rank diffdock poses

utils/docking/diffdock/rank-diffdock-poses-tool/.bumpversion.cfg

@@ -0,0 +1,29 @@
+[bumpversion]
+current_version = 0.1.0
+commit = False
+tag = False
+parse = (?P<major>\d+)\.(?P<minor>\d+)\.(?P<patch>\d+)(\-(?P<release>[a-z]+)(?P<dev>\d+))?
+serialize = 
+	{major}.{minor}.{patch}-{release}{dev}
+	{major}.{minor}.{patch}
+
+[bumpversion:part:release]
+optional_value = _
+first_value = dev
+values = 
+	dev
+	_
+
+[bumpversion:part:dev]
+
+[bumpversion:file:pyproject.toml]
+search = version = "{current_version}"
+replace = version = "{new_version}"
+
+[bumpversion:file:VERSION]
+
+[bumpversion:file:README.md]
+
+[bumpversion:file:plugin.json]
+
+[bumpversion:file:src/polus/mm/utils/rank_diffdock_poses/__init__.py]

utils/docking/diffdock/rank-diffdock-poses-tool/.dockerignore

@@ -0,0 +1,4 @@
+.venv
+out
+tests
+__pycache__

utils/docking/diffdock/rank-diffdock-poses-tool/.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/docking/diffdock/rank-diffdock-poses-tool/.gitignore

@@ -0,0 +1 @@
+poetry.lock

utils/docking/diffdock/rank-diffdock-poses-tool/CHANGELOG.md

@@ -0,0 +1,5 @@
+# CHANGELOG
+
+## 0.1.0
+
+Initial release.

utils/docking/diffdock/rank-diffdock-poses-tool/Dockerfile

@@ -0,0 +1,22 @@
+# docker build -f Dockerfile -t polusai/rank-diffdock-poses-tool .
+FROM python
+
+ENV EXEC_DIR="/opt/executables"
+ENV POLUS_LOG="INFO"
+RUN mkdir -p ${EXEC_DIR}
+
+
+# Work directory defined in the base container
+# WORKDIR ${EXEC_DIR}
+
+COPY pyproject.toml ${EXEC_DIR}
+COPY VERSION ${EXEC_DIR}
+COPY README.md ${EXEC_DIR}
+COPY CHANGELOG.md ${EXEC_DIR}
+
+COPY src ${EXEC_DIR}/src
+ADD Dockerfile .
+
+RUN pip3 install ${EXEC_DIR} --no-cache-dir
+
+CMD ["--help"]

utils/docking/diffdock/rank-diffdock-poses-tool/README.md

@@ -0,0 +1,14 @@
+# rank_diffdock_poses (0.1.0)
+
+DiffDock Diffusion pose ranking
+
+## Options
+
+This plugin takes     3     input arguments and 1 output argument:
+
+| Name          | Description             | I/O    | Type   | Default |
+|---------------|-------------------------|--------|--------|---------|
+| diffdock_poses |  | Input | File[] | File[] |
+| top_n_confident |  | Input | float | float |
+| top_percent_confidence |  | Input | float | float |
+| output_poses |  | Output | File[] | File[] |

utils/docking/diffdock/rank-diffdock-poses-tool/VERSION

@@ -0,0 +1 @@
+0.1.0

utils/docking/diffdock/rank-diffdock-poses-tool/build-docker.sh

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

utils/docking/diffdock/rank-diffdock-poses-tool/ict.yml

@@ -0,0 +1,50 @@
+specVersion: "0.1.0"
+name: rank_diffdock_poses
+version: 0.1.0
+container: rank-diffdock-poses-tool
+entrypoint:
+title: rank_diffdock_poses
+description: DiffDock Diffusion pose ranking
+author: Brandon Walker
+contact: [email protected]
+repository:
+documentation:
+citation:
+
+inputs:
+  - name: diffdock_poses
+    required: true
+    description:
+    type: File[]
+    format:
+      uri: edam:format_3814
+  - name: top_n_confident
+    required: true
+    description:
+    type: float
+    defaultValue: 1000
+  - name: top_percent_confidence
+    required: true
+    description:
+    type: float
+    defaultValue: 100
+outputs:
+  - name: output_poses
+    required: true
+    description:
+    type: File[]
+    format:
+      uri: edam:format_3814
+ui:
+  - key: inputs.diffdock_poses
+    title: "diffdock_poses: "
+    description: ""
+    type: File[]
+  - key: inputs.top_n_confident
+    title: "top_n_confident: "
+    description: ""
+    type: float
+  - key: inputs.top_percent_confidence
+    title: "top_percent_confidence: "
+    description: ""
+    type: float

utils/docking/diffdock/rank-diffdock-poses-tool/pyproject.toml

@@ -0,0 +1,29 @@
+[tool.poetry]
+name = "polus-mm-utils-rank-diffdock-poses"
+version = "0.1.0"
+description = "DiffDock Diffusion pose ranking"
+authors = ["Data Scientist <[email protected]>"]
+readme = "README.md"
+packages = [{include = "polus", from = "src"}]
+
+[tool.poetry.dependencies]
+python = ">=3.9,<3.12.5"
+sophios = "0.1.1"
+
+[tool.poetry.group.dev.dependencies]
+bump2version = "^1.0.1"
+pytest = "^7.4"
+pytest-sugar = "^0.9.6"
+pre-commit = "^3.2.1"
+black = "^23.3.0"
+mypy = "^1.1.1"
+ruff = "^0.0.270"
+
+[build-system]
+requires = ["poetry-core"]
+build-backend = "poetry.core.masonry.api"
+
+[tool.pytest.ini_options]
+pythonpath = [
+  "."
+]

utils/docking/diffdock/rank-diffdock-poses-tool/rank_diffdock_poses_0@1@0.cwl

@@ -0,0 +1,76 @@
+#!/usr/bin/env cwl-runner
+cwlVersion: v1.0
+
+class: CommandLineTool
+
+label: DiffDock Diffusion pose ranking
+
+doc: |-
+  DiffDock Diffusion pose ranking
+
+baseCommand: ["python", "-m", "polus.mm.utils.rank_diffdock_poses"]
+
+hints:
+  DockerRequirement:
+    dockerPull: polusai/rank-diffdock-poses-tool@sha256:ff03d4c4a4a908ea0b00ee79de05e633b5edf9e5067d71f62251cc034a6fee62
+
+requirements:
+  InlineJavascriptRequirement: {}
+
+inputs:
+
+  diffdock_poses:
+    label: diffdock poses
+    type:
+      type: array
+      items: File
+    inputBinding:
+      prefix: --diffdock_poses
+    format: edam:format_3814
+
+  top_n_confident:
+    type: float
+    label: top n most confident poses to keep
+    inputBinding:
+      prefix: --top_n_confident
+    # set default to essentially keep all poses
+    default: 1000
+
+  top_percent_confidence:
+    type: float
+    label: top percent of most confident poses to keep
+    inputBinding:
+      prefix: --top_percent_confidence
+    # set default to keep all poses
+    default: 100
+
+outputs:
+
+  output_poses:
+    type: File[]
+    label: top ranked poses
+    outputBinding:
+      glob: ranked_poses.txt # This determines what binds to self[0]
+      loadContents: true
+      outputEval: |
+        ${
+          // file looks like
+          // file_index
+          const lines = self[0].contents.split("\n").filter(line => line.trim() !== '');
+          const lst = [];
+          for (var i = 0; i < lines.length; i++) {
+            var splitLine = lines[i].split(" ");
+            // now find the File from inputs.diffdock_poses
+            var mol_idx = parseInt(splitLine[0]);
+            var file = inputs.diffdock_poses[mol_idx];
+            lst.push(file);
+          }
+          return lst;
+        }
+    format: edam:format_3814
+
+$namespaces:
+  edam: https://edamontology.org/
+
+$schemas:
+- https://raw.githubusercontent.com/edamontology/edamontology/master/EDAM_dev.owl

utils/docking/diffdock/rank-diffdock-poses-tool/src/polus/mm/utils/rank_diffdock_poses/__init__.py

@@ -0,0 +1,7 @@
+"""rank_diffdock_poses."""
+
+__version__ = "0.1.0"
+
+from polus.mm.utils.rank_diffdock_poses.rank_diffdock_poses import (  # noqa # pylint: disable=unused-import
+    rank_diffdock_poses,
+)

utils/docking/diffdock/rank-diffdock-poses-tool/src/polus/mm/utils/rank_diffdock_poses/__main__.py

@@ -0,0 +1,57 @@
+"""Package entrypoint for the rank_diffdock_poses package."""
+
+# Base packages
+import argparse
+import logging
+from os import environ
+from pathlib import Path
+
+from polus.mm.utils.rank_diffdock_poses.rank_diffdock_poses import rank_diffdock_poses
+
+logging.basicConfig(
+    format="%(asctime)s - %(name)-8s - %(levelname)-8s - %(message)s",
+    datefmt="%d-%b-%y %H:%M:%S",
+)
+POLUS_LOG = getattr(logging, environ.get("POLUS_LOG", "INFO"))
+logger = logging.getLogger("polus.mm.utils.rank_diffdock_poses.")
+logger.setLevel(POLUS_LOG)
+
+
+def main() -> None:
+    """rank_diffdock_poses."""
+    parser = argparse.ArgumentParser(description="rank_diffdock_poses.")
+    parser.add_argument(
+        "--diffdock_poses",
+        nargs="+",
+        type=Path,
+        required=True,
+        help="List of diffdock pose paths.",
+    )
+    parser.add_argument(
+        "--top_n_confident",
+        type=int,
+        required=True,
+        help="Top N confident poses.",
+    )
+    parser.add_argument(
+        "--top_percent_confidence",
+        type=int,
+        required=True,
+        help="Top percent confidence threshold.",
+    )
+
+    args = parser.parse_args()
+
+    logger.info(f"diffdock_poses: {args.diffdock_poses}")
+    logger.info(f"top_n_confident: {args.top_n_confident}")
+    logger.info(f"top_percent_confidence: {args.top_percent_confidence}")
+
+    rank_diffdock_poses(
+        diffdock_poses=args.diffdock_poses,
+        top_n_confident=args.top_n_confident,
+        top_percent_confidence=args.top_percent_confidence,
+    )
+
+
+if __name__ == "__main__":
+    main()

utils/docking/diffdock/rank-diffdock-poses-tool/src/polus/mm/utils/rank_diffdock_poses/rank_diffdock_poses.py

@@ -0,0 +1,57 @@
+"""This module ranks the poses from a DiffDock output based on confidence scores."""
+import re
+from pathlib import Path
+
+
+def rank_diffdock_poses(
+    diffdock_poses: list[Path],
+    top_n_confident: int,
+    top_percent_confidence: int,
+) -> None:
+    """rank_diffdock_poses.
+
+    Args:
+        diffdock_poses: List of poses from DiffDock output
+        top_n_confident: Number of poses to keep based on confidence score
+        top_percent_confidence: Percentage of poses to keep based on confidence score
+    Returns:
+        None
+    """
+    confidences = [parse_confidence(name) for name in diffdock_poses]
+    diffdock_poses_str = [str(name) for name in diffdock_poses]
+    confidence_to_pose: dict[float, Path] = dict(zip(confidences, diffdock_poses))
+    file_to_index: dict[str, int] = dict(
+        zip(diffdock_poses_str, range(len(diffdock_poses))),
+    )
+
+    # First filter by absolute value top_n_confident
+    # if user only wants to use top_percent_confidence,
+    # can set top_n_confident to trivially high number
+    # if user only wants to use top_n_confident,
+    # then can set top_percent_confidence to 100
+    sorted_list = sorted(confidence_to_pose.items(), reverse=True)
+    sorted_pose_list = [v for (k, v) in sorted_list]
+    poses = sorted_pose_list[:top_n_confident]
+    # Next filter by top percentage of confident poses
+    num_poses = int(top_percent_confidence * 0.01 * len(poses))
+    poses = poses[:num_poses]
+    # Write to ranked_filename
+    path = Path("ranked_poses.txt")
+    with path.open("w", encoding="utf-8") as file:
+        file.writelines([f"{file_to_index[str(string)]} \n" for string in poses])
+
+
+def parse_confidence(file_name: Path) -> float:
+    """This function returns the confidence score from a filename.
+
+    Filenames must follow the format 'rankX_confidenceY.mol',
+    where X is a positive integer and Y is a float.
+    This format is the default for DiffDock outputs.".
+
+    Args:
+        file_name (Path): The filename of output pose
+
+    Returns:
+        float: The confidence value from pose
+    """
+    return float(re.findall("rank[0-9]+_confidence(.*).sdf", str(file_name))[0])

utils/docking/diffdock/rank-diffdock-poses-tool/tests/__init__.py

@@ -0,0 +1 @@
+"""Tests for rank_diffdock_poses."""