AtomSpec

Atom representation. Depending on the input file format, not all fields may be defined.

Source

Members

atom :string

Atom name; may be more specific than 'elem' (e.g 'CA' for alpha carbon)

Type:
  • string
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b :number

Atom b factor data

Type:
  • number
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bondOrder :Array

Array of this atom's bond orders, corresponding to bonds identfied by 'bonds'

Type:
  • Array
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bondStyles :Array

custom bond styling by position in bonds

Type:
  • Array
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bonds :Array

Array of atom ids this atom is bonded to

Type:
  • Array
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callback :function

Callback click handler function to be executed on this atom and its parent viewer

Type:
  • function
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chain :string

Chain this atom belongs to, if specified in input file (e.g 'A' for chain A)

Type:
  • string
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clickable :boolean

Set this flag to true to enable click selection handling for this atom

Type:
  • boolean
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color :ColorSpec

Atom's color, as hex code or built-in color string

Type:
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elem :string

Element abbreviation (e.g. 'H', 'Ca', etc)

Type:
  • string
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hetflag :boolean

Set to true if atom is a heteroatom

Type:
  • boolean
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hover_callback :function

Callback hover handler function to be executed on this atom and its parent viewer

Type:
  • function
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hoverable :boolean

Set this flag to true to enable hover selection handling for this atom

Type:
  • boolean
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index :number

Index of atom in molecule

Type:
  • number
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invert :boolean

for selection, inverts the meaning of the selection

Type:
  • boolean
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lchain :string

Label chain (not author)

Type:
  • string
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lresi :number

Label residues number (not author)

Type:
  • number
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lresn :string

Residue label name

Type:
  • string
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pdbline :string

If applicable, this atom's record entry from the input PDB file (used to output new PDB from models)

Type:
  • string
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properties :Record.<string, any>

Optional mapping of additional properties

Type:
  • Record.<string, any>
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resi :number

Residue number

Type:
  • number
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resn :string

Parent residue name

Type:
  • string
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serial :number

Atom's serial id number

Type:
  • number
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singleBonds :boolean

true if this atom forms only single bonds or no bonds at all

Type:
  • boolean
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ss :string

Secondary structure identifier (for cartoon render; e.g. 'h' for helix)

Type:
  • string
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style :AtomStyleSpec

style of atom

Type:
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surfaceColor :ColorSpec

Hex code for color to be used for surface patch over this atom

Type:
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unhover_callback :function

Callback handling "unhover" to be executed on this atom and its parent viewer

Type:
  • function
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x :number

Atom's x coordinate

Type:
  • number
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y :number

Atom's y coordinate

Type:
  • number
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z :number

Atom's z coordinate

Type:
  • number
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