obmin

utils/.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

utils/pre-process/minimize/obmin-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/obmin/__init__.py]

utils/pre-process/minimize/obmin-tool/.dockerignore

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+.venv
+out
+tests
+__pycache__

utils/pre-process/minimize/obmin-tool/.gitignore

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+poetry.lock

utils/pre-process/minimize/obmin-tool/CHANGELOG.md

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

utils/pre-process/minimize/obmin-tool/Dockerfile

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+# docker build -f Dockerfile -t mrbrandonwalker/openbabel-tool .
+FROM condaforge/mambaforge
+# NOT mambaforge-pypy3 (openbabel is incompatible with pypy)
+RUN mamba install -c conda-forge openbabel

utils/pre-process/minimize/obmin-tool/README.md

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+# obmin (0.1.0)
+
+Minimize a molecule using Open Babel
+
+## Options
+
+This plugin takes 3 input arguments and 1 output argument:
+
+| Name          | Description             | I/O    | Type   | Default |
+|---------------|-------------------------|--------|--------|---------|
+| script | Minimize script | Input | string | string |
+| input_mol2_path | Input mol2 file | Input | File | File |
+| output_mol2_path | Output mol2 filename | Input | string | string |
+| output_mol2_path | Output mol2 file | Output | File | File |

utils/pre-process/minimize/obmin-tool/VERSION

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+0.1.0

utils/pre-process/minimize/obmin-tool/ict.yml

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+specVersion: "0.1.0"
+name: obmin
+version: 0.1.0
+container: obmin-tool
+entrypoint:
+title: obmin
+description: Minimize a molecule using OpenBabel
+author: Brandon Walker, OpenBabel
+contact: [email protected]
+repository:
+documentation:
+citation:
+
+inputs:
+  - name: script
+    required: true
+    description:
+    type: string
+  - name: input_mol2_path
+    required: true
+    description:
+    type: File
+    format:
+      uri: edam:format_3816
+  - name: output_mol2_path
+    required: true
+    description:
+    type: string
+    defaultValue: system.mol2
+    format:
+      uri: edam:format_3816
+outputs:
+  - name: output_mol2_path
+    required: true
+    description:
+    type: File
+    format:
+      uri: edam:format_3816
+ui:
+  - key: inputs.script
+    title: "script: "
+    description: ""
+    type: string
+  - key: inputs.input_mol2_path
+    title: "input_mol2_path: "
+    description: ""
+    type: File
+  - key: inputs.output_mol2_path
+    title: "output_mol2_path: "
+    description: ""
+    type: string

utils/pre-process/minimize/obmin-tool/obmin.cwl

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+#!/usr/bin/env cwl-runner
+cwlVersion: v1.0
+
+class: CommandLineTool
+
+label: Run a Bash script
+
+doc: |
+  Run a Bash script
+
+baseCommand: bash
+
+hints:
+  DockerRequirement:
+    dockerPull: mrbrandonwalker/openbabel-tool
+
+inputs:
+  script:
+    type: string
+    inputBinding:
+      position: 1
+
+  input_mol2_path:
+    type: File
+    format: edam:format_3816
+    inputBinding:
+      position: 2
+
+  output_mol2_path:
+    type: string
+    format: edam:format_3816
+#    inputBinding:
+#      position: 3
+    default: system.mol2
+
+outputs:
+  output_mol2_path:
+    type: File
+    format: edam:format_3816 # 'Textual format'
+    streamable: true
+    outputBinding:
+      glob: $(inputs.output_mol2_path)
+
+stdout: $(inputs.output_mol2_path)
+
+$namespaces:
+  edam: https://edamontology.org/
+
+$schemas:
+- https://raw.githubusercontent.com/edamontology/edamontology/master/EDAM_dev.owl

utils/pre-process/minimize/obmin-tool/obminimize.sh

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+#!/bin/bash -e
+# -cg is the default minimization algorithm, but it falsely claims to reach
+# convergence on the second timestep. (same with -newton)
+# Use steepest descent because it's the only one that works!
+obminimize -sd -o mol2 "$1" > temp.mol2 # -xu is ignored here
+obabel temp.mol2 -o mol2 -O "$2" -xu

utils/pre-process/minimize/obmin-tool/pyproject.toml

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+[tool.poetry]
+name = "polus-mm-utils-obmin"
+version = "0.1.0"
+description = "Run a Bash script"
+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/pre-process/minimize/obmin-tool/tests/__init__.py

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+"""Tests for obmin."""

utils/pre-process/minimize/obmin-tool/tests/test_obmin.py

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+"""Tests for obmin."""
+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_obmin() -> None:
+    """Test obmin."""
+    cwl_file = Path("obmin.cwl")
+    input_to_props = parse_cwl_arguments(cwl_file)
+    input_to_props["script"] = "/obminimize.sh"
+    file_path_str = "benzene.mol2"
+    file_path = str(Path(__file__).resolve().parent / Path(file_path_str))
+    input_to_props["input_mol2_path"]["path"] = file_path
+    input_yaml_path = Path("obmin.yml")
+    create_input_yaml(input_to_props, input_yaml_path)
+    call_cwltool(cwl_file, input_yaml_path)
+    assert Path("system.mol2").exists()