Atom Biology General Molecule Reaction Tools Trial Virus

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Install Ketcher on Apache Web Server
How to install Ketcher on an Apache Web server? If you want to install Ketcher on a Web server for others to try it remotely, you can follow this tutorial to install it an Apache Web server. 1. Follow the previous tutorial to download and install Ketcher on your local computer in the "./standalone" ... 2024-10-14, 1203🔥, 0💬

What Is Ketcher JavaScript API
What is Ketcher JavaScript API? Ketcher JavaScript API is programming interface provided by Ketcher for your JavaScript code to interact with the Ketcher editor. To access Ketcher JavaScript API, you need to access the "ketcher" object as a property of the content "window" object of the "iframe" whe... 2024-07-25, 1552🔥, 0💬

contentWindow.ketcher - Access "ketcher" Object
How to access the "ketcher" object when Ketcher is loaded in an HTML "iframe" element? As mentioned in the last tutorial, if Ketcher is loaded in an HTML "iframe" element, you can access the "ketcher" object with the follow JavaScript code: lst = document.getElementsByTagName( "iframe");frm = lst[0]... 2024-07-25, 1220🔥, 0💬

Ketcher File Structure
How is the Ketcher file structured? At a high level, a Ketcher file is structured to represent an object with a required property "root", which has a property "nodes" to hold an array of graphical objects. The hight level structure of a Ketcher file looks like this: { "root": { "nodes": [ <ob... 2024-04-14, 683🔥, 0💬

Import Ketcher File to Editor
How to import Ketcher file to the Ketcher editor? If you created a Ketcher file, you can verify it by importing it to the Ketcher editor as described below: 1. Create a Ketcher file, cyclobutane.ket, with a text editor: { "root": { "nodes": [ { "$ref": "mol0" } ] }, "mol0": { "type": "molecule", "at... 2024-03-23, 611🔥, 0💬

Export Ketcher File from Editor
How to export structure from Ketcher editor in Ketcher file format? The best way to learn the Ketcher file format is to export different types of chemical structures for the Ketcher editor in Ketcher file format as described below: 1. Open Ketcher editor as shown in previous tutorials. 2. Select the... 2024-03-23, 547🔥, 0💬

ketcher.setMolecule() - Import Molecule into Ketcher
How to import a molecule structure into the Ketcher with the ketcher.setMolecule() method? To import a molecule structure into the Ketcher, you can use the setMolecule(structure) method provided by the Ketcher API as shown in below: 1. Load the Ketcher editor in an "iframe" HTML element: <ifr... 2024-03-17, 1345🔥, 0💬

ketcher.getMolfile() - Export Molecule in Molfile Format
How to export the molecule structure in Molfile format from the Ketcher with the ketcher.getMolfile() method? To export the molecule structure in Molfile format from the Ketcher, you can use the getMolfile() method provided by the Ketcher API as shown in below: 1. Load the Ketcher editor in an "ifra... 2024-03-17, 1097🔥, 0💬

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<seq>" } ] }, "mol<seq>": { "type": "molecule",... 2024-03-07, 593🔥, 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, 514🔥, 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, 619🔥, 0💬

Adding Text Labels in Ketcher File
How to add text labels in a Ketcher file? You can insert a "text" object structure into the "nodes" array to add a text label in a Ketcher file as shown below: { "type": "text", "data": { "content": <text-definition&gt ;,"position": <location-object&gt ;,"pos": <bounding... 2024-02-28, 587🔥, 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, 634🔥, 0💬

Ketcher File Structure for Reaction
What is the Ketcher file structure for a chemical reaction? The Ketcher file structure for a chemical reaction is an extension of the Ketcher file structure for a molecule. Additional molecule objects are added as reactants, reagents, solvents, and products of the reaction. A long arrow is also adde... 2024-02-18, 607🔥, 0💬

Ketcher File Format for Chemical Structures
Where to find FAQ (Frequently Asked Questions) on Ketcher File Format for Chemical Structures? Here is a list of tutorials to answer many frequently asked questions compiled by FYIcenter.com team on Ketcher File Format for Chemical Structures. What Is Ketcher File Format Ketcher File Structure Expor... 2024-02-11, 660🔥, 0💬

What Is Ketcher File Format
What is Ketcher File Format? A Ketcher file is a JSON document that stores the entire content created in the Ketcher editor. It supports the following features: Supports molecule 3-D structures. Supports chemical reactions. Supports styled text labels. Supports S-Groups. Here is a simple example of ... 2024-02-11, 592🔥, 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, 687🔥, 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, 540🔥, 0💬

Call getSmiles() and getSmarts() Nested
How to call getSmiles() and getSmarts() methods in 2 promises one nested in the other? One way to avoid the bug mentioned in the previous tutorial is to call ketcher.getSmiles() and ketcher.getSmarts() methods in 2 promises one nested in the other. This can be done by calling ketcher.getSmiles() fir... 2024-01-24, 678🔥, 0💬

Call getSmiles() and getSmarts() Parallelly
Why do getSmiles() and getSmarts() methods return the same result, if they are called in 2 parallel promises? There seems to be a bug in Ketcher v2.11.0 release. If you call getSmiles() and getSmarts() methods one after the other, you are creating 2 promises The first promise seems to be overriding ... 2024-01-24, 642🔥, 0💬

Export Chemical Structure in All Formats
How to export the chemical structure in all Formats? If you want to export the chemical structure from the Ketcher editor in all formats, you can call those get*() methods in chained promises as shown the HTML document below: <html> <!-- export-structure-in-all-format s.htmlCopy... 2024-01-15, 776🔥, 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, 592🔥, 0💬

Export Chemical Structure in All Formats Failed
What will happen if I export the chemical structure in all formats in parallel promises? If you export the chemical structure in all formats in parallel promises by calling get*() methods, you will get unpredictable results. This is caused by a code bug in the Ketcher v2.11.0 release. The following ... 2024-01-10, 796🔥, 0💬

Ketcher Editor Interface
Where to find FAQ (Frequently Asked Questions) on Ketcher Editor Interface? Here is a list of tutorials to answer many frequently asked questions compiled by FYIcenter.com team on Ketcher Editor Interface. What Is Ketcher Editor Interface editor.struct() - Get Entire Structure editor.struct().atoms ... 2024-01-10, 774🔥, 0💬

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Atom Biology General Molecule Reaction Tools Trial Virus