Instrument Data To Allotrope
aws-samples/amazon-bedrock-agents-healthcare-lifesciences
Convert laboratory instrument output files (PDF, CSV, Excel, TXT) to Allotrope Simple Model (ASM) JSON format or flattened 2D CSV.
Standalone evaluation of an existing PDB directory with Proteina-Complexa.
Install Complexa Evaluate Pdbs
$ npx skills add NVIDIA-BioNeMo/bionemo-agent-toolkit --skill complexa-evaluate-pdbs -a claude-codeProject install by default; add -g for ~/.claude/skills/.
$ gh skill install NVIDIA-BioNeMo/bionemo-agent-toolkit complexa-evaluate-pdbs --agent claude-codeProject scope by default; add --scope user for a personal install. Needs GitHub CLI 2.90.0 or later (public preview).
$ git clone --depth 1 https://github.com/NVIDIA-BioNeMo/bionemo-agent-toolkit.git skills-src && mkdir -p .claude/skills && cp -r skills-src/skills/bionemo-agent-toolkit/skills/complexa-evaluate-pdbs .claude/skills/complexa-evaluate-pdbs && rm -rf skills-srcUse ~/.claude/skills/ instead of .claude/skills for a personal install. The folder must contain SKILL.md.
Claude Code skills documentation · loads skills from .claude/skills/
Install the "complexa-evaluate-pdbs" agent skill from https://github.com/NVIDIA-BioNeMo/bionemo-agent-toolkit/tree/main/skills/bionemo-agent-toolkit/skills/complexa-evaluate-pdbs into .claude/skills/complexa-evaluate-pdbs/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "complexa-evaluate-pdbs", then confirm the skill loads.Claude Code copies the folder itself, the same result as the manual copy. Check what it changed before you commit it.
$skill-installer install https://github.com/NVIDIA-BioNeMo/bionemo-agent-toolkit/tree/main/skills/bionemo-agent-toolkit/skills/complexa-evaluate-pdbsType this inside Codex. $skill-installer <name> installs a curated skill from openai/skills. The installer writes to $CODEX_HOME/skills (default ~/.codex/skills). Restart Codex if the skill does not show up.
$ npx skills add NVIDIA-BioNeMo/bionemo-agent-toolkit --skill complexa-evaluate-pdbs -a codexProject install goes to .agents/skills/; add -g for ~/.codex/skills/.
$ gh skill install NVIDIA-BioNeMo/bionemo-agent-toolkit complexa-evaluate-pdbs --agent codexProject scope by default (.agents/skills/); add --scope user for a personal install.
$ git clone --depth 1 https://github.com/NVIDIA-BioNeMo/bionemo-agent-toolkit.git skills-src && mkdir -p .agents/skills && cp -r skills-src/skills/bionemo-agent-toolkit/skills/complexa-evaluate-pdbs .agents/skills/complexa-evaluate-pdbs && rm -rf skills-srcUse ~/.agents/skills/ instead of .agents/skills for a personal install.
Codex skills documentation · loads skills from .agents/skills/
Install the "complexa-evaluate-pdbs" agent skill from https://github.com/NVIDIA-BioNeMo/bionemo-agent-toolkit/tree/main/skills/bionemo-agent-toolkit/skills/complexa-evaluate-pdbs into .agents/skills/complexa-evaluate-pdbs/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "complexa-evaluate-pdbs", then confirm the skill loads.Codex copies the folder itself, the same result as the manual copy. Check what it changed before you commit it.
$ npx skills add NVIDIA-BioNeMo/bionemo-agent-toolkit --skill complexa-evaluate-pdbs -a cursorProject install goes to .agents/skills/; add -g for ~/.cursor/skills/.
$ gh skill install NVIDIA-BioNeMo/bionemo-agent-toolkit complexa-evaluate-pdbs --agent cursorProject scope by default (.agents/skills/); add --scope user for a personal install.
$ git clone --depth 1 https://github.com/NVIDIA-BioNeMo/bionemo-agent-toolkit.git skills-src && mkdir -p .cursor/skills && cp -r skills-src/skills/bionemo-agent-toolkit/skills/complexa-evaluate-pdbs .cursor/skills/complexa-evaluate-pdbs && rm -rf skills-srcUse ~/.cursor/skills/ instead of .cursor/skills for a personal install.
Cursor skills documentation · loads skills from .cursor/skills/, .agents/skills/, .claude/skills/, .codex/skills/
Install the "complexa-evaluate-pdbs" agent skill from https://github.com/NVIDIA-BioNeMo/bionemo-agent-toolkit/tree/main/skills/bionemo-agent-toolkit/skills/complexa-evaluate-pdbs into .cursor/skills/complexa-evaluate-pdbs/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "complexa-evaluate-pdbs", then confirm the skill loads.Cursor copies the folder itself, the same result as the manual copy. Check what it changed before you commit it.
$ gemini skills install https://github.com/NVIDIA-BioNeMo/bionemo-agent-toolkit.git --path skills/bionemo-agent-toolkit/skills/complexa-evaluate-pdbs--scope user (default) or --scope workspace; --path is the subfolder of the repo that holds the skill; --consent skips the security confirmation prompt.
$ npx skills add NVIDIA-BioNeMo/bionemo-agent-toolkit --skill complexa-evaluate-pdbs -a gemini-cliProject install goes to .agents/skills/; add -g for ~/.gemini/skills/.
$ gh skill install NVIDIA-BioNeMo/bionemo-agent-toolkit complexa-evaluate-pdbs --agent gemini-cliProject scope by default (.agents/skills/); add --scope user for a personal install.
$ git clone --depth 1 https://github.com/NVIDIA-BioNeMo/bionemo-agent-toolkit.git skills-src && mkdir -p .gemini/skills && cp -r skills-src/skills/bionemo-agent-toolkit/skills/complexa-evaluate-pdbs .gemini/skills/complexa-evaluate-pdbs && rm -rf skills-srcUse ~/.gemini/skills/ instead of .gemini/skills for a personal install, then run /skills reload.
Gemini CLI skills documentation · loads skills from .gemini/skills/, .agents/skills/
Install the "complexa-evaluate-pdbs" agent skill from https://github.com/NVIDIA-BioNeMo/bionemo-agent-toolkit/tree/main/skills/bionemo-agent-toolkit/skills/complexa-evaluate-pdbs into .gemini/skills/complexa-evaluate-pdbs/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "complexa-evaluate-pdbs", then confirm the skill loads.Gemini CLI copies the folder itself, the same result as the manual copy. Check what it changed before you commit it.
$ gh skill install NVIDIA-BioNeMo/bionemo-agent-toolkit complexa-evaluate-pdbsInstalls for Copilot at project scope by default; add --scope user for a personal install. Preview a skill first with gh skill preview. Needs GitHub CLI 2.90.0 or later (public preview).
$ npx skills add NVIDIA-BioNeMo/bionemo-agent-toolkit --skill complexa-evaluate-pdbs -a github-copilotProject install goes to .agents/skills/; add -g for ~/.copilot/skills/.
$ git clone --depth 1 https://github.com/NVIDIA-BioNeMo/bionemo-agent-toolkit.git skills-src && mkdir -p .github/skills && cp -r skills-src/skills/bionemo-agent-toolkit/skills/complexa-evaluate-pdbs .github/skills/complexa-evaluate-pdbs && rm -rf skills-srcUse ~/.copilot/skills/ instead of .github/skills for a personal install. Commit .github/skills so cloud agent and code review can use it.
GitHub Copilot skills documentation · loads skills from .github/skills/, .claude/skills/, .agents/skills/
Install the "complexa-evaluate-pdbs" agent skill from https://github.com/NVIDIA-BioNeMo/bionemo-agent-toolkit/tree/main/skills/bionemo-agent-toolkit/skills/complexa-evaluate-pdbs into .github/skills/complexa-evaluate-pdbs/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "complexa-evaluate-pdbs", then confirm the skill loads.GitHub Copilot copies the folder itself, the same result as the manual copy. Check what it changed before you commit it.
$ npx skills add NVIDIA-BioNeMo/bionemo-agent-toolkit --skill complexa-evaluate-pdbs -a opencodeOpenCode documents no install command of its own. Project install goes to .agents/skills/; add -g for ~/.config/opencode/skills/.
$ gh skill install NVIDIA-BioNeMo/bionemo-agent-toolkit complexa-evaluate-pdbs --agent opencodeProject scope by default (.agents/skills/); add --scope user for a personal install.
$ git clone --depth 1 https://github.com/NVIDIA-BioNeMo/bionemo-agent-toolkit.git skills-src && mkdir -p .opencode/skills && cp -r skills-src/skills/bionemo-agent-toolkit/skills/complexa-evaluate-pdbs .opencode/skills/complexa-evaluate-pdbs && rm -rf skills-srcUse ~/.config/opencode/skills/ instead of .opencode/skills for a personal install.
OpenCode skills documentation · loads skills from .opencode/skills/, .claude/skills/, .agents/skills/
Install the "complexa-evaluate-pdbs" agent skill from https://github.com/NVIDIA-BioNeMo/bionemo-agent-toolkit/tree/main/skills/bionemo-agent-toolkit/skills/complexa-evaluate-pdbs into .opencode/skills/complexa-evaluate-pdbs/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "complexa-evaluate-pdbs", then confirm the skill loads.OpenCode copies the folder itself, the same result as the manual copy. Check what it changed before you commit it.
Facts
- Skill name
complexa-evaluate-pdbs- GitHub stars
- 478
- Token cost
- ~3.3k tokens
- SKILL.md length
- 1,033 words
- Files
- 4
- Skills in repo
- 14
- Repo updated
- First seen
- Licence
- Custom licence
At a glance
Standalone evaluation of an existing PDB directory with Proteina-Complexa.
- Works in 6 steps: Pre-flight → Identify the design type → Gather inputs (AskUserQuestion) → …
- The user wants to evaluate PDB files
- SKILL.md covers What this skill enables, Step 1: Pre-flight, Step 2: Identify the design type and Step 3: Gather inputs…, plus 7 more sections
- Calls python, bash and python3
What it does
Complexa Evaluate Pdbs is an agent skill from NVIDIA-BioNeMo/bionemo-agent-toolkit. Standalone evaluation of an existing PDB directory with Proteina-Complexa. Use when the user wants to "evaluate PDB files", "re-fold these designs", "compute interface pAE", "compute ipLDDT for a folder", "run AF2 / RF3 / ESMFold on my designs", "score binder candidates", "designability of this folder", "scRMSD for designs", "motif RMSD for these PDBs", "complexa analysis", "complexa evaluate from a PDB directory", "evaluate from pdb dir", or to score third-party outputs (BindCraft, AlphaProteo, RFdiffusion…
Its SKILL.md is about 3.3k tokens, which your agent loads only when the skill is triggered. The skill folder holds 5 other files (for example `evals/evals.json`, `evals/trigger_evals.json` and `reference/eval_configs.md`). Compatibility notes: complexa CLI installed (pip install -e .); CUDA GPU; AF2DIR (colabdesign) or RF3CKPTPATH+RF3EXECPATH (rf3latest); ESMFold weights for monomer paths
It sits in Documents & Office, covering CSV and tabular files. The repository describes itself as: Turn any agent into a life science expert with NVIDIA BioNeMo skills.
When your agent uses it
- The user wants to evaluate PDB files
- Re-fold these designs
- Compute interface pAE
- Compute ipLDDT for a folder
Example prompts
- “evaluate PDB files”
- “re-fold these designs”
- “compute interface pAE”
- “/complexa-evaluate-pdbs”
Requirements
- Python 3
- Compatibility (from SKILL.md): complexa CLI installed (pip install -e .); CUDA GPU; AF2_DIR (colabdesign) or RF3_CKPT_PATH+RF3_EXEC_PATH (rf3_latest); ESMFold weights for monomer paths
- Pre-approved tools (allowed-tools): Bash, Read, Write, AskUserQuestion
Workflow steps
6 steps, taken from the step headings in SKILL.md.
- Pre-flight
- Identify the design type
- Gather inputs (AskUserQuestion)
- Run evaluate → analyze
- Parse results
- Emit manifest
What it can do on your machine
Read from SKILL.md and the folder at commit 2113472. It shows what the files ask for, not the result of running them.
Tool permissions
Pre-approves these tools, so the agent can use them without asking each time:
BashReadWriteAskUserQuestion
From allowed-tools in the SKILL.md frontmatter.
Runs code
Shell commands in SKILL.md call:
pythonbashpython3
From the folder's file list and the shell code blocks in SKILL.md.
Network
No URLs in SKILL.md.
From URLs in SKILL.md, links to its own repository left out.
Credentials
Names no API keys, tokens, secrets or passwords.
From names ending in _API_KEY, _TOKEN, _SECRET, _KEY or _PASSWORD in SKILL.md.
Compatibility
complexa CLI installed (pip install -e .); CUDA GPU; AF2_DIR (colabdesign) or RF3_CKPT_PATH+RF3_EXEC_PATH (rf3_latest); ESMFold weights for monomer paths
From compatibility in the SKILL.md frontmatter.
Context cost
Complexa Evaluate Pdbs loads about 3.3k tokens when it runs. Until then it costs about 193 tokens; SKILL.md has 1,033 words of instructions outside code blocks.
Estimates: characters ÷ 4, the usual rule of thumb; real counts depend on the model's tokenizer. Scripts and assets cost tokens only if the agent reads them.
Safety
Auto-check: notes
The automated check noted patterns worth knowing about, such as sudo or a known installer.
- NoteMentions a .env fileSKILL.md:216
OLDSEEK_EXEC` not on `PATH`. Either fix `.env` (preferred) or disable: `++aggregation.compute_diversity=false ++aggregat - NotePre-approves every shell command (allowed-tools: Bash)SKILL.md
allowed-tools: Bash, Read, Write, AskUserQuestion
Automated static check — not a guarantee. Review scripts before installing. It scans the text of SKILL.md for risky patterns (piping downloads into a shell, reading credential files, hidden Unicode, destructive commands); files beside SKILL.md are not scanned.
SKILL.md
Its licence (Custom licence) doesn't allow us to republish the file, so here is its outline and opening line. It has 1,033 words (~3,329 tokens).
“Score a directory of pre-existing PDB files against the same metrics Proteina-Complexa uses internally. Wraps complexa analysis ++sample_storage_path=: the CLI runs the evaluate step (refold + interface metrics + monomer metrics) and then the analyze step (success thresholds, diversity, pass-rate…”
- name
- complexa-evaluate-pdbs
- allowed-tools
- Bash, Read, Write, AskUserQuestion
- compatibility
- complexa CLI installed (pip install -e .); CUDA GPU; AF2_DIR (colabdesign) or RF3_CKPT_PATH+RF3_EXEC_PATH (rf3_latest); ESMFold weights for monomer paths
Files
SKILL.md and 3 other files in skills/bionemo-agent-toolkit/skills/complexa-evaluate-pdbs of NVIDIA-BioNeMo/bionemo-agent-toolkit.
- SKILL.md
- evals/evals.json
- evals/trigger_evals.json
- reference/eval_configs.md
Open the folder on GitHubat commit 2113472
Compare with similar skills
Complexa Evaluate Pdbs next to the 5 skills that share the most tags, products or categories with it. Stars are the repository's; “used in” counts other GitHub owners with a copy.
| Skill | Stars | Used in | Tokens | Auto-check | Licence | Repo updated |
|---|---|---|---|---|---|---|
| Complexa Evaluate Pdbs this skillNVIDIA-BioNeMo/bionemo-agent-toolkit | 478 | — | ~3.3k | Automated safety check: Notes | Custom licence | |
| Instrument Data To Allotropeaws-samples/amazon-bedrock-agents-healthcare-lifesciences | 274 | 2 repos | ~2.7k | Automated safety check: Pass | Apache-2.0 | |
| Sector Analysttradermonty/claude-trading-skills | 3k | 1 repos | ~2.3k | Automated safety check: Pass | MIT | |
| Cliare Artifact Reviewmodiqo/cliare | 469 | — | ~2.4k | Automated safety check: Pass | Apache-2.0 | |
| Convert Fileduckdb/duckdb-skills | 599 | 1 repos | ~720 | Automated safety check: Notes | MIT | |
| Research Integrity Auditxuzhougeng/wisp-science | 1k | — | ~2.6k | Automated safety check: Pass | AGPL-3.0 |
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Related
Categories
Questions about Complexa Evaluate Pdbs
What does Complexa Evaluate Pdbs do?
Standalone evaluation of an existing PDB directory with Proteina-Complexa. Complexa Evaluate Pdbs is an agent skill from NVIDIA-BioNeMo/bionemo-agent-toolkit. Standalone evaluation of an existing PDB directory with Proteina-Complexa.
When should I use Complexa Evaluate Pdbs?
Complexa Evaluate Pdbs fits situations like: the user wants to evaluate PDB files; re-fold these designs; compute interface pAE; compute ipLDDT for a folder.
How do I install Complexa Evaluate Pdbs in Claude Code?
Run `npx skills add NVIDIA-BioNeMo/bionemo-agent-toolkit --skill complexa-evaluate-pdbs -a claude-code`. Or copy the skill folder (skills/bionemo-agent-toolkit/skills/complexa-evaluate-pdbs in NVIDIA-BioNeMo/bionemo-agent-toolkit) into .claude/skills/complexa-evaluate-pdbs in your project. Claude Code loads it when a task matches its description.
How do I install Complexa Evaluate Pdbs in Codex?
Run `npx skills add NVIDIA-BioNeMo/bionemo-agent-toolkit --skill complexa-evaluate-pdbs -a codex`. Or copy the skill folder (skills/bionemo-agent-toolkit/skills/complexa-evaluate-pdbs in NVIDIA-BioNeMo/bionemo-agent-toolkit) into .agents/skills/complexa-evaluate-pdbs in your project. Codex loads it when a task matches its description.
Can I use Complexa Evaluate Pdbs in Cursor, Gemini CLI or GitHub Copilot?
Cursor, Gemini CLI, GitHub Copilot and OpenCode also load SKILL.md folders. With the skills CLI, run `npx skills add NVIDIA-BioNeMo/bionemo-agent-toolkit --skill complexa-evaluate-pdbs -a cursor` (or -a gemini-cli, github-copilot or opencode for the others). To copy it by hand, put the folder in .cursor/skills/complexa-evaluate-pdbs, .gemini/skills/complexa-evaluate-pdbs, .github/skills/complexa-evaluate-pdbs and .opencode/skills/complexa-evaluate-pdbs in your project.
What does Complexa Evaluate Pdbs need to run?
Going by SKILL.md and its folder, Complexa Evaluate Pdbs needs the command-line tools its instructions call (python, bash and python3). Our summary lists: Python 3. Its frontmatter pre-approves these tools: Bash, Read, Write, AskUserQuestion. Compatibility (from SKILL.md): complexa CLI installed (pip install -e .); CUDA GPU; AF2_DIR (colabdesign) or RF3_CKPT_PATH+RF3_EXEC_PATH (rf3_latest); ESMFold weights for monomer paths.
Does Complexa Evaluate Pdbs access the network?
SKILL.md contains no URLs. Any network use would come from the scripts or tools the agent runs. This is read from the text; nothing was executed.
Is Complexa Evaluate Pdbs safe to install?
Our automated static check of SKILL.md found notes only (mentions a .env file; pre-approves every shell command (allowed-tools: bash)), nothing it rates as a warning. It is not a guarantee. Review the folder before installing.
What licence does Complexa Evaluate Pdbs use?
Complexa Evaluate Pdbs has a licence file (the repository's licence) that doesn't match a standard licence. Read it on GitHub before reusing the skill.
How many tokens does Complexa Evaluate Pdbs use?
About 3.3k tokens (SKILL.md is roughly 13k characters). Agents keep only the skill's name and description in context until a task matches; then they load SKILL.md in full.
What are the alternatives to Complexa Evaluate Pdbs?
Skills that share tags, products or a category with Complexa Evaluate Pdbs: Instrument Data To Allotrope (aws-samples/amazon-bedrock-agents-healthcare-lifesciences, 274 stars), Sector Analyst (tradermonty/claude-trading-skills, 3k stars), Cliare Artifact Review (modiqo/cliare, 469 stars) and Convert File (duckdb/duckdb-skills, 599 stars). The comparison table on this page puts their stars, adoption, token cost, safety result and licence side by side.
Who maintains Complexa Evaluate Pdbs?
NVIDIA-BioNeMo (a GitHub organization) maintains it in NVIDIA-BioNeMo/bionemo-agent-toolkit, which has 478 GitHub stars. The repository holds 14 skills in this directory. The repository was last updated on October 6, 2026.
Source: NVIDIA-BioNeMo/bionemo-agent-toolkit on GitHub. Facts on this page come from the repository at the commit we read; the author's words are quoted as theirs.