ljmartin

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---
name: TranscribePNGFolder
description: Use this skill whenever the user wants to transcribe PDF contents, contained in PNG files in a local folder, into text or markdown. The source PDFs include academic papers, reports, manuals, or any PDF with mixed text and figures. The skill iterates over the PNG files, uses a vision model to transcribe the text and describe any figures in place, collating everything into a single clean markdown document. Triggers: "transcribe this PDF in directory", "extract text from PDF", "convert PDF contained in directory to markdown", "summarise this PDF" (as a first step).
---

TranscribePNGFolder Skill

Overview

Transcribes PDF contents from PNG to a markdown document by:

	data_structure
	#
	loop_
	_atom_site.group_PDB
	_atom_site.type_symbol
	_atom_site.label_atom_id
	_atom_site.label_alt_id
	_atom_site.label_comp_id
	_atom_site.label_asym_id
	_atom_site.label_entity_id

	import pandas as pd
	from rdkit import Chem

	from rdkit.Chem import AllChem
	from rdkit.Chem import rdMolDescriptors
	from rdkit.Chem import AllChem, rdMolDescriptors, rdMolAlign, rdMolTransforms

	import numpy as np
	from tqdm.notebook import tqdm

	import modal

	image = (
	modal.Image.micromamba(python_version="3.10")
	.apt_install('gcc')
	.apt_install('git', 'wget')
	.micromamba_install('openmm==8.0.0', 'pdbfixer','kalign2=2.04', 'hhsuite=3.3.0',
	'mmseqs2', channels=['conda-forge', 'bioconda'])
	.run_commands('pip install "colabfold[alphafold-minus-jax] @ git+https://github.com/sokrypton/ColabFold"')
	.run_commands('pip install "colabfold[alphafold]"')

	import modal

	image = (
	modal.Image.debian_slim()
	.pip_install("uv")
	.run_commands("uv pip install --system --compile-bytecode chai_lab==0.4.2")
	.run_commands('mkdir -p /usr/local/lib/python3.11/site-packages/downloads/models_v2')
	.apt_install("wget")
	.run_commands('wget -O /usr/local/lib/python3.11/site-packages/downloads/conformers_v1.apkl https://chaiassets.com/chai1-inference-depencencies/conformers_v1.apkl')
	.run_commands('wget -O /usr/local/lib/python3.11/site-packages/downloads/models_v2/trunk.pt https://chaiassets.com/chai1-inference-depencencies/models_v2/trunk.pt')