Class: Molecule

structure.Molecule

Molecule

Constructor

new Molecule()

Atomic model

Author:
  • Jean-Christophe Taveau

Extends

Members

(static) threeToOne :string

Three to One Letter Converter for amino-acids and nucleotides

Type:
  • string
Example
var aa   = Structure.threeToOne("GLN"); // returns 'Q' in uppercase
var nucl = Structure.threeToOne("DA"); // returns 'a' in lowercase

atoms :Array(Atom)

Atoms - Array of module:mol.Atom

Type:
  • Array(Atom)
Properties:
Name Type Description
atom Atom
Properties
Name Type Description
type string

ATOM or HETATM
serial number

ID of the atom in the file
name string

Atom name according to the chemical nomenclature
altLoc char

Alternate Location of the atom
group string

Group name the atom belongs (three-chars code)
groupID string

Location of the group (residue or nucleotide) in the chain.
chain char

Chain ID
x number

X-coordinate
y number

Y-coordinate
z number

Z-coordinate
symbol string

Chemical symbol
See:

bbox

Bounding Box

Properties:
Name Type Description
min vec3

Top-left-front corner of the bounding box

Properties
Name Type Description
x number

X-coordinate of the 'min' corner
y number

Y-coordinate of the 'min' corner
y number

Z-coordinate of the 'min' corner
max vec3

Bottom-right-back corner of the bounding box

Properties
Name Type Description
x number

X-coordinate of the 'max' corner
y number

Y-coordinate of the 'max' corner
z number

Z-coordinate of the 'max' corner
Inherited From:

bonds :Array(Bond)

Bonds

Type:
  • Array(Bond)
See:
  • mol.Bond

centroid :vec3

Center of Gravity - Centroid

Type:
  • vec3
Properties:
Name Type Description
centroid vec3

Center of gravity or centroid of this structure

Properties
Name Type Description
x number

X-coordinate
y number

Y-coordinate
y number

Z-coordinate
Inherited From:

chains

Chains

colors :Array(RGBColor)

RGB Colors

Type:
  • Array(RGBColor)

ID :string

Identifier

Type:
  • string
Inherited From:

information :object

Information

Type:
  • object
Inherited From:

Methods

atomFinder(callback) → {Array(Atom)}

Filter the atoms in function of their properties

Parameters:
Name Type Description
callback function

A function for filtering
Returns:
Type
Array(Atom)
Example
// Extract CA atoms from mystructure
var selA = mystructure.atomFinder(
    function (atom) {
        if ( atom.name === 'CA') {
             return true;
        } 
    }
);

calcPhiPsi()

Compute the phi and psi dihedral angles of this structure. The angles are stored in the CA atom of each group.

Example
// Compute phi and psi dihedral angles from mystructure
mystructure.calcPhiPsi();
console.log(mystructure.getAtomByLabel("[10].CA").phi);  //

fasta() → {string}

Return the primary sequence in FASTA format

Returns:

The sequence in FASTA format

Type
string

finder(src, callback) → {Array(Atom)}

Filter the atoms or bonds in function of their properties

Parameters:
Name Type Description
src string

The type of objects (ATOM or BOND ) on which the filter is applied
callback function

A function for filtering
Returns:
Type
Array(Atom)
Example
// Extract CA atoms from mystructure
var selA = mystructure.finder(
    'ATOM', 
    function (atom) {
        if ( atom.name === 'CA') {
             return true;
        } 
    }
);

getAtomByLabel(pattern) → {Atom}

Get first atom corresponding to the pattern In MOWGLI, each atom has a label following the following syntax:

  • <PDBID>.<modelID>.<chainID>[<secStruct>].<groupName>([<groupSerial>].<atomName>[<atomSerial>]
  • A.[1].CA corresponds to the alpha carbon belonging to the first residue of chain A of the PDB structure 1ZNI
  • .CA corresponds to the first alpha carbon found in this structure
Parameters:
Name Type Description
pattern string

A simplified regular expression
Returns:
Type
Atom
Example
// Get the first atom carbon alpha (CA) found in chain B 
var atom = mystructure.getAtomByLabel("B*.CA");

isMolecule() → {boolean}

Is this structure an atomic model? (instance of class Molecule)

Inherited From:
Returns:
  • true if this structure is an atomic model.
Type
boolean

isRaster() → {boolean}

Is this structure a 2D/3D-raster? (instance of class Raster)

Inherited From:
Returns:
  • true if this structure is a 2D- or 3D-raster (image or volume/map).
Type
boolean

secondary() → {string}

Return the secondary structures in FASTA format -- if available.

Returns:

The secondary structures of sequence in FASTA format

Type
string

setTitle(str)

Set Title

Parameters:
Name Type Description
str string

Set a new title
Inherited From: