| name | pdb-viewer |
| description | Use this skill when user wants to view one or multiple PDB / SDF files in the 3D structure viewer. Trigger when user mentions: open pdb, open sdf, 3D structure, view protein, view molecule, or provides local .pdb/.sdf file(s) to view. Supports viewing multiple files simultaneously by chaining path parameters with '&'. |
PDB 3D Structure Viewer Skill
Overview
Open one or multiple local PDB / SDF files in the 3D structure viewer. The viewer URL is read from the PDB_VIEWER_URL environment variable (default: https://canvas.golab.chat).
Workflow
- check if the given pdb/sdf file(s) exist:
- copy the file(s) into ./upload directory
- construct the viewer hyperlink by:
- For single file: use
path=/app/huntianling/uploads/{{FILE_NAME}}
- For multiple files: chain with
&, e.g., path=file1.pdb&path=file2.sdf
- replace {{VIEWER_URL}} with the actual viewer URL
Hyperlink Template
Single File
<a href="{{VIEWER_URL}}/#/three-structure?path=/app/huntianling/uploads/{{FILE_NAME}}" target="_blank">View: {{FILE_NAME}}</a>
Multiple Files
<a href="{{VIEWER_URL}}/#/three-structure?path=/app/huntianling/uploads/{{FILE_NAME_1}}&path=/app/huntianling/uploads/{{FILE_NAME_2}}" target="_blank">View: {{FILE_NAME_1}} & {{FILE_NAME_2}}</a>
Examples
Single File
For file: /app/huntianling/uploads/01KKG0GM1X3MY196VW83EYA79G-Tyk2_protein.pdb
Result: <a href="https://canvas.golab.chat/#/three-structure?path=/app/huntianling/uploads/01KKG0GM1X3MY196VW83EYA79G-Tyk2_protein.pdb" target="_blank">View: 01KKG0GM1X3MY196VW83EYA79G-Tyk2_protein.pdb</a>
Multiple Files (Protein + Ligand)
For files:
/app/huntianling/uploads/tyk2_protein.pdb/app/huntianling/uploads/ligand_docked.sdf
Result: <a href="https://canvas.golab.chat/#/three-structure?path=/app/huntianling/uploads/tyk2_protein.pdb&path=/app/huntianling/uploads/ligand_docked.sdf" target="_blank">View: tyk2_protein.pdb & ligand_docked.sdf</a>
