pymol_align_protein_ca

utils/pymol-align-protein-ca-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/pymol_align_protein_ca/__init__.py]

utils/pymol-align-protein-ca-plugin/.dockerignore

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+.venv
+out
+tests
+__pycache__

utils/pymol-align-protein-ca-plugin/.gitattributes

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+*.gro filter=lfs diff=lfs merge=lfs -text
+*.xyz filter=lfs diff=lfs merge=lfs -text
+*.trr filter=lfs diff=lfs merge=lfs -text

utils/pymol-align-protein-ca-plugin/.gitignore

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+poetry.lock

utils/pymol-align-protein-ca-plugin/CHANGELOG.md

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

utils/pymol-align-protein-ca-plugin/Dockerfile

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+FROM condaforge/mambaforge
+
+RUN apt-get update && apt-get install libgl1-mesa-glx -y
+
+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
+# errors installing pymol-open-source from poetry so using conda
+COPY environment.yml ${EXEC_DIR}
+RUN mamba env create -f ${EXEC_DIR}/environment.yml
+RUN echo "source activate project_env" > ~/.bashrc
+ENV PATH /opt/conda/envs/env/bin:$PATH
+
+COPY src ${EXEC_DIR}/src
+
+ADD Dockerfile .
+
+RUN conda run -n project_env pip install ${EXEC_DIR} --no-cache-dir
+
+CMD ["--help"]

utils/pymol-align-protein-ca-plugin/README.md

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+# pymol_align_protein_ca (0.1.0)
+
+Align Protein and CA atoms for a trajectory using Pymol
+
+## Options
+
+This plugin takes     6     input arguments and 1 output argument:
+
+| Name          | Description             | I/O    | Type   | Default |
+|---------------|-------------------------|--------|--------|---------|
+| input_1_path | Input receptor file path | Input | File | File |
+| input_2_path | Input ligand file path | Input | File | File |
+| input_3_path | Input structure file path | Input | File | File |
+| input_4_path | Input trajectory file path | Input | File | File |
+| output_file_path | Path to the output file | Input | string | string |
+| output_file_path | Path to the output file | Output | File | File |

utils/pymol-align-protein-ca-plugin/VERSION

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+0.1.0

utils/pymol-align-protein-ca-plugin/build-docker.sh

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+#!/bin/bash
+
+version=$(<VERSION)
+docker build . -t polusai/pymol-align-protein-ca-tool:${version}

utils/pymol-align-protein-ca-plugin/environment.yml

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+name: project_env
+channels:
+  - conda-forge
+dependencies:
+  - python==3.10
+  - pymol-open-source==3.0.0

utils/pymol-align-protein-ca-plugin/ict.yml

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+specVersion: "0.1.0"
+name: pymol_align_protein_ca
+version: 0.1.0
+container: pymol-align-protein-ca-plugin
+entrypoint:
+title: pymol_align_protein_ca
+description: Align Protein and CA atoms for a trajectory using Pymol
+author: Data Scientist
+contact: [email protected]
+repository:
+documentation:
+citation:
+
+inputs:
+  - name: input_1_path
+    required: true
+    description: Input receptor file path
+    type: File
+    format:
+      uri: edam:format_1476, edam:format_3877
+  - name: input_2_path
+    required: true
+    description: Input ligand file path
+    type: File
+    format:
+      uri: edam:format_1476, edam:format_3877
+  - name: input_3_path
+    required: true
+    description: Input structure file path
+    type: File
+    format:
+      uri: edam:format_2033
+  - name: input_4_path
+    required: true
+    description: Input trajectory file path
+    type: File
+    format:
+      uri: edam:format_3910
+  - name: output_file_path
+    required: true
+    description: Path to the output file
+    type: string
+    defaultValue: system.pdb
+    format:
+      uri: edam:format_1476
+outputs:
+  - name: output_file_path
+    required: true
+    description: Path to the output file
+    type: File
+    format:
+      uri: edam:format_1476
+ui:
+  - key: inputs.input_1_path
+    title: "input_1_path: "
+    description: "Input receptor file path"
+    type: File
+  - key: inputs.input_2_path
+    title: "input_2_path: "
+    description: "Input ligand file path"
+    type: File
+  - key: inputs.input_3_path
+    title: "input_3_path: "
+    description: "Input structure file path"
+    type: File
+  - key: inputs.input_4_path
+    title: "input_4_path: "
+    description: "Input trajectory file path"
+    type: File
+  - key: inputs.output_file_path
+    title: "output_file_path: "
+    description: "Path to the output file"
+    type: string

utils/pymol-align-protein-ca-plugin/pymol_align_protein_ca_0@1@0.cwl

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+#!/usr/bin/env cwl-runner
+cwlVersion: v1.0
+
+class: CommandLineTool
+
+label: Align Protein and CA atoms for a trajectory using Pymol
+
+doc: |-
+  Align Protein and CA atoms for a trajectory using Pymol
+
+baseCommand: ["conda", "run", "-n", "project_env", "pymol"]
+arguments: ["-rcQ", "/opt/executables/src/polus/mm/utils/pymol_align_protein_ca/__main__.py ", "--"]
+# NOTE: Based on the last example here
+# See https://pymolwiki.org/index.php/Command_Line_Options
+
+hints:
+  DockerRequirement:
+    dockerPull: polusai/pymol-align-protein-ca-tool@sha256:3d51e1e6cd560b64b33159e153b68560b00701ac81307bce259dbf8d454395fd
+
+inputs:
+  input_1_path:
+    label: Input receptor file path
+    doc: |-
+      Input receptor file path
+    type: File
+    format: edam:format_1476, edam:format_3877 # pdb, xyz
+    inputBinding:
+      prefix: --input_1_path
+
+  input_2_path:
+    label: Input ligand file path
+    doc: |-
+      Input ligand file path
+    type: File
+    format: edam:format_1476, edam:format_3877 # pdb, xyz
+    inputBinding:
+      prefix: --input_2_path
+
+  input_3_path:
+    label: Input structure file path
+    doc: |-
+      Input structure file path
+    type: File
+    format: edam:format_2033 # Gromacs structure *.gro
+    inputBinding:
+      prefix: --input_3_path
+
+  input_4_path:
+    label: Input trajectory file path
+    doc: |-
+      Input trajectory file path
+    type: File
+    format: edam:format_3910 # Gromacs trajectory *.trr
+    inputBinding:
+      prefix: --input_4_path
+
+  output_file_path:
+    label: Path to the output file
+    doc: |-
+      Path to the output file
+    type: string
+    format:
+    - edam:format_1476 # pdb
+    inputBinding:
+      prefix: --output_file_path
+    default: system.pdb
+
+
+outputs:
+  output_file_path:
+    label: Path to the output file
+    doc: |-
+      Path to the output file
+    type: File
+    format: edam:format_1476 # pdb
+    outputBinding:
+      glob: $(inputs.output_file_path)
+
+$namespaces:
+  edam: https://edamontology.org/
+
+$schemas:
+- https://raw.githubusercontent.com/edamontology/edamontology/master/EDAM_dev.owl

utils/pymol-align-protein-ca-plugin/pyproject.toml

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+[tool.poetry]
+name = "polus-mm-utils-pymol-align-protein-ca"
+version = "0.1.0"
+description = "Align Protein and CA atoms for a trajectory using Pymol"
+authors = ["Data Scientist <[email protected]>"]
+readme = "README.md"
+packages = [{include = "polus", from = "src"}]
+
+[tool.poetry.dependencies]
+python = ">=3.9,<3.13"
+typer = "^0.7.0"
+sophios = "0.1.4"
+mdanalysis = "2.7.0"
+
+[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/pymol-align-protein-ca-plugin/src/polus/mm/utils/pymol_align_protein_ca/__init__.py

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+"""pymol_align_protein_ca."""
+
+__version__ = "0.1.0"
+
+from polus.mm.utils.pymol_align_protein_ca.pymol_align_protein_ca import (  # noqa # pylint: disable=unused-import
+    pymol_align_protein_ca,
+)

utils/pymol-align-protein-ca-plugin/src/polus/mm/utils/pymol_align_protein_ca/__main__.py

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+"""Package entrypoint for the pymol_align_protein_ca package."""
+
+# Base packages
+import logging
+from os import environ
+
+import typer
+from polus.mm.utils.pymol_align_protein_ca.pymol_align_protein_ca import (
+    pymol_align_protein_ca,
+)
+
+logging.basicConfig(
+    format="%(asctime)s - %(name)-8s - %(levelname)-8s - %(message)s",
+    datefmt="%d-%b-%y %H:%M:%S",
+)
+POLUS_LOG = getattr(logging, environ.get("POLUS_LOG", "INFO"))
+logger = logging.getLogger("polus.mm.utils.pymol_align_protein_ca.")
+logger.setLevel(POLUS_LOG)
+
+app = typer.Typer(help="pymol_align_protein_ca.")
+
+
+@app.command()
+def main(
+    input_1_path: str = typer.Option(
+        ...,
+        "--input_1_path",
+        help="Input receptor file path",
+    ),
+    input_2_path: str = typer.Option(
+        ...,
+        "--input_2_path",
+        help="Input ligand file path",
+    ),
+    input_3_path: str = typer.Option(
+        ...,
+        "--input_3_path",
+        help="Input structure file path",
+    ),
+    input_4_path: str = typer.Option(
+        ...,
+        "--input_4_path",
+        help="Input trajectory file path",
+    ),
+    output_file_path: str = typer.Option(
+        ...,
+        "--output_file_path",
+        help="Path to the output file",
+    ),
+) -> None:
+    """pymol_align_protein_ca."""
+    logger.info(f"input_1_path: {input_1_path}")
+    logger.info(f"input_2_path: {input_2_path}")
+    logger.info(f"input_3_path: {input_3_path}")
+    logger.info(f"input_4_path: {input_4_path}")
+    logger.info(f"output_file_path: {output_file_path}")
+
+    pymol_align_protein_ca(
+        input_1_path=input_1_path,
+        input_2_path=input_2_path,
+        input_3_path=input_3_path,
+        input_4_path=input_4_path,
+        output_file_path=output_file_path,
+    )
+
+
+if __name__ == "__main__":
+    app()