AD
Data & Repro
Adaptyv
Adaptyv is a cloud laboratory platform that provides automated protein testing and validation services. Submit protein sequences via API or…
K-Dense-AI/claude-scientific-skillsView
Data & Repro
BI
bio-pdb-geometric-analysis
Maintainer FreedomIntelligence · Last updated April 1, 2026
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).
Original source
FreedomIntelligence/OpenClaw-Medical-Skills
https://github.com/FreedomIntelligence/OpenClaw-Medical-Skills/tree/main/skills/bio-pdb-geometric-analysis
- Maintainer
- FreedomIntelligence
- License
- MIT
- Last updated
- April 1, 2026
Skill Snapshot
Key Details From SKILL.md
Key Notes
- Python: Bio.PDB.Superimposer() for RMSD, NeighborSearch for contacts.
- 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.
- distance = atom1 - atom2 print(f'Distance: {distance:.2f} Angstroms').
Source Doc
Excerpt From SKILL.md
Distance Between Atoms
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']
## Or use numpy
import numpy as np
distance = np.linalg.norm(atom1.coord - atom2.coord)
Angle Between Three Atoms
from Bio.PDB import PDBParser, calc_angle
parser = PDBParser(QUIET=True)
structure = parser.get_structure('protein', 'protein.pdb')
residue = structure[0]['A'][100]
n = residue['N']
ca = residue['CA']
c = residue['C']
Use cases
- Use when measuring distances, angles, and dihedrals, superimposing structures, calculating RMSD, or computing solvent accessible surface area (SASA).
Not for
- Do not rely on this catalog entry alone for installation or maintenance details.
Upstream Related Skills
- structure-io - Parse and write structure files
- structure-navigation - Access chains, residues, atoms
- structure-modification - Transform coordinates, modify structures
- alignment/pairwise-alignment - Sequence alignment for structure comparison
Related skills
Related skills
AL
Data & Repro
alphafold
Validate protein designs using AlphaFold2 structure prediction. Use this skill when: (1) Validating designed sequences fold correctly, (2) P…
FreedomIntelligence/OpenClaw-Medical-SkillsView
AL
Data & Repro
AlphaFold DB
AlphaFold DB is a public repository of AI-predicted 3D protein structures for over 200 million proteins, maintained by DeepMind and EMBL-EBI…
K-Dense-AI/claude-scientific-skillsView
AN
Data & Repro
antibody-design-agent
Antibody design: epitope mapping, CDR engineering, bispecific construction.
FreedomIntelligence/OpenClaw-Medical-SkillsView