autodock_vina_rescore

utils/autodock-vina-rescore-plugin/.bumpversion.cfg

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+[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/autodock_vina_rescore/__init__.py]

utils/autodock-vina-rescore-plugin/.dockerignore

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+.venv
+out
+tests
+__pycache__

utils/autodock-vina-rescore-plugin/.gitattributes

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+*.pdb filter=lfs diff=lfs merge=lfs -text
+*.pdbqt filter=lfs diff=lfs merge=lfs -text

utils/autodock-vina-rescore-plugin/.gitignore

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+poetry.lock

utils/autodock-vina-rescore-plugin/CHANGELOG.md

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+# CHANGELOG
+
+## 0.1.0
+
+Initial release.

utils/autodock-vina-rescore-plugin/Dockerfile

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+FROM condaforge/miniforge3
+# NOT miniforge-pypy3 (The build process is incompatible with pypy)
+
+# RUN conda install -c conda-forge vina
+
+RUN apt-get update && apt-get install -y git
+RUN git clone https://github.com/ccsb-scripps/AutoDock-Vina.git
+
+# Prevent being prompted for geographical region
+ARG DEBIAN_FRONTEND=noninteractive
+
+# Build vina binary
+RUN apt-get update && apt-get install -y build-essential libboost-all-dev swig
+RUN cd AutoDock-Vina/build/linux/release && make
+# Since there is no make install, manually copy vina
+RUN cp AutoDock-Vina/build/linux/release/vina /usr/bin/
+
+# Build and install python bindings
+RUN conda install -c conda-forge numpy boost-cpp swig
+RUN cd AutoDock-Vina/build/python && python setup.py build install
+
+ADD Dockerfile .

utils/autodock-vina-rescore-plugin/README.md

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+# autodock_vina_rescore (0.1.0)
+
+Wrapper of the AutoDock Vina software.
+
+## Options
+
+This plugin takes     6     input arguments and 3 output argument:
+
+| Name          | Description             | I/O    | Type   | Default |
+|---------------|-------------------------|--------|--------|---------|
+| input_ligand_pdbqt_path | Path to the input PDBQT ligand, Type: string, File type: input, Accepted formats: pdbqt, Example file: https://github.com/bioexcel/biobb_vs/raw/master/biobb_vs/test/data/vina/vina_ligand.pdbqt | Input | File | File |
+| input_receptor_pdbqt_path | Path to the input PDBQT receptor, Type: string, File type: input, Accepted formats: pdbqt, Example file: https://github.com/bioexcel/biobb_vs/raw/master/biobb_vs/test/data/vina/vina_receptor.pdbqt | Input | File | File |
+| local_only | Do local search only | Input | boolean | boolean |
+| score_only | Do not do any conformational search; simply rescore. | Input | boolean | boolean |
+| output_ligand_pdbqt_path | Path to the output PDBQT ligand, Type: string, File type: output, Accepted formats: pdbqt, Example file: https://github.com/bioexcel/biobb_vs/raw/master/biobb_vs/test/reference/vina/ref_output_vina.pdbqt | Input | string | string |
+| output_log_path | Path to the log file, Type: string, File type: output, Accepted formats: log, Example file: https://github.com/bioexcel/biobb_vs/raw/master/biobb_vs/test/reference/vina/ref_output_vina.log | Input | string | string |
+| output_ligand_pdbqt_path | Path to the output PDBQT files | Output | {'type': 'array', 'items': 'File'} | {'type': 'array', 'items': 'File'} |
+| output_log_path | Path to the log file | Output | File | File |
+| docking_score | Estimated Free Energy of Binding | Output | float | float |

utils/autodock-vina-rescore-plugin/VERSION

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+0.1.0

utils/autodock-vina-rescore-plugin/autodock_vina_rescore_0@1@0.cwl

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+
+#!/usr/bin/env cwl-runner
+cwlVersion: v1.0
+
+# NOTE: This file is nearly identical to autodock_vina_batch with the primary difference that
+# --input_batch_pdbqt_path is replaced with --input_ligand_pdbqt_path.
+# (For no obvious reason, --score_only only works with --ligand, not --batch)
+
+class: CommandLineTool
+
+label: Wrapper of the AutoDock Vina software.
+
+doc: |-
+  This class performs docking of the ligand to a set of grids describing the target protein via the AutoDock Vina software.
+
+baseCommand: vina # NOTE: Only version >=1.2 supports --batch!
+arguments:
+- "--autobox"
+# NOTE: The documentation for --score_only claims "search space can be omitted" which is not quite correct;
+# if you omit --center_* and --size_* you get "ERROR: Grid box dimensions must be greater than 0 Angstrom."
+# However, adding --autobox works.
+
+hints:
+  DockerRequirement:
+    dockerPull: polusai/autodock-vina-tool@sha256:98e353a67fbe76c010647bc80e15c86bf1f1c34fef25f58a41ada1a831496114
+
+requirements:
+  InlineJavascriptRequirement: {}
+# InitialWorkDirRequirement is needed for --local_only, because vina writes out
+# the optimized geometry in the same directory as input_ligand_pdbqt_path,
+# which needs to be writeable.
+  InitialWorkDirRequirement:
+    listing:
+    - $(inputs.input_ligand_pdbqt_path)
+
+inputs:
+  input_ligand_pdbqt_path:
+    label: Path to the input PDBQT ligand
+    doc: |-
+      Path to the input PDBQT ligand
+      Type: string
+      File type: input
+      Accepted formats: pdbqt
+      Example file: https://github.com/bioexcel/biobb_vs/raw/master/biobb_vs/test/data/vina/vina_ligand.pdbqt
+    type: File
+    format: edam:format_1476
+    inputBinding:
+      position: 1
+      prefix: --ligand
+
+  input_receptor_pdbqt_path:
+    label: Path to the input PDBQT receptor
+    doc: |-
+      Path to the input PDBQT receptor
+      Type: string
+      File type: input
+      Accepted formats: pdbqt
+      Example file: https://github.com/bioexcel/biobb_vs/raw/master/biobb_vs/test/data/vina/vina_receptor.pdbqt
+    type: File
+    format: edam:format_1476
+    inputBinding:
+      position: 2
+      prefix: --receptor
+
+  local_only:
+    label: Do local search only
+    doc: Do local search only
+    type: boolean?
+    #format:
+    #- edam_format_2330 # textual format
+    inputBinding:
+      prefix: --local_only
+
+  score_only:
+    label: Do not do any conformational search; simply rescore.
+    doc: Do not do any conformational search; simply rescore.
+    type: boolean?
+    #format:
+    #- edam_format_2330 # textual format
+    inputBinding:
+      prefix: --score_only
+
+  output_ligand_pdbqt_path:
+    label: Path to the output PDBQT ligand
+    doc: |-
+      Path to the output PDBQT ligand
+      Type: string
+      File type: output
+      Accepted formats: pdbqt
+      Example file: https://github.com/bioexcel/biobb_vs/raw/master/biobb_vs/test/reference/vina/ref_output_vina.pdbqt
+    type: string?
+    format: edam:format_1476
+
+  output_log_path:
+    label: Path to the log file
+    doc: |-
+      Path to the log file
+      Type: string
+      File type: output
+      Accepted formats: log
+      Example file: https://github.com/bioexcel/biobb_vs/raw/master/biobb_vs/test/reference/vina/ref_output_vina.log
+    type: string
+    format: edam:format_2330
+    default: system.log
+
+outputs:
+  output_ligand_pdbqt_path:
+    label: Path to the output PDBQT files
+    doc: |-
+      Path to the output PDBQT files
+    #type: File[]
+    type:
+      type: array
+      items: File
+    outputBinding:
+      glob: ./*_out.pdbqt # Use ./* because leading *'s are reserved syntax for Yaml aliases.
+      outputEval: |
+        ${
+          if (self.length > 0) { // if --local_only
+            return self;
+          } else { // if --score_only
+            return [inputs.input_ligand_pdbqt_path]
+          }
+        }
+    format: edam:format_1476
+
+  output_log_path:
+    label: Path to the log file
+    doc: |-
+      Path to the log file
+    type: File
+    outputBinding:
+      glob: $(inputs.output_log_path)
+    format: edam:format_2330
+
+  docking_score:
+    label: Estimated Free Energy of Binding
+    doc: |-
+      Estimated Free Energy of Binding
+    type: float
+    outputBinding:
+      glob: $(inputs.output_log_path)
+      loadContents: true
+      outputEval: |
+        ${
+          var lines = self[0].contents.split("\n");
+          // The correct line should be of the form
+          // Estimated Free Energy of Binding   : -6.053 (kcal/mol) [=(1)+(2)+(3)+(4)]
+          var bfe_line = lines.filter(function(s) {return s.split(" ")[0] == "Estimated"})[0];
+          var docking_score_string = bfe_line.split(" ").filter(function(s) {return !isNaN(parseFloat(s))})[0];
+          var docking_score = parseFloat(docking_score_string);
+          return docking_score
+        }
+
+stdout: $(inputs.output_log_path)
+
+$namespaces:
+  edam: https://edamontology.org/
+
+$schemas:
+- https://raw.githubusercontent.com/edamontology/edamontology/master/EDAM_dev.owl

utils/autodock-vina-rescore-plugin/build-docker.sh

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+#!/bin/bash
+
+version=$(<VERSION)
+docker build . -t polusai/polusai/autodock-vina-tool:${version}

utils/autodock-vina-rescore-plugin/ict.yml

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+specVersion: "0.1.0"
+name: autodock_vina_rescore
+version: 0.1.0
+container: autodock-vina-rescore-plugin
+entrypoint:
+title: autodock_vina_rescore
+description: Wrapper of the AutoDock Vina software.
+author: Data Scientist
+contact: [email protected]
+repository:
+documentation:
+citation:
+
+inputs:
+  - name: input_ligand_pdbqt_path
+    required: true
+    description: Path to the input PDBQT ligand, Type string, File type input, Accepted formats pdbqt, Example file https//github.com/bioexcel/biobb_vs/raw/master/biobb_vs/test/data/vina/vina_ligand.pdbqt
+    type: File
+    format:
+      uri: edam:format_1476
+  - name: input_receptor_pdbqt_path
+    required: true
+    description: Path to the input PDBQT receptor, Type string, File type input, Accepted formats pdbqt, Example file https//github.com/bioexcel/biobb_vs/raw/master/biobb_vs/test/data/vina/vina_receptor.pdbqt
+    type: File
+    format:
+      uri: edam:format_1476
+  - name: local_only
+    required: true
+    description: Do local search only
+    type: boolean
+  - name: score_only
+    required: true
+    description: Do not do any conformational search; simply rescore.
+    type: boolean
+  - name: output_ligand_pdbqt_path
+    required: true
+    description: Path to the output PDBQT ligand, Type string, File type output, Accepted formats pdbqt, Example file https//github.com/bioexcel/biobb_vs/raw/master/biobb_vs/test/reference/vina/ref_output_vina.pdbqt
+    type: string
+    format:
+      uri: edam:format_1476
+  - name: output_log_path
+    required: true
+    description: Path to the log file, Type string, File type output, Accepted formats log, Example file https//github.com/bioexcel/biobb_vs/raw/master/biobb_vs/test/reference/vina/ref_output_vina.log
+    type: string
+    defaultValue: system.log
+    format:
+      uri: edam:format_2330
+outputs:
+  - name: output_ligand_pdbqt_path
+    required: true
+    description: Path to the output PDBQT files
+    type: {'type': 'array', 'items': 'File'}
+    format:
+      uri: edam:format_1476
+  - name: output_log_path
+    required: true
+    description: Path to the log file
+    type: File
+    format:
+      uri: edam:format_2330
+  - name: docking_score
+    required: true
+    description: Estimated Free Energy of Binding
+    type: float
+ui:
+  - key: inputs.input_ligand_pdbqt_path
+    title: "input_ligand_pdbqt_path: "
+    description: "Path to the input PDBQT ligand, Type string, File type input, Accepted formats pdbqt, Example file https//github.com/bioexcel/biobb_vs/raw/master/biobb_vs/test/data/vina/vina_ligand.pdbqt"
+    type: File
+  - key: inputs.input_receptor_pdbqt_path
+    title: "input_receptor_pdbqt_path: "
+    description: "Path to the input PDBQT receptor, Type string, File type input, Accepted formats pdbqt, Example file https//github.com/bioexcel/biobb_vs/raw/master/biobb_vs/test/data/vina/vina_receptor.pdbqt"
+    type: File
+  - key: inputs.local_only
+    title: "local_only: "
+    description: "Do local search only"
+    type: checkbox
+  - key: inputs.score_only
+    title: "score_only: "
+    description: "Do not do any conformational search; simply rescore."
+    type: checkbox
+  - key: inputs.output_ligand_pdbqt_path
+    title: "output_ligand_pdbqt_path: "
+    description: "Path to the output PDBQT ligand, Type string, File type output, Accepted formats pdbqt, Example file https//github.com/bioexcel/biobb_vs/raw/master/biobb_vs/test/reference/vina/ref_output_vina.pdbqt"
+    type: string
+  - key: inputs.output_log_path
+    title: "output_log_path: "
+    description: "Path to the log file, Type string, File type output, Accepted formats log, Example file https//github.com/bioexcel/biobb_vs/raw/master/biobb_vs/test/reference/vina/ref_output_vina.log"
+    type: string

utils/autodock-vina-rescore-plugin/pyproject.toml

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+[tool.poetry]
+name = "polus-mm-utils-autodock-vina-rescore"
+version = "0.1.0"
+description = "Wrapper of the AutoDock Vina software."
+authors = ["Data Scientist <[email protected]>"]
+readme = "README.md"
+
+[tool.poetry.dependencies]
+python = ">=3.9,<3.12"
+typer = "^0.7.0"
+cwl-utils = "0.33"
+cwltool = "3.1.20240404144621"
+
+[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/autodock-vina-rescore-plugin/tests/__init__.py

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+"""Tests for autodock_vina_rescore."""

utils/autodock-vina-rescore-plugin/tests/test_autodock_vina_rescore.py

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+"""Tests for autodock_vina_rescore."""
+from pathlib import Path
+
+from sophios.api.pythonapi import Step
+from sophios.api.pythonapi import Workflow
+
+
+def test_autodock_vina_rescore_cwl() -> None:
+    """Test autodock_vina_rescore CWL."""
+    cwl_file = Path("autodock_vina_rescore_0@1@0.cwl")
+
+    autodock_vina_rescore_step = Step(clt_path=cwl_file)
+
+    ligand_path = "ligand.pdbqt"
+    ligand_path = str(Path(__file__).resolve().parent / Path(ligand_path))
+    receptor_path = "receptor.pdbqt"
+    receptor_path = str(Path(__file__).resolve().parent / Path(receptor_path))
+
+    autodock_vina_rescore_step.input_ligand_pdbqt_path = ligand_path
+    autodock_vina_rescore_step.input_receptor_pdbqt_path = receptor_path
+    autodock_vina_rescore_step.score_only = True
+    autodock_vina_rescore_step.output_log_path = "vina_rescore_pdbind.log"
+
+    steps = [autodock_vina_rescore_step]
+    filename = "autodock_vina_rescore"
+    viz = Workflow(steps, filename)
+
+    viz.run()
+
+    # Check for the existence of the output file
+    outdir = Path("outdir")
+    assert any(
+        file.name == "autodock_vina_rescore" for file in outdir.rglob("*")
+    ), "The file autodock_vina_rescore was not found."