mdtraj-trajectory-analysis
De la autor
mdtraj molecular dynamics trajectory analysis (Python). Reads DCD/XTC/TRR/NetCDF/H5/PDB topologies and trajectories; computes RMSD vs time, radius of gyration, per-residue RMSF, residue-residue contact frequency maps, phi/psi torsions for Ramachandran plots (general + Gly/Pro), and 8-state DSSP secondary structure. Modules: trajectory I/O, geometry (distances/angles/dihedrals), structural analysis (RMSD/Rg/RMSF/SASA), contacts, hydrogen bonds, secondary structure (DSSP), NMR observables. For broader atom-selection grammar use mdanalysis-trajectory; for running MD simulations use OpenMM/GROMACS.
Instalare
npx skills add jaechang-hits/SciAgent-Skills --skill mdtraj-trajectory-analysis -a claude-code
Se instalează în .claude/skills/mdtraj-trajectory-analysis/ · Fiecare comandă descarcă skill-ul direct de pe GitHub cu utilitarul open source skills.
Fără descărcare: licența acestui skill (LGPL-2.1) nu ne permite să-i redistribuim fișierele. Comenzile de instalare le iau direct de pe GitHub.
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Verificări de siguranță pe SKILL.md
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De ce 84
aiqbench calculează scorul de încredere din semnale publice. Nu este un audit de securitate, așa că citește un skill înainte să-l instalezi.
Skill-uri similare
Cele mai apropiate de acesta prin ce fac și când sunt folosite.
- mdanalysis-trajectoryjaechang-hits/SciAgent-SkillsAnalyze MD trajectories from GROMACS, AMBER, NAMD, CHARMM, LAMMPS. Reads topology/trajectory into Universe objects; supports RMSD, RMSF, radius of gyration, contact maps, H-bonds, PCA, and custom distance/angle calculations. Use for post-simulation structural analysis; use OpenMM/GROMACS for running simulations.Altele★ 382
- molecular-dynamicsK-Dense-AI/scientific-agent-skillsRuns and analyzes molecular dynamics simulations with OpenMM and MDAnalysis. Sets up protein/small molecule systems, defines force fields, runs energy minimization and production MD, and analyzes trajectories (RMSD, RMSF, contact maps, free energy surfaces). For structural biology, drug binding, and biophysics.Știință★ 54.1K
- pymatgenK-Dense-AI/scientific-agent-skillsAnalyzes, validates, converts, and transforms materials structures and computed materials data with pymatgen. Use for local phase diagrams, symmetry sensitivity, electronic-structure I/O, and bounded Materials Project queries.Altele★ 54.1K
- matlab-plan-robot-motionmatlab/matlab-agentic-toolkitPlan manipulator motion and generate trajectories in MATLAB. Use when the task involves moving a robot arm between configurations or poses — whether the user says "trajectory," "motion," "path," "move from A to B," or "plan." This skill applies regardless of whether the user explicitly mentions collisions or obstacles; if geometry exists in the workspace, collision safety is implicit. Triggers on: manipulatorRRT, manipulatorCHOMP, dlCHOMP, contopptraj, trapveltraj, collision-free path, motion planner, RRT, CHOMP, TOPPRA, path shortening, obstacle avoidance for manipulators, time-optimal trajectory, velocity limits, acceleration limits, occupancyMap3D, meshtsdf, collision objects as environment, trajectory between waypoints, joint interpolation, move between poses, constant velocity, trapezoidal profile, feed rate. Also triggers when a user has IK solutions or waypoints and needs to connect them — whether for time-optimal motion, constant-speed welding/cutting, or any other trajectory parameterization.Planificare★ 1.2K
- roadmap-managementa5c-ai/babysitterRoadmap parsing, analysis, and mutation operations for ROADMAP.md. Handles phase and milestone lifecycle including add, insert (decimal), remove, complete, and requirements coverage analysis.Planificare★ 1.9K
- tldr-deepvibeeval/vibecosystemRun full 5-layer analysis (AST, call graph, CFG, DFG, slice) on a specific function for deep debugging or understanding.Planificare★ 540
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