bio-pdb-structure-navigation
Navigate protein structure hierarchy using Biopython Bio.PDB SMCRA model. Use when accessing models, chains, residues, and atoms, iterating over structure levels, or extracting sequences from PDB files.
npx skills add FreedomIntelligence/OpenClaw-Medical-Skills --skill bio-pdb-structure-navigation --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+ 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 Navigation **"Access residues and atoms in a PDB structure"** → Navigate the Structure-Model-Chain-Residue-Atom hierarchy to iterate over components, extract sequences, and access atomic coordinates. - Python: `structure[0]['A'][100]['CA'].get_vector()` for direct access Navigate the Structure-Model-Chain-Residue-Atom (SMCRA) hierarchy to access and iterate over structure components. ## Required Imports ```python from Bio.PDB import PDBParser, PPBuilder, Selection from Bio.Data.PDBData import protein_letters_3to1 ``` ## SMCRA Hierarchy ``` Structure | +-- Model (0, 1, ...) # NMR ensembles, crystal asymmetric unit | +-- Chain (A, B, ...) # Polypeptide chains, ligands | +-- Residue # Amino acids, nucleotides, hetero groups | +-- Atom # Individual atoms ``` ## Accessing Hierarchy Levels
- Version Compatibility
- Required Imports
- SMCRA Hierarchy
- Accessing Hierarchy Levels
- Iterating Over Structure
- Residue Identification
- Atom Properties
- Getting Full Identifiers
- Checking for Children
- Getting Parent Entity
- Extracting Polypeptide Sequences
- Using CaPPBuilder for Broken Chains
- Converting Residue Names
- Using Selection.unfoldentities
What does the bio-pdb-structure-navigation skill do?
Navigate protein structure hierarchy using Biopython Bio.PDB SMCRA model. Use when accessing models, chains, residues, and atoms, iterating over structure levels, or extracting sequences from PDB files.
How do I install it?
Run `npx skills add FreedomIntelligence/OpenClaw-Medical-Skills --skill bio-pdb-structure-navigation --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.