Extract DFT coordinates from PDFs and generate Gaussian input files.
npx skills add https://github.com/InternScience/ChemClaw --skill pdf-dft-extractor
Please help me install this Agent Skill. Skill: pdf-dft-extractor Source: https://github.com/InternScience/ChemClaw/tree/main/skills/pdf-dft-extractor Command: npx skills add https://github.com/InternScience/ChemClaw --skill pdf-dft-extractor
This skill addresses the manual bottleneck of converting molecular coordinates embedded in PDF documents into ready-to-run Gaussian input files (gjf). It specifically targets supplementary materials and other PDFs that contain computed coordinates, enabling batch extraction and organized output folders per PDF.
Run the extractor on a single PDF to generate gjf files and a summary in the output folder.
High-intent search queries and answers about installing and using this skill.
To extract DFT coordinates from a PDF for Gaussian calculations, the skill converts the document to structured Markdown via MinerU, identifies the molecular coordinates, and generates ready-to-run Gaussian input files (gjf) with sanitized per-molecule naming.
Yes, you can batch process multiple PDFs to generate Gaussian input files. The skill supports batch processing entire directories and automatically creates isolated output folders for each PDF to keep the extracted gjf files organized.
The best way to convert supplementary material PDFs into gjf files is using an automated extraction pipeline. This skill specifically targets supplementary materials, parsing the converted Markdown to enforce coordinate extraction and robust gjf generation.
Yes, you need MinerU to extract Cartesian coordinates from PDF documents. The skill relies on the MinerU PDF converter to transform the PDF into Markdown, which is then parsed to isolate the molecular coordinates for downstream quantum chemistry calculations.
Your extracted Gaussian input file has a modified molecule name because the skill enforces file-name sanitization. This process ensures the generated gjf files have valid, robust naming conventions required for downstream quantum chemistry calculations.
ShenWang96Parse PDFs, Word, PPT, and images into structured Markdown with MinerU.
Hello-QMAutomate Gaussian quantum chemistry calculation setup, execution, and output management.
RonnasaydProcess large files with token and memory optimization strategies.
mr-daedaliumExtract text and tabular data from PDF documents using Python libraries.
