smina

utils/docking/smina/smina-docking-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/smina_docking/__init__.py]

utils/docking/smina/smina-docking-tool/.dockerignore

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+.venv
+out
+tests
+__pycache__

utils/docking/smina/smina-docking-tool/.gitattributes

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+*.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/smina/smina-docking-tool/.gitignore

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+poetry.lock

utils/docking/smina/smina-docking-tool/CHANGELOG.md

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

utils/docking/smina/smina-docking-tool/Dockerfile

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+# docker build -f Dockerfile -t polusai/smina-tool .
+FROM condaforge/mambaforge-pypy3
+
+# Prevent being prompted for geographical region
+ARG DEBIAN_FRONTEND=noninteractive
+
+# Install essential packages
+RUN apt-get update && apt-get install -y git build-essential libboost-all-dev libopenbabel-dev libeigen3-dev cmake
+ENV PATH="${PATH}:/smina-code/build"
+
+# Download Smina code and compile binary
+## The URL (https://github.com/mwojcikowski/smina) is the Smina repo in GitHub and final updated in 2018
+## The URL (https://git.code.sf.net/p/smina/code) is the Smina repo in original SourceForge \
+## (https://sourceforge.net/p/smina/code/ci/master/tree/) and final updated in 2021.
+RUN git clone https://git.code.sf.net/p/smina/code smina-code && \
+    cd smina-code && mkdir build && cd build && cmake .. && make -j12
+
+RUN echo "alias smina=/smina-code/build/smina" >> ~/.bashrc
+ADD Dockerfile .

utils/docking/smina/smina-docking-tool/README.md

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+# smina_docking (0.1.0)
+
+Smina docking tool to perform protein-ligand docking
+
+## Options
+
+This plugin takes 6 input arguments and 2 output argument:
+
+| Name          | Description             | I/O    | Type   | Default |
+|---------------|-------------------------|--------|--------|---------|
+| receptor_file | Path to the input receptor file, Type: string?, File type: input, Accepted formats: pdb, pdbqt, sdf, mol, mol2 | Input | File | File |
+| ligand_file | Path to the input ligand file, Type: string?, File type: input, Accepted formats: pdb, pdbqt, sdf, mol, mol2 | Input | File | File |
+| ligand_box | Path to the input docking box file, Type: string?, File type: input, Accepted formats: pdb, pdbqt, sdf, mol, mol2 | Input | File | File |
+| scoring | Which scoring function to use, can be vina, vinardo, or a customized scoring function | Input | string | string |
+| output_dock_file | Output dock filename, contains docking poses | Input | string | string |
+| output_path | Output file name | Input | string | string |
+| output_dock_file | Output dock file, contains docking poses | Output | File | File |
+| output_path | Output file | Output | File | File |

utils/docking/smina/smina-docking-tool/VERSION

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+0.1.0

utils/docking/smina/smina-docking-tool/ict.yml

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+specVersion: "0.1.0"
+name: smina_docking
+version: 0.1.0
+container: smina-docking-tool
+entrypoint:
+title: smina_docking
+description: Smina docking tool to perform protein-ligand docking
+author: Brandon Walker, Nazanin Donyapour
+contact: [email protected], [email protected]
+repository:
+documentation:
+citation:
+
+inputs:
+  - name: receptor_file
+    required: true
+    description: Path to the input receptor file, Type string?, File type input, Accepted formats pdb, pdbqt, sdf, mol, mol2
+    type: File
+    format:
+      uri: edam:format_1476, edam:format_3814, edam:format_3815, edam:format_3816
+  - name: ligand_file
+    required: true
+    description: Path to the input ligand file, Type string?, File type input, Accepted formats pdb, pdbqt, sdf, mol, mol2
+    type: File
+    format:
+      uri: edam:format_1476, edam:format_3814, edam:format_3815, edam:format_3816
+  - name: ligand_box
+    required: true
+    description: Path to the input docking box file, Type string?, File type input, Accepted formats pdb, pdbqt, sdf, mol, mol2
+    type: File
+    format:
+      uri: edam:format_1476, edam:format_3814, edam:format_3815, edam:format_3816
+  - name: scoring
+    required: true
+    description:
+    type: string
+    defaultValue: vina
+  - name: output_dock_file
+    required: true
+    description:
+    type: string
+    defaultValue: docked.pdb
+    format:
+      uri: edam:format_1476
+  - name: output_path
+    required: true
+    description:
+    type: string
+outputs:
+  - name: output_dock_file
+    required: true
+    description:
+    type: File
+    format:
+      uri: edam:format_1476
+  - name: output_path
+    required: true
+    description:
+    type: File
+ui:
+  - key: inputs.receptor_file
+    title: "receptor_file: "
+    description: "Path to the input receptor file, Type string?, File type input, Accepted formats pdb, pdbqt, sdf, mol, mol2"
+    type: File
+  - key: inputs.ligand_file
+    title: "ligand_file: "
+    description: "Path to the input ligand file, Type string?, File type input, Accepted formats pdb, pdbqt, sdf, mol, mol2"
+    type: File
+  - key: inputs.ligand_box
+    title: "ligand_box: "
+    description: "Path to the input docking box file, Type string?, File type input, Accepted formats pdb, pdbqt, sdf, mol, mol2"
+    type: File
+  - key: inputs.scoring
+    title: "scoring: "
+    description: ""
+    type: string
+  - key: inputs.output_dock_file
+    title: "output_dock_file: "
+    description: ""
+    type: string
+  - key: inputs.output_path
+    title: "output_path: "
+    description: ""
+    type: string

utils/docking/smina/smina-docking-tool/pyproject.toml

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+[tool.poetry]
+name = "polus-mm-utils-smina-docking"
+version = "0.1.0"
+description = "Smina docking tool to perform protein-ligand docking"
+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/docking/smina/smina-docking-tool/smina_docking_0.1.0.cwl

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+#!/usr/bin/env cwl-runner
+
+cwlVersion: v1.0
+class: CommandLineTool
+
+label: Smina docking tool to perform protein-ligand docking
+
+baseCommand: ["smina"]
+
+hints:
+  DockerRequirement:
+    dockerPull: polusai/smina-tool@sha256:c75dab4e45a2881ada98b10679f3fde27ed9948a673192bcf0acf942417c8631
+
+requirements:
+  InlineJavascriptRequirement: {}
+  InitialWorkDirRequirement:
+    listing:
+      - $(inputs.ligand_file)
+
+inputs:
+
+  receptor_file:
+    label: receptor structure.
+    doc: |-
+      Path to the input receptor file
+      Type: string?
+      File type: input
+      Accepted formats: pdb, pdbqt, sdf, mol, mol2
+    type: File?
+    format: edam:format_1476, edam:format_3814, edam:format_3815, edam:format_3816
+    inputBinding:
+      position: 1
+      prefix: -r
+
+  ligand_file:
+    label: ligand structure.
+    doc: |-
+      Path to the input ligand file
+      Type: string?
+      File type: input
+      Accepted formats: pdb, pdbqt, sdf, mol, mol2
+    type: File?
+    format: edam:format_1476, edam:format_3814, edam:format_3815, edam:format_3816
+    inputBinding:
+      position: 2
+      prefix: -l
+
+  ligand_box:
+    label: 3D structure to define ligand box center and size
+    doc: |-
+      Path to the input docking box file
+      Type: string?
+      File type: input
+      Accepted formats: pdb, pdbqt, sdf, mol, mol2
+    type: File?
+    format: edam:format_1476, edam:format_3814, edam:format_3815, edam:format_3816
+    inputBinding:
+      position: 3
+      prefix: --autobox_ligand
+
+  scoring:
+    label: scoring function option, default is vina, options can be (vina, vinardo, or a customized scoring function)
+    type: string?
+    inputBinding:
+      position: 4
+      prefix: --scoring
+    default: "vina"
+
+  output_dock_file:
+    label: output docking poses.
+    type: string?
+    format: edam:format_1476
+    inputBinding:
+      position: 5
+      prefix: -o
+    default: "docked.pdb"
+
+# Is this still necessary?
+  output_path:
+    type: string
+
+outputs:
+
+  output_dock_file:
+    type: File
+    outputBinding:
+      glob: $(inputs.output_dock_file)
+    format: edam:format_1476
+
+  output_path:
+    type: File
+    outputBinding:
+      glob: $(inputs.output_path)
+
+
+stdout: $(inputs.output_path)
+
+$namespaces:
+  edam: https://edamontology.org/
+  cwltool: http://commonwl.org/cwltool#
+
+$schemas:
+- https://raw.githubusercontent.com/edamontology/edamontology/master/EDAM_dev.owl

utils/docking/smina/smina-docking-tool/tests/__init__.py

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+"""Tests for smina_docking."""

utils/docking/smina/smina-docking-tool/tests/test_smina_docking.py

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+"""Tests for smina_docking."""
+import sys
+from pathlib import Path
+
+current_dir = Path(__file__).resolve().parent
+target_dir = current_dir.parent.parent.parent / "cwl_utils"
+sys.path.append(str(target_dir))
+
+from cwl_utilities import call_cwltool  # noqa: E402
+from cwl_utilities import create_input_yaml  # noqa: E402
+from cwl_utilities import parse_cwl_arguments  # noqa: E402
+
+
+def test_smina_docking() -> None:
+    """Test smina_docking."""
+    cwl_file = Path("smina_docking_0.1.0.cwl")
+    input_to_props = parse_cwl_arguments(cwl_file)
+    file_path_str = "5umx_protein.pdb"
+    file_path = str(Path(__file__).resolve().parent / Path(file_path_str))
+    input_to_props["receptor_file"]["path"] = file_path
+    input_to_props["receptor_file"]["class"] = "File"
+    file_path_str = "5umx_ligand.sdf"
+    file_path = str(Path(__file__).resolve().parent / Path(file_path_str))
+    input_to_props["ligand_file"]["path"] = file_path
+    input_to_props["ligand_file"]["class"] = "File"
+    input_to_props["ligand_box"]["path"] = file_path
+    input_to_props["ligand_box"]["class"] = "File"
+    input_yaml_path = Path("smina_docking_0.1.0.yml")
+    create_input_yaml(input_to_props, input_yaml_path)
+    stdout, stderr = call_cwltool(cwl_file, input_yaml_path)
+    assert Path("string").exists()