fix amides plugin

utils/fix-amides-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/fix_amides/__init__.py]

utils/fix-amides-plugin/.dockerignore

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+.venv
+out
+tests
+__pycache__

utils/fix-amides-plugin/.gitignore

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+poetry.lock

utils/fix-amides-plugin/CHANGELOG.md

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

utils/fix-amides-plugin/README.md

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+# fix_amides (0.1.0)
+
+Fix amide groups from residues.
+
+## Options
+
+This plugin takes 3 input arguments and 1 output argument:
+
+| Name          | Description             | I/O    | Type   | Default |
+|---------------|-------------------------|--------|--------|---------|
+| input_pdb_path | Input PDB file path, Type: string, File type: input, Accepted formats: pdb, Example file: https://github.com/bioexcel/biobb_model/raw/master/biobb_model/test/data/model/5s2z.pdb | Input | File | File |
+| output_pdb_path | Output PDB file path, Type: string, File type: output, Accepted formats: pdb, Example file: https://raw.githubusercontent.com/bioexcel/biobb_model/master/biobb_model/test/reference/model/output_amide_pdb_path.pdb | Input | string | string |
+| config | Advanced configuration options for biobb_model FixAmides. This should be passed as a string containing a dict. The possible options to include here are listed under 'properties' in the biobb_model FixAmides documentation: https://biobb-model.readthedocs.io/en/latest/model.html#module-model.fix_amides | Input | string | string |
+| output_pdb_path | Output PDB file path | Output | File | File |

utils/fix-amides-plugin/VERSION

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+0.1.0

utils/fix-amides-plugin/fix_amides.cwl

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+#!/usr/bin/env cwl-runner
+cwlVersion: v1.0
+
+class: CommandLineTool
+
+label: Fix amide groups from residues.
+
+doc: |-
+  Flip the clashing amide groups to avoid clashes.
+
+baseCommand: fix_amides
+
+hints:
+  DockerRequirement:
+    dockerPull: quay.io/biocontainers/biobb_model:4.1.0--pyhdfd78af_0
+
+inputs:
+  input_pdb_path:
+    label: Input PDB file path
+    doc: |-
+      Input PDB file path
+      Type: string
+      File type: input
+      Accepted formats: pdb
+      Example file: https://github.com/bioexcel/biobb_model/raw/master/biobb_model/test/data/model/5s2z.pdb
+    type: File
+    format: edam:format_1476
+    inputBinding:
+      position: 1
+      prefix: --input_pdb_path
+
+  output_pdb_path:
+    label: Output PDB file path
+    doc: |-
+      Output PDB file path
+      Type: string
+      File type: output
+      Accepted formats: pdb
+      Example file: https://raw.githubusercontent.com/bioexcel/biobb_model/master/biobb_model/test/reference/model/output_amide_pdb_path.pdb
+    type: string
+    format: edam:format_1476
+    inputBinding:
+      position: 2
+      prefix: --output_pdb_path
+    default: system.pdb
+
+  config:
+    label: Advanced configuration options for biobb_model FixAmides
+    doc: |-
+      Advanced configuration options for biobb_model FixAmides. This should be passed as a string containing a dict. The possible options to include here are listed under 'properties' in the biobb_model FixAmides documentation: https://biobb-model.readthedocs.io/en/latest/model.html#module-model.fix_amides
+    type: string?
+    inputBinding:
+      prefix: --config
+
+outputs:
+  output_pdb_path:
+    label: Output PDB file path
+    doc: |-
+      Output PDB file path
+    type: File
+    outputBinding:
+      glob: $(inputs.output_pdb_path)
+    format: edam:format_1476
+
+$namespaces:
+  edam: https://edamontology.org/
+
+$schemas:
+- https://raw.githubusercontent.com/edamontology/edamontology/master/EDAM_dev.owl

utils/fix-amides-plugin/ict.yml

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+specVersion: "0.1.0"
+name: fix_amides
+version: 0.1.0
+container: fix-amides-plugin
+entrypoint:
+title: fix_amides
+description: Fix amide groups from residues.
+author: Data Scientist
+contact: [email protected]
+repository:
+documentation:
+citation:
+
+inputs:
+  - name: input_pdb_path
+    required: true
+    description: Input PDB file path, Type string, File type input, Accepted formats pdb, Example file https//github.com/bioexcel/biobb_model/raw/master/biobb_model/test/data/model/5s2z.pdb
+    type: File
+    format:
+      uri: edam:format_1476
+  - name: output_pdb_path
+    required: true
+    description: Output PDB file path, Type string, File type output, Accepted formats pdb, Example file https//raw.githubusercontent.com/bioexcel/biobb_model/master/biobb_model/test/reference/model/output_amide_pdb_path.pdb
+    type: string
+    defaultValue: system.pdb
+    format:
+      uri: edam:format_1476
+  - name: config
+    required: true
+    description: Advanced configuration options for biobb_model FixAmides. This should be passed as a string containing a dict. The possible options to include here are listed under 'properties' in the biobb_model FixAmides documentation https//biobb-model.readthedocs.io/en/latest/model.html#module-model.fix_amides
+    type: string
+outputs:
+  - name: output_pdb_path
+    required: true
+    description: Output PDB file path
+    type: File
+    format:
+      uri: edam:format_1476
+ui:
+  - key: inputs.input_pdb_path
+    title: "input_pdb_path: "
+    description: "Input PDB file path, Type string, File type input, Accepted formats pdb, Example file https//github.com/bioexcel/biobb_model/raw/master/biobb_model/test/data/model/5s2z.pdb"
+    type: File
+  - key: inputs.output_pdb_path
+    title: "output_pdb_path: "
+    description: "Output PDB file path, Type string, File type output, Accepted formats pdb, Example file https//raw.githubusercontent.com/bioexcel/biobb_model/master/biobb_model/test/reference/model/output_amide_pdb_path.pdb"
+    type: string
+  - key: inputs.config
+    title: "config: "
+    description: "Advanced configuration options for biobb_model FixAmides. This should be passed as a string containing a dict. The possible options to include here are listed under 'properties' in the biobb_model FixAmides documentation https//biobb-model.readthedocs.io/en/latest/model.html#module-model.fix_amides"
+    type: string