Atom Biology General Molecule Reaction Tools Trial Virus

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Ketcher File Structure for Molecule
What is the Ketcher file structure for a molecule structure? 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&lt;seq&gt;" } ] }, "mol&lt;seq&gt;": { "type": "molecule",... 2024-03-07, 1233🔥, 0💬

indigo.calculate() - Calculates Chemical Properties
How to calculate chemical properties of a given structure with the indigo.calculate() method? If you want to calculate chemical properties like mass and weight of a given chemical structure you can use the indigo.calculate() method on the Ketcher Indigo interface. Here is an HTML document that shows... 2023-11-09, 1223🔥, 0💬

Call getSmiles() and getSmarts() Chained
How to call getSmiles() and getSmarts() methods in 2 promises one chained to the other? Another way to avoid the bug mentioned in the previous tutorial is to call ketcher.getSmiles() and ketcher.getSmarts() methods in 2 chained promises. Chained promises use fulfilled and rejected handlers of the pr... 2024-01-15, 1212🔥, 0💬

Molecule with Substituted Functional Group
How to specify a S-Group (Substituted Functional Group) in a molecule structure in Ketcher file format? There are 2 options to specify a S-Group (Substituted Functional Group) in a molecule structure: 1. Specify S-Group without Group Substructure: Just replace the atom symbol at the s-group attachin... 2024-02-28, 1206🔥, 0💬

editor.options() - Get Editor Options
How to get a list of options used by the Ketcher editor with the editor.options() method? If you want to get a list of options used by the Ketcher editor, you can use the editor.options() method on the Ketcher Editor interface. Here is an HTML document that shows you how to get a list of options cur... 2023-11-18, 1197🔥, 0💬

Bond Type Codes in Ketcher File
What are bond type codes supported by Ketcher file? Ketcher file supports the following bond type codes: Single bond - "type": 1 Double bond - "type": 2 Triple Bond - "type": 3 Any bond - "type": 8 Aromatic bond - "type": 4 Single/double bond - "type": 5 Single/aromatic bond - "type": 6 Double/aroma... 2024-02-18, 1192🔥, 0💬

editor.struct().loops - Get Loop List
How to get a list of loops currently in the Ketcher editor with the editor.struct().loops property? If you want to get a list of loops currently in the Ketcher editor, you can use the editor.struct().loops property on the Ketcher Editor interface. Here is an HTML document that shows you how to get a... 2023-11-23, 1183🔥, 0💬

One Molecule with Disconnected Parts
Can I specify a single molecule object with multiple disconnected parts in a Ketcher file? 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 betw... 2024-01-31, 1173🔥, 0💬

editor.struct().atoms - Get Atom List
How to get a list of atoms currently in the Ketcher editor with the editor.struct().atoms property? If you want to get a list of atoms currently in the Ketcher editor, you can use the editor.struct().atoms property on the Ketcher Editor interface. Here is an HTML document that shows you how to get a... 2023-12-01, 1126🔥, 0💬

editor.struct().bonds - Get Bond List
How to get a list of bonds currently in the Ketcher editor with the editor.struct().bonds property? If you want to get a list of bonds currently in the Ketcher editor, you can use the editor.struct().bonds property on the Ketcher Editor interface. Here is an HTML document that shows you how to get a... 2023-12-01, 1106🔥, 0💬

Show InChI String on Ketcher
How to display the InChI string of the molecule in Ketcher editor? You can follow steps below to display the InChI string of the molecule in Ketcher editor. 1. Open Ketcher editor as shown in previous tutorial. 2. Select the "Benzene" button in the template toolbar at the bottom of the editor window... 2023-10-27, 1103🔥, 0💬

Molecule Structure with Directed Bonds
How to specify a directed bond at a stereocenter in a molecule structure in Ketcher file format? You need to use the optional "stereo" property to specify a directed bond at a stereocenter in a molecule structure. For example: "stereo": 1 - for a upward bond "stereo": 6 - for a downward bond Note th... 2024-03-07, 1039🔥, 0💬

Scaling Issue on Importing Ketcher File
Why is my reaction schema scaled badly when imported from the Ketcher editor UI? The Ketcher editor UI seems to have a code bug. When a reaction schema stored in a Ketcher file is imported from the editor user interface, atom locations and the reaction arrow may be scaled down or up when mapping to ... 2024-01-31, 1025🔥, 0💬

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Atom Biology General Molecule Reaction Tools Trial Virus