bio-pdb-geometric-analysis
Perform geometric calculations on protein structures using Biopython Bio.PDB. Use when measuring distances, angles, and dihedrals, superimposing structures, calculating RMSD, or computing solvent accessible surface area (SASA).
npx skills add FreedomIntelligence/OpenClaw-Medical-Skills --skill bio-pdb-geometric-analysis --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+, numpy 1.26+ 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. # Geometric Analysis **"Calculate RMSD between two protein structures"** → Measure atomic distances/angles/dihedrals, superimpose structures, compute RMSD, and find inter-residue contacts. - Python: `Bio.PDB.Superimposer()` for RMSD, `NeighborSearch` for contacts Measure distances, angles, and dihedrals. Superimpose structures and calculate RMSD. Find neighbor atoms and contacts. ## Required Imports ```python from Bio.PDB import PDBParser, NeighborSearch, Superimposer from Bio.PDB import calc_angle, calc_dihedral import numpy as np ``` ## Distance Between Atoms ```python from Bio.PDB import PDBParser parser = PDBParser(QUIET=True) structure = parser.get_structure('protein', 'protein.pdb') chain = structure[0]['A'] atom1 = chain[100]['CA'] atom2 = chain[200]['CA'] # Direct subtraction
- Version Compatibility
- Required Imports
- Distance Between Atoms
- Distance Matrix
- Angle Between Three Atoms
- Dihedral Angles
- Ramachandran Angles for All Residues
- Finding Neighbor Atoms
- Finding Residue Contacts
- Contact Levels
- Superimposing Structures
- Calculating RMSD
- CEAligner for Dissimilar Structures
- Center of Mass
What does the bio-pdb-geometric-analysis skill do?
Perform geometric calculations on protein structures using Biopython Bio.PDB. Use when measuring distances, angles, and dihedrals, superimposing structures, calculating RMSD, or computing solvent accessible surface area (SASA).
How do I install it?
Run `npx skills add FreedomIntelligence/OpenClaw-Medical-Skills --skill bio-pdb-geometric-analysis --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.