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Ketcher File Structure for Molecule
What is the Ketcher file structure for a molecule structure?
✍: FYIcenter.com
To represent a single molecule in a Ketcher file, you need to include a referenced-object in the "nodes" array as shown below:
{ "root": { "nodes": [ { "$ref": "mol<seq>" } ] }, "mol<seq>": { "type": "molecule", ... } }
The molecule object structure should include an "atoms" array and a "bonds" array as shown below:
"mol<seq>": { "type": "molecule", "atoms": [ <atom>, <atom>, ... <atom> ], "bonds": [ <bond>, <bond>, ... <bond> ] }
The "atom" object must have 2 required properties: "label" for the atom symbol, and "location" for the atom coordinates. For example, the following structure represents a carbon atom located at (0, 0, 0):
{ "label": "C", "location": [ 0, 0, 0 ] }
The "bond" object must have 2 required properties: "type" indicating the type of the bond, and "atoms" specifying the connecting atoms of the bond. For example, the following structure represents a single bond connecting atom #0 and atom #1:
{ "type": 1, "atoms": [ 0, 1 ] }
Here is a Ketcher file for a carbon dioxide molecule:
{ "root": { "nodes": [ { "$ref": "mol0" } ] }, "mol0": { "type": "molecule", "atoms": [ { "label": "O", "location": [ 0, 0, 0 ] }, { "label": "C", "location": [ 1, 0, 0 ] }, { "label": "O", "location": [ 2, 0, 0 ] } ], "bonds": [ { "type": 1, "atoms": [ 0, 1 ] }, { "type": 1, "atoms": [ 1, 2 ] } ] } }
⇒ Molecule Structure with Directed Bonds
⇐ Import Ketcher File to Editor
2024-03-07, 352🔥, 0💬
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