ConformAtlas
Mapping conformational landscapes from molecular simulations. Free-energy landscapes with bootstrap uncertainty, metastable states, barriers and kinetics from MD trajectories: PCA, TICA, Markov state models, convergence diagnostics and multi-system comparison. Python package and CLI
What XERJ indexed
Snapshot
The whole repository at commit 64f8fcc9f9. It is the newest commit on main.
Selected work
Licence
The repository
LICENSE file checked at the pinned commit; the author agreed to inclusion.
The XERJ corpus
The owner added it on hub.xerj.org after signing in with GitHub, on 2026-10-28. Same terms as the repository. Answers name the repo, the commit and the file:line.
selected for the XERJ Corpus Hublicence clearedsuggested use: adapt with attribution
computational-biologycomputational-chemistryconformational-analysisenhanced-samplingfree-energy-landscapegromacsmarkov-state-modelmdanalysis
Example questions
- How does ConformAtlas implement computational-biology?
- Show the computational-chemistry code in ConformAtlas.
Inside the indexed corpus
- 191 files, 7.3 MB in total, about 38.9 KB per file.
- Languages by size: Python 97.7%, Jinja 2.3%.
- On GitHub since 2026-09-19, last push 2026-10-21, 22 commits on main.
Licence on GitHub and in the corpus
GitHub reported MIT for AtharvaTilewale/ConformAtlas on 2026-10-31, and the LICENSE file at commit 64f8fcc9f9 was reviewed as MIT. They match, so answers from this corpus carry the same terms as the live repository.
Contributors
Atharva Tilewale (@AtharvaTilewale) has 6 selected repositories on the hub.
Their other repository pages: AtharvaTilewale/boltz2-notebook, AtharvaTilewale/ChemLitmus, AtharvaTilewale/FELBuilder, AtharvaTilewale/meowmd, AtharvaTilewale/SmileSherlock.
Using XERJ with ConformAtlas
- ripgrep vs a code index for coding agents: 30 tasks
- Best MCP servers for local code search in 2026, compared
- Best grep alternative for AI coding agents (2026)
- Ask questions about a GitHub repo without cloning it
The prompt
Paste it into your AI agent. It clones AtharvaTilewale/ConformAtlas at the pinned commit and indexes it on your machine.
Search the GitHub repository AtharvaTilewale/ConformAtlas with XERJ (https://hub.xerj.org/corpus/atharvatilewale--conformatlas). Run these in a shell, in order, and check each result before the next: 1. xerj --help (success: it prints usage). If xerj is missing: curl -fsSL https://xerj.org/get | sh 2. git clone https://github.com/AtharvaTilewale/ConformAtlas ConformAtlas && git -C ConformAtlas checkout 64f8fcc9f9831c4dafd8e68373ad73a2fe6b9c60 3. Start a local node and leave it running: xerj --insecure --data-dir ./xerj-data 4. xerj autoindex ./ConformAtlas --url http://127.0.0.1:9200 --prefix conformatlas --progress plain 5. xerj autoindex map --url http://127.0.0.1:9200 Then answer my question from the indexed files and cite the ax_path of every hit. Query syntax: https://xerj.org/llms.txt Licence: MIT. Keep the copyright notice and credit the authors.
Related
Atharva TilewaleHealth and clinical reference corporaAtharvaTilewale/FELBuilderasifverse4/100-days-of-computational-chemistrydavewalker5/MolecularClockSimulation
Stats: GitHub API, fetched 2026-10-31. Snapshot: the git tree at the pinned commit. Selected work and consent: the XERJ registry.