Collections:
One Molecule with Disconnected Parts
Can I specify a single molecule object with multiple disconnected parts in a Ketcher file?
✍: FYIcenter.com
Yes, you can specify a single molecule object with multiple disconnected parts in a Ketcher file.
Here is a simple example of Ketcher file with a single "molecule" object of a 4-carbon chain. But the bond between the second and third carbon is removed with 2 disconnected remaining parts:
{ "root": { "nodes": [ { "$ref": "mol0" } ] }, "mol0": { "type": "molecule", "atoms": [ { "label": "C", "location": [ 0.59, 0.0, 0 ] }, { "label": "C", "location": [ 1.46, 0.5, 0 ] }, { "label": "C", "location": [ 2.33, 0.0, 0 ] }, { "label": "C", "location": [ 3.19, 0.5, 0 ] } ], "bonds": [ { "type": 1, "atoms": [ 0, 1 ] }, { "type": 1, "atoms": [ 2, 3 ] } ] } }
You can import the above Ketcher file to the Ketcher editor. But it will be considered as a 2-molecule structure. If you export it as a Ketcher file, you will see 2 "molecule" objects like this:
{ "root": { "nodes": [ { "$ref": "mol0" }, { "$ref": "mol1" } ] }, "mol0": { "type": "molecule", "atoms": [ { "label": "C", "location": [ 0.59, 0.0, 0 ] }, { "label": "C", "location": [ 1.46, 0.5, 0 ] } ], "bonds": [ { "type": 1, "atoms": [ 0, 1 ] } ] }, "mol1": { "type": "molecule", "atoms": [ { "label": "C", "location": [ 2.33, 0.0, 0 ] }, { "label": "C", "location": [ 3.19, 0.5, 0 ] } ], "bonds": [ { "type": 1, "atoms": [ 0, 1 ] } ] } }
⇒ Scaling Issue on Importing Ketcher File
⇐ Ketcher File Structure for Reaction
2024-01-31, 201🔥, 0💬
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