autodock-vina-filter plugin

utils/autodock-vina-filter-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_filter/__init__.py]

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

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+.venv
+out
+tests
+__pycache__

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

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

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

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+poetry.lock

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

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

utils/autodock-vina-filter-plugin/Dockerfile

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+FROM condaforge/mambaforge
+
+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}
+
+# Install needed packages here
+
+COPY src ${EXEC_DIR}/src
+
+RUN pip3 install ${EXEC_DIR} --no-cache-dir
+
+CMD ["--help"]

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

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+# autodock_vina_filter (0.1.0)
+
+Filters results of the AutoDock Vina software.
+
+## Options
+
+This plugin takes     11     input arguments and 5 output argument:
+
+| Name          | Description             | I/O    | Type   | Default |
+|---------------|-------------------------|--------|--------|---------|
+| input_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 | File | File |
+| input_log_paths | Path to the log files, 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 | File[] | File[] |
+| docking_score_cutoff | Cutoff threshold for filtering docking scores, Type: float | Input | float | float |
+| max_num_poses_per_ligand | Maximum number of poses per initial ligand, Type: int | Input | int | int |
+| max_num_poses_total | Maximum number of poses total, Type: int | Input | int | int |
+| input_txt_path | Experimental binding free energy data file (if any) | Input | File | File |
+| rescore | Use True if autodock vina was run with --rescore | Input | boolean | boolean |
+| input_ligand_pdbqt_path | Path to the input PDBQT ligands, 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 | {'type': 'array', 'items': {'type': 'array', 'items': 'File'}} | {'type': 'array', 'items': {'type': 'array', 'items': 'File'}} |
+| output_ligand_pdbqt_path | Path to the output PDBQT ligand files, 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 |
+| input_receptor_pdbqt_path | Path to the input PDBQT receptors, 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 | {'type': 'array', 'items': {'type': 'array', 'items': 'File'}} | {'type': 'array', 'items': {'type': 'array', 'items': 'File'}} |
+| output_receptor_pdbqt_path | Path to the output PDBQT receptor files, 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_ligand_pdbqt_path | Path to the output PDBQT file | Output | File[] | File[] |
+| output_receptor_pdbqt_path | Path to the output PDBQT file | Output | File[] | File[] |
+| docking_scores | Estimated Free Energies of Binding | Output | {'type': 'array', 'items': 'float'} | {'type': 'array', 'items': 'float'} |
+| experimental_binding_data | Experimental binding data (if any) | Output | ['null', {'type': 'array', 'items': 'float'}] | ['null', {'type': 'array', 'items': 'float'}] |
+| experimental_dGs | Experimental binding free energy dG values (if any) | Output | ['null', {'type': 'array', 'items': 'float'}] | ['null', {'type': 'array', 'items': 'float'}] |

utils/autodock-vina-filter-plugin/VERSION

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+0.1.0