autodock-vina-run

.gitattributes

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

utils/docking/autodock-vina/autodock-vina-run-tool/.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_run/__init__.py]

utils/docking/autodock-vina/autodock-vina-run-tool/.dockerignore

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+.venv
+out
+tests
+__pycache__

utils/docking/autodock-vina/autodock-vina-run-tool/.gitignore

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+poetry.lock

utils/docking/autodock-vina/autodock-vina-run-tool/CHANGELOG.md

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

utils/docking/autodock-vina/autodock-vina-run-tool/README.md

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+# autodock_vina_run (0.1.0)
+
+Wrapper of the AutoDock Vina software.
+
+## Options
+
+This plugin takes 6 input arguments and 2 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 |
+| input_box_path | Path to the PDB containig the residues belonging to the binding site, Type: string, File type: input, Accepted formats: pdb, Example file: https://github.com/bioexcel/biobb_vs/raw/master/biobb_vs/test/data/vina/vina_box.pdb | Input | File | File |
+| output_pdbqt_path | Path to the output PDBQT file, 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 |
+| config | Advanced configuration options for biobb_vs AutoDockVinaRun. This should be passed as a string containing a dict. The possible options to include here are listed under 'properties' in the biobb_vs AutoDockVinaRun documentation: https://biobb-vs.readthedocs.io/en/latest/vina.html#module-vina.autodock_vina_run | Input | string | string |
+| output_pdbqt_path | Path to the output PDBQT file | Output | File | File |
+| output_log_path | Path to the log file | Output | File | File |

utils/docking/autodock-vina/autodock-vina-run-tool/VERSION

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+0.1.0

utils/docking/autodock-vina/autodock-vina-run-tool/autodock_vina_run_0@1@0.cwl

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+#!/usr/bin/env cwl-runner
+cwlVersion: v1.0
+
+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: autodock_vina_run
+
+hints:
+  DockerRequirement:
+    dockerPull: quay.io/biocontainers/biobb_vs:4.0.0--pyhdfd78af_2
+
+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: --input_ligand_pdbqt_path
+
+  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: --input_receptor_pdbqt_path
+
+  input_box_path:
+    label: Path to the PDB containig the residues belonging to the binding site
+    doc: |-
+      Path to the PDB containig the residues belonging to the binding site
+      Type: string
+      File type: input
+      Accepted formats: pdb
+      Example file: https://github.com/bioexcel/biobb_vs/raw/master/biobb_vs/test/data/vina/vina_box.pdb
+    type: File
+    format: edam:format_1476
+    inputBinding:
+      position: 3
+      prefix: --input_box_path
+
+  output_pdbqt_path:
+    label: Path to the output PDBQT file
+    doc: |-
+      Path to the output PDBQT file
+      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
+    inputBinding:
+      position: 4
+      prefix: --output_pdbqt_path
+    default: system.pdbqt
+
+  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
+    inputBinding:
+      prefix: --output_log_path
+    default: system.log
+
+  config:
+    label: Advanced configuration options for biobb_vs AutoDockVinaRun
+    doc: |-
+      Advanced configuration options for biobb_vs AutoDockVinaRun. This should be passed as a string containing a dict. The possible options to include here are listed under 'properties' in the biobb_vs AutoDockVinaRun documentation: https://biobb-vs.readthedocs.io/en/latest/vina.html#module-vina.autodock_vina_run
+    type: string?
+    inputBinding:
+      prefix: --config
+
+outputs:
+  output_pdbqt_path:
+    label: Path to the output PDBQT file
+    doc: |-
+      Path to the output PDBQT file
+    type: File
+    outputBinding:
+      glob: $(inputs.output_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: $(inputs.output_log_path)
+    format: edam:format_2330
+
+$namespaces:
+  edam: https://edamontology.org/
+
+$schemas:
+- https://raw.githubusercontent.com/edamontology/edamontology/master/EDAM_dev.owl

utils/docking/autodock-vina/autodock-vina-run-tool/build-docker.sh

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

utils/docking/autodock-vina/autodock-vina-run-tool/ict.yml

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+specVersion: "0.1.0"
+name: autodock_vina_run
+version: 0.1.0
+container: autodock-vina-run-tool
+entrypoint:
+title: autodock_vina_run
+description: Wrapper of the AutoDock Vina software.
+author: Brandon Walker, Nazanin Donyapour
+contact: [email protected], [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: input_box_path
+    required: true
+    description: Path to the PDB containig the residues belonging to the binding site, Type string, File type input, Accepted formats pdb, Example file https//github.com/bioexcel/biobb_vs/raw/master/biobb_vs/test/data/vina/vina_box.pdb
+    type: File
+    format:
+      uri: edam:format_1476
+  - name: output_pdbqt_path
+    required: true
+    description: Path to the output PDBQT file, 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
+    defaultValue: system.pdbqt
+    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
+  - name: config
+    required: true
+    description: Advanced configuration options for biobb_vs AutoDockVinaRun. This should be passed as a string containing a dict. The possible options to include here are listed under 'properties' in the biobb_vs AutoDockVinaRun documentation https//biobb-vs.readthedocs.io/en/latest/vina.html#module-vina.autodock_vina_run
+    type: string
+outputs:
+  - name: output_pdbqt_path
+    required: true
+    description: Path to the output PDBQT file
+    type: 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
+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.input_box_path
+    title: "input_box_path: "
+    description: "Path to the PDB containig the residues belonging to the binding site, Type string, File type input, Accepted formats pdb, Example file https//github.com/bioexcel/biobb_vs/raw/master/biobb_vs/test/data/vina/vina_box.pdb"
+    type: File
+  - key: inputs.output_pdbqt_path
+    title: "output_pdbqt_path: "
+    description: "Path to the output PDBQT file, 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
+  - key: inputs.config
+    title: "config: "
+    description: "Advanced configuration options for biobb_vs AutoDockVinaRun. This should be passed as a string containing a dict. The possible options to include here are listed under 'properties' in the biobb_vs AutoDockVinaRun documentation https//biobb-vs.readthedocs.io/en/latest/vina.html#module-vina.autodock_vina_run"
+    type: string

utils/docking/autodock-vina/autodock-vina-run-tool/pyproject.toml

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+[tool.poetry]
+name = "polus-mm-utils-autodock-vina-run"
+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"
+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/autodock-vina/autodock-vina-run-tool/tests/__init__.py

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+"""Tests for autodock_vina_run."""

utils/docking/autodock-vina/autodock-vina-run-tool/tests/test_autodock_vina_run.py

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+"""Tests for autodock_vina_run."""
+from pathlib import Path
+
+from sophios.api.pythonapi import Step
+from sophios.api.pythonapi import Workflow
+
+
+def test_autodock_vina_run() -> None:
+    """Test autodock_vina_run."""
+    cwl_file = Path("autodock_vina_run_0@[email protected]")
+
+    # Create the step for the CWL file
+    autodock_vina_step = Step(clt_path=cwl_file)
+
+    # Set up the inputs for the step
+    ligand_file_path = str(Path(__file__).resolve().parent / "vina_ligand.pdbqt")
+    receptor_file_path = str(Path(__file__).resolve().parent / "vina_receptor.pdbqt")
+    box_file_path = str(Path(__file__).resolve().parent / "vina_box.pdb")
+
+    autodock_vina_step.input_ligand_pdbqt_path = ligand_file_path
+    autodock_vina_step.input_receptor_pdbqt_path = receptor_file_path
+    autodock_vina_step.input_box_path = box_file_path
+    autodock_vina_step.output_log_path = "system.log"
+    autodock_vina_step.output_pdbqt_path = "system.pdbqt"
+
+    # Define the workflow with the step
+    steps = [autodock_vina_step]
+    filename = "autodock_vina_workflow"
+    workflow = Workflow(steps, filename)
+
+    # Run the workflow
+    workflow.run()
+
+    # Check for the existence of the output file
+    outdir = Path("outdir")
+    assert any(
+        file.name == "system.pdbqt" for file in outdir.rglob("*")
+    ), "The file system.pdbqt was not found."