Sidebar & Activation

Structure Sidebar

The structure sidebar (codemol/structure_sidebar.py) appears automatically when 2+ structures are loaded. It provides a visual list of loaded structures with click-to-activate behavior.

┌──────────────────────────────┐
│ Structures                   │
│ ┌──────────────────────────┐ │
│ │ ● 1AKE  (active)        │ │
│ │   4AKE                   │ │
│ │   3HTB                   │ │
│ └──────────────────────────┘ │
└──────────────────────────────┘

Auto-Open Behavior

The sidebar is managed by StructureManager:

1. First structure loaded → sidebar stays hidden
2. Second structure loaded → sidebar slides open (animated)
3. All structures cleared → sidebar slides closed

# In StructureManager
def _check_sidebar_visibility(self):
    if self._ctx.session.has_multiple():
        _animate_sidebar(self._sidebar, 0, 200)  # open
    else:
        _animate_sidebar(self._sidebar, 200, 0)  # close

Activation Flow

When the user clicks a structure in the sidebar:

sequenceDiagram
    participant Sidebar
    participant StructureManager
    participant Session as StructureSession
    participant Engine
    participant Window

    Sidebar->>StructureManager: clicked("4AKE")
    StructureManager->>Session: activate("4AKE", cmd)
    Session->>Engine: save scene for "1AKE"
    Session->>Engine: disable "1AKE" + objects
    Session->>Engine: enable "4AKE" + objects
    Session->>Engine: recall scene for "4AKE"
    StructureManager->>Window: update scope to "4AKE"
    Window->>Window: update title bar
    Sidebar->>Sidebar: highlight "4AKE" row

Scoping After Activation

After activation, the window's scope changes. All subsequent commands are automatically scoped to the active structure:

# User activates "4AKE" via sidebar
# Then types:
/rep cartoon protein
# Executes as: cmd.show("cartoon", "model 4AKE and (polymer.protein)")

Keyboard Shortcuts

Shortcut	Action
Click structure name	Activate that structure
Double-click	Activate + zoom to fit

Visual State Per Structure

Each structure maintains independent:

• Representations (cartoon, sticks, surface)
• Colors
• Measurements
• Camera position (via scene save/restore)
• Visibility of associated objects