alphafold2
Predict protein structure for monomers and multimers with AlphaFold2 via the ColabFold runner (Mirdita et al. 2022,…
Use when creating a Word DOCX report from Markdown, converting Markdown tables and lists to DOCX, or choosing a workflow for editing an existing DOCX while preserving its structure and styles. Use this workflow before running Markdown-to-DOCX shell commands. Includes report
$ npx -y skills add aipoch/open-science --skill docx-generation --agent claude-codeHow it fires
How this skill gets triggered: by you, by Claude, or both.
/docx-generationContext preview
The summary Claude sees to decide when to auto-load this skill.
Use when creating a Word DOCX report from Markdown, converting Markdown tables and lists to DOCX, or choosing a workflow for editing an existing DOCX while preserving its structure and styles. Use this workflow before running Markdown-to-DOCX shell commands. Includes report
name: docx-generation description: Use when creating a Word DOCX report from Markdown, converting Markdown tables and lists to DOCX, or choosing a workflow for editing an existing DOCX while preserving its structure and styles. Use this workflow before running Markdown-to-DOCX shell commands. Includes report typography, table layout, a reusable reference document, and a Python converter. license: Apache-2.0
Choose a workflow that preserves the user's requested content, structure, and presentation. User requirements take precedence over defaults. Keep tables, headings, and lists as native document structures.
For ordinary reports, use the bundled converter with an existing Pandoc 3.12.1 executable and Python 3.9 or newer. It uses a versioned reference document, separates ordinary table paragraphs from the Compact style shared by lists, and records converter/template provenance inside the DOCX. It does not install software. Run this converter rather than a bare `pandoc source.md -o output.docx` command: that command bypasses the report template and its typography, page geometry, table spacing, and provenance.
In Open Science, first prepare the workflow through the registered Notebook helper:
{
"kernelSkillIds": ["docx-generation"],
"code": "docx_workflow = prepare_docx_conversion('.')\nprint(docx_workflow)"
}Call the function directly, without importing it. Repeat `kernelSkillIds` in every cell using this function. The helper writes the fixed converter and reference into a new directory inside the authorized Notebook working directory and returns `script_path`, `reference_path`, and `workflow_directory`. This uses the registered skill transport; the Notebook and shell cannot necessarily read the framework's skill directory.
Then run the returned `script_path` through the session's approved shell tool:
python "<returned-script_path>" "<source.md>" "<output.docx>"
Use the interpreter configured for the session. If the helper is unavailable, report that prerequisite through the normal execution recovery flow; do not probe or copy from the isolated framework skill directory. In environments outside Open Science that already allow reading this package, the original `scripts/convert.py` is also a standalone CLI.
Optional arguments:
The bundled report profile uses A4 with 2 cm margins, 10.5 pt body text with approximately 1.33 line spacing, coordinated heading sizes (17/14/11.5 pt), and tighter list spacing. Tables use 9.5 pt text, 3 pt vertical and 4 pt horizontal cell padding, visible outer and internal grid lines, and bold headers without background shading. Top-level tables with automatic width fill the text area; explicit widths and column proportions remain intact. The default faces are Arial and PingFang SC for East Asian text; fonts are not embedded, and viewers substitute missing fonts. For a specific viewing platform or font requirement, use a reference with appropriate available fonts. A reference document's body content is not copied into the output. Use another workflow when the task requires filling a template's existing content.
Do not substitute the bundled template when the user supplied a template or requested a different design. For special page layouts or table widths, use an appropriate reference or targeted document editing; do not impose fixed page/column dimensions on every document.
For Pandoc Markdown pipe tables, retain intentional delimiter-row widths. Padding or reformatting a wide Markdown table can change the column proportions inferred by Pandoc.
The converter emits one JSON receipt with the output path, MIME type, versions, and template hash. It requires a new output filename and leaves existing files intact. If the supported Pandoc version is unavailable, report the missing prerequisite or use another suitable document-generation workflow under the session's normal environment rules. This skill does not require Pandoc for every DOCX task.
Modify the existing package with an appropriate document library or narrowly scoped OOXML edits. Preserve unrelated styles, numbering, relationships, sections, and embedded objects. Avoid rebuilding a richly formatted source through Markdown when the task requires preserving its layout. For complex tables and precise forms, choose a library suited to that structure; library choice alone does not guarantee style preservation.
Pass the generated file's local path and MIME type to `write_artifact_file`. When Notebook or shell execution produced it, include the exact execution `runId` as `producerRunId`. The converter receipt is not an Artifact receipt; claim availability only after the Artifact tool succeeds.
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