bio-pdb-structure-io
Parse and write protein structure files using Biopython Bio.PDB. Use when reading PDB, mmCIF, and MMTF files, downloading structures from RCSB PDB, or writing structures to various formats.
npx skills add FreedomIntelligence/OpenClaw-Medical-Skills --skill bio-pdb-structure-io --agent claude-code
Same command for any agent — swap --agent for codex, cursor, copilot.
Weekly change comes from our own snapshots, not the repository page — it measures attention, not adoption.
## Version Compatibility Reference examples tested with: BioPython 1.83+, scanpy 1.10+ Before using code patterns, verify installed versions match. If versions differ: - Python: `pip show <package>` then `help(module.function)` to check signatures If code throws ImportError, AttributeError, or TypeError, introspect the installed package and adapt the example to match the actual API rather than retrying. # Structure I/O **"Read a PDB file"** → Parse protein structure files (PDB, mmCIF, MMTF), download from RCSB PDB, and write structures to various formats. - Python: `Bio.PDB.PDBParser().get_structure('id', 'file.pdb')`, `Bio.PDB.MMCIFParser()` Parse, download, and write protein structure files in PDB, mmCIF, and MMTF formats. ## Required Imports ```python from Bio.PDB import PDBParser, MMCIFParser, PDBIO, MMCIFIO, PDBList from Bio.PDB.MMCIF2Dict import MMCIF2Dict ``` ## Supported Formats | Format | Parser | Writer | Description | |--------|--------|--------|-------------| | PDB | `PDBParser` | `PDBIO` | Legacy format, limited to 99999 atoms | | mmCIF | `MMCIFParser` | `MMCIFIO` | Modern standard, full metadata | | MMTF | `MMTFParser` | - | Compact binary (read-only in Biopython) | |
- Version Compatibility
- Required Imports
- Supported Formats
- Parsing PDB Files
- Parsing mmCIF Files
- Parsing MMTF Files
- Parsing BinaryCIF Files
- Downloading from RCSB PDB
- Batch Downloading
- Writing PDB Files
- Writing mmCIF Files
- Selective Output with Select Class
- Select Class Methods
- Extracting Header Information
What does the bio-pdb-structure-io skill do?
Parse and write protein structure files using Biopython Bio.PDB. Use when reading PDB, mmCIF, and MMTF files, downloading structures from RCSB PDB, or writing structures to various formats.
How do I install it?
Run `npx skills add FreedomIntelligence/OpenClaw-Medical-Skills --skill bio-pdb-structure-io --agent claude-code` — it drops the skill into your project so the agent can pick it up. Swap the --agent value for codex, cursor or copilot if you use one of those.
Where does this skill come from?
From FreedomIntelligence/OpenClaw-Medical-Skills, a repository with 2,909 stars. We read it straight from the repository tree rather than a submitted listing, so what you see here is what is actually published.
Is a popular skill a good skill?
Not necessarily. Stars measure attention, not adoption — a repository can trend for a week and be abandoned. That is why we show the weekly change from our own snapshots next to the total, instead of a single flattering number.