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bio-pdb-geometric-analysis
维护者 FreedomIntelligence · 最近更新 2026年4月1日
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).
原始来源
FreedomIntelligence/OpenClaw-Medical-Skills
https://github.com/FreedomIntelligence/OpenClaw-Medical-Skills/tree/main/skills/bio-pdb-geometric-analysis
- 维护者
- FreedomIntelligence
- 许可
- MIT
- 最近更新
- 2026年4月1日
技能摘要
来自 SKILL.md 的关键信息
核心说明
- Python：Bio.PDB.Superimposer() ，用于 RMSD，NeighborSearch ，用于 contacts。
- Calculate RMSD between two protein structures" → Measure atomic distances/angles/dihedrals，superimpose structures，compute RMSD，、 find inter-residue contacts. Python：Bio.PDB.Superimposer() ，用于 RMSD，NeighborSearch ，用于 contacts。
- Measure distances，angles，、 dihedrals. Superimpose structures 、 calculate RMSD. Find neighbor atoms 、 contacts。
- distance = atom1 - atom2 print(f'Distance：{distance：.2f} Angstroms')。
原始文档
SKILL.md 摘录
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']
适用场景
- 适合在measuring distances，angles，、 dihedrals，superimposing structures，calculating RMSD，或 computing solvent accessible surface area (SASA)时使用。
不适用场景
- Do not rely on this catalog entry alone ，用于 installation 或 maintenance details。
上游相关技能
- 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
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