost

@@ -0,0 +1,26 @@
+#!/bin/bash
+
+# end when error
+set -e
+
+image_name=$1
+script_path=$2
+
+if [[ ${#@} -lt 1 ]]; then
+    echo "Usage: run_docker_ost <IMAGE_NAME> [<SCRIPT_PATH>]"
+    exit 1
+fi
+
+if [[ -z ${script_path} ]]; then
+    docker run -ti --rm -v $(pwd):/home ${image_name}
+else
+    if [[ -e $script_path ]]; then
+        abspath=$(readlink -f $script_path)
+        dirpath=$(dirname $abspath)
+        name=$(basename $script_path)
+        docker run --rm -v ${dirpath}:/home ${image_name} /home/${name} ${@:3}
+    else
+        # it is maybe an action if it does not exist
+        docker run --rm -v $(pwd):/home ${image_name} ${script_path} ${@:3}
+    fi
+fi