fix-side-chain (#68)

Co-authored-by: Brandon Duane Walker <[email protected]>

utils/pre-process/structure-change/fix-side-chain-tool/.bumpversion.cfg

@@ -0,0 +1,29 @@
+[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_side_chain/__init__.py]

utils/pre-process/structure-change/fix-side-chain-tool/.dockerignore

@@ -0,0 +1,4 @@
+.venv
+out
+tests
+__pycache__

utils/pre-process/structure-change/fix-side-chain-tool/.gitattributes

@@ -0,0 +1,3 @@
+*.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/structure-change/fix-side-chain-tool/.gitignore

@@ -0,0 +1 @@
+poetry.lock

utils/pre-process/structure-change/fix-side-chain-tool/CHANGELOG.md

@@ -0,0 +1,5 @@
+# CHANGELOG
+
+## 0.1.0
+
+Initial release.

utils/pre-process/structure-change/fix-side-chain-tool/README.md

@@ -0,0 +1,14 @@
+# fix_side_chain (0.1.0)
+
+Class to model the missing atoms in amino acid side chains of a PDB.
+
+## 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/2ki5.pdb | Input | File | File |
+| output_pdb_path | Output PDB file path, Type: string, File type: output, Accepted formats: pdb, Example file: https://github.com/bioexcel/biobb_model/raw/master/biobb_model/test/reference/model/output_pdb_path.pdb | Input | string | string |
+| config | Advanced configuration options for biobb_model FixSideChain. This should be passed as a string containing a dict. The possible options to include here are listed under 'properties' in the biobb_model FixSideChain documentation: https://biobb-model.readthedocs.io/en/latest/model.html#module-model.fix_side_chain | Input | string | string |
+| output_pdb_path | Output PDB file path | Output | File | File |

utils/pre-process/structure-change/fix-side-chain-tool/VERSION

@@ -0,0 +1 @@
+0.1.0

utils/pre-process/structure-change/fix-side-chain-tool/fix_side_chain.cwl

@@ -0,0 +1,69 @@
+#!/usr/bin/env cwl-runner
+cwlVersion: v1.0
+
+class: CommandLineTool
+
+label: Class to model the missing atoms in amino acid side chains of a PDB.
+
+doc: |-
+  Model the missing atoms in amino acid side chains of a PDB using biobb_structure_checking if the use_modeller property is added the Modeller suite will also be used to rebuild the missing atoms.
+
+baseCommand: fix_side_chain
+
+hints:
+  DockerRequirement:
+    dockerPull: quay.io/biocontainers/biobb_model:4.0.1--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/2ki5.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://github.com/bioexcel/biobb_model/raw/master/biobb_model/test/reference/model/output_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 FixSideChain
+    doc: |-
+      Advanced configuration options for biobb_model FixSideChain. This should be passed as a string containing a dict. The possible options to include here are listed under 'properties' in the biobb_model FixSideChain documentation: https://biobb-model.readthedocs.io/en/latest/model.html#module-model.fix_side_chain
+    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/pre-process/structure-change/fix-side-chain-tool/ict.yml

@@ -0,0 +1,51 @@
+specVersion: "0.1.0"
+name: fix_side_chain
+version: 0.1.0
+container: fix-side-chain-tool
+entrypoint:
+title: fix_side_chain
+description: Class to model the missing atoms in amino acid side chains of a PDB.
+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/2ki5.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//github.com/bioexcel/biobb_model/raw/master/biobb_model/test/reference/model/output_pdb_path.pdb
+    type: string
+    defaultValue: system.pdb
+    format:
+      uri: edam:format_1476
+  - name: config
+    required: true
+    description: Advanced configuration options for biobb_model FixSideChain. This should be passed as a string containing a dict. The possible options to include here are listed under 'properties' in the biobb_model FixSideChain documentation https//biobb-model.readthedocs.io/en/latest/model.html#module-model.fix_side_chain
+    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/2ki5.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//github.com/bioexcel/biobb_model/raw/master/biobb_model/test/reference/model/output_pdb_path.pdb"
+    type: string
+  - key: inputs.config
+    title: "config: "
+    description: "Advanced configuration options for biobb_model FixSideChain. This should be passed as a string containing a dict. The possible options to include here are listed under 'properties' in the biobb_model FixSideChain documentation https//biobb-model.readthedocs.io/en/latest/model.html#module-model.fix_side_chain"
+    type: string

utils/pre-process/structure-change/fix-side-chain-tool/pyproject.toml

@@ -0,0 +1,30 @@
+[tool.poetry]
+name = "polus-mm-utils-fix-side-chain"
+version = "0.1.0"
+description = "Class to model the missing atoms in amino acid side chains of a PDB."
+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/structure-change/fix-side-chain-tool/tests/__init__.py

@@ -0,0 +1 @@
+"""Tests for fix_side_chain."""

utils/pre-process/structure-change/fix-side-chain-tool/tests/test_fix_side_chain.py

@@ -0,0 +1,24 @@
+"""Tests for fix_side_chain."""
+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_fix_side_chain() -> None:
+    """Test fix_side_chain."""
+    cwl_file = Path("fix_side_chain.cwl")
+    input_to_props = parse_cwl_arguments(cwl_file)
+    file_path_str = "2ki5.pdb"
+    file_path = str(Path(__file__).resolve().parent / Path(file_path_str))
+    input_to_props["input_pdb_path"]["path"] = file_path
+    input_yaml_path = Path("fix_side_chain.yml")
+    create_input_yaml(input_to_props, input_yaml_path)
+    stdout, stderr = call_cwltool(cwl_file, input_yaml_path)
+    assert Path("system.pdb").exists()