Atom Biology General Molecule Reaction Tools Trial Virus

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Reaction with Stereocenters in CDXML Format Error
Why am I getting CDXML loader errors on reactions with stereocenters? Ketcher 2.11.0 has a code bug that gives you a CDXML loader error if you try to load a reaction with stereocenters in CDXML (ChemDraw XML) format as shown in this tutorial. 1. Open Ketcher editor as shown in previous tutorial. 2. ... 2024-01-10, 1219🔥, 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, 1216🔥, 0💬

Introduction to Ketcher
Where to find FAQ (Frequently Asked Questions) on basic understanding of Ketcher, Chemical Structure Editor in JavaScript? Here is a list of tutorials to answer many frequently asked questions compiled by FYIcenter.com team on basic understanding of Ketcher, Chemical Structure Editor in JavaScript. ... 2023-11-02, 1204🔥, 0💬

Refresh Molecule in JSME Editor
How to refresh (read and reset) molecule created in JSME editor with the Web server? If you want refresh molecule properties displayed in the JSME editor, you can use a PHP script on the Web server to read and reset the molecule structure in the JSME editor. 1. Create an HTML form with an input fiel... 2023-04-13, 1185🔥, 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, 1178🔥, 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": [ &lt;ob... 2024-04-14, 1177🔥, 0💬

openbabel.cheminfo.org/v1/convert - Web API
How to make a HTTP request to the Open Babel Web API at openbabel.cheminfo.org/v1/conv ert?You can call the Open Babel Web API at https://openbabel.cheminfo.org /v1/convertwith a HTTP POST request as shown below. 1. Use "curl" command to call the Web API to generate a 3D SDF file from a given SMILES... 2023-01-24, 1163🔥, 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, 1143🔥, 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, 1126🔥, 0💬

editor.struct() - Get Entire Structure
How to get the entire structure currently in the Ketcher editor with the editor.struct() method? If you want to get detailed information about the entire structure currently in the Ketcher editor, you can call the editor.struct() method on the Ketcher Editor interface. Here is an HTML document that ... 2023-12-08, 1114🔥, 0💬

editor.structSelected() - Get Selected Sub-Structure
How to get the selected sub-structure currently in the Ketcher editor with the editor.structSelected() method? If you want to get detailed information about the selected sub-structure currently in the Ketcher editor, you can use the editor.structSelected() method on the Ketcher Editor interface. Her... 2023-11-23, 1113🔥, 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, 1101🔥, 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, 1081🔥, 0💬

Restore Structure from Server to Ketcher
How to restore a chemical structure from the Web server to the Ketcher editor? If you want to build a chemical structure editor with the capability to save the structure on the Web server and restore it later to the Ketcher, you should follow steps described below: 1. Using JavaScript to export the ... 2023-10-11, 1081🔥, 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, 1073🔥, 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": &lt;text-definition&gt ;,"position": &lt;location-object&gt ;,"pos": &lt;bounding... 2024-02-28, 1063🔥, 0💬

Install JSME 2017-02-26 Version
How to download and install JSME? If you want to try JSME on your own computer, you can follow this tutorial to download and install it. 1. Go to JSME Website at https://www.peter-ertl.com/jsm e/. 2. Click "Download the JSME 2017-02-26" to start downloading. 3. Save the download file as "JSME_2017-0... 2023-01-18, 1052🔥, 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, 1051🔥, 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&lt;seq&gt;" } ] }, "mol&lt;seq&gt;": { "type": "molecule",... 2024-03-07, 1019🔥, 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, 1017🔥, 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, 1005🔥, 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, 998🔥, 0💬

Failed to Load D4DF9EC9DD21B943E35F3D5696D5D2A1.cache.js
Why JSME editor is not showing after upgrade to the 2022-09-26 version? If you upgraded JSME to the 2022-09-26 version from an older version, the JSME editor may fail to show up in your browser. In the browser developer console, you will see that a required JSME JavaScript file, D4DF9EC9DD21B943E35F... 2023-04-13, 989🔥, 0💬

JSApplet.Inchi.computeInchi() - Generate InChI
How to generate InChI and InChIKey with the JSApplet.Inchi.computeInchi() method? The latest version of JSME allows you to generate InChI and InChIKey from a given molecule in SDF format. Here are the steps you can follow to do this in JavaScript code: 1. Create an empty object called "JSApplet" and... 2023-01-18, 985🔥, 0💬

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Atom Biology General Molecule Reaction Tools Trial Virus