Selection Aliases¶

Overview¶

codemol provides user-friendly aliases for common selection expressions. When you type protein in a command, it resolves to polymer.protein before reaching the rendering engine.

Built-in Aliases¶

Alias	Resolves To	Description
`protein`	`polymer.protein`	Protein chains
`ligand`	`organic`	Small-molecule ligands
`solvent`	`solvent`	Water molecules
`metals`	`metals`	Metal ions
`backbone`	`backbone`	Backbone atoms (N, CA, C, O)
`sidechain`	`sidechain`	Side-chain atoms
`ions`	`inorganic`	Inorganic ions
`nucleic`	`polymer.nucleic`	Nucleic acid chains

How Resolution Works¶

The resolve() function in selection_aliases.py handles alias expansion:

resolve("protein")     # → "polymer.protein"
resolve("chain A")     # → "chain A"  (not an alias, passes through)
resolve("ligand")      # → "organic"

Resolution happens inside dispatch(), after argument fitting but before scoping:

graph LR
    A[User arg: protein] --> B[resolve]
    B --> C[polymer.protein]
    C --> D[scope]
    D --> E["model 1AKE and (polymer.protein)"]

User Overrides with `/set`¶

Users can override built-in aliases or create new ones using /config set:

/config set alias protein "polymer.protein and not resn ACE NME"
/config set alias active_site "resi 45-60 and chain A"

Overrides persist in ~/.codemol/config.json and take priority over built-in aliases.

Aliases in Practice¶

/rep cartoon protein         # → cartoon polymer.protein
/show ligand                 # → show organic
/hide solvent                # → hide solvent
/color bychain protein       # → bychain polymer.protein
/interactions hbonds ligand  # → hbonds organic

Combining aliases with selection syntax

You can mix aliases with standard selection expressions:

/rep sticks ligand and chain A
# Resolves to: sticks organic and chain A