structure-file-prep

name	structure_file_prep
description	Structure/sequence file preparation with VenusFactory file tools. Use for FASTA parsing, PDB chain extraction, PDB↔mmCIF conversion (MAXIT), apo checks, batch PDB→FASTA, and UniProt ID from RCSB metadata. Do NOT use for structure prediction (protein_structure_pipeline) or homology search.
license	Apache-2.0
metadata	{"version":"1.0","skill-author":"VenusFactory2"}

Structure & Sequence File Prep

Project Tools (VenusFactory2)

Tool	Purpose
read_fasta	Parse multi-FASTA → headers/sequences
extract_uids_from_fasta	Pull UIDs from headers
uid_file_to_chunks	Chunk UID lists for batch jobs
pdb_chain_sequences	Per-chain sequences from PDB
get_seq_from_pdb_chain_a	Chain A sequence shortcut
pdb_dir_to_fasta	Directory of PDBs → FASTA
check_pdb_apo	Ligand-free / apo heuristic
maxit_structure_convert	pdb2cif / cif2pdb / cif2mmcif (needs MAXIT)
extract_uniprot_id_from_rcsb_metadata	UniProt from RCSB metadata JSON
unzip_archive / ungzip_file	Unpack downloads

Workflows

PDB → design/mutation ready

1. check_pdb_apo (if apo backbone required)
2. pdb_chain_sequences → choose designed chains
3. Optional maxit_structure_convert for format mismatches

RCSB metadata → UniProt → AlphaFold

1. download_rcsb_entry_metadata_by_pdb_id
2. extract_uniprot_id_from_rcsb_metadata
3. Hand off to alphafold_database / protein_structure_pipeline

Common mistakes

• Hardcoding chain lengths without pdb_chain_sequences
• Calling MAXIT strategies other than pdb2cif/cif2pdb/cif2mmcif
• Feeding directories to tools that expect a single file path