Atom Biology General Molecule Reaction Tools Trial Virus

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Examples Provided in JSME
Where to find more examples on using JSME? The JSME distribution package provides a number example on how to use JSME. If you open "./JSME_2022-09-26/index.html" in a Web browser, you see the following examples: JSME_minimal.html - minimalistic example how to incorporate JSME into a web page JSME_te... 2023-01-18, 1709🔥, 0💬

Substructure Search with Fingerprints
Can I do Substructure Search with fingerprints using Open Babel? Yes, you can do Substructure Search with fingerprints using Open Babel. All you have to do is to take substructure as the query molecule and run a similarity search using the fingerprint output option "-o fpt ". When Open Babel calcula... 2020-12-02, 1700🔥, 0💬

indigo.generateImageAsBase64() - Generate Image as Base64
How to generate images of a given structure as a Base64 encoded string with the indigo.generateImageAsBase64() method? If you want to generate an image of a given structure in PNG, JPEG, or SVG format and Base64 encoded, you can use the indigo.generateImageAsBase64() method on the Ketcher Indigo int... 2023-11-09, 1698🔥, 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, 1695🔥, 0💬

ketcher.getRxn() - Export Reaction in RXN Format
How to export the reaction structure in RXN format from the Ketcher with the ketcher.getRxn() method? To export the reaction structure in RXN format from the Ketcher, you can use the getRxn() method provided by the Ketcher API as shown in below: 1. Load the Ketcher editor in an "iframe" HTML element... 2023-12-10, 1690🔥, 0💬

Save Structure from Ketcher to Server
How to save structures created in Ketcher editor to the Web server? If you want to save the chemical structure created in the Ketcher editor to the backend Web server, you need write JavaScript code to extract the molecule data and send it as an HTML form parameter to the server. 1. Create a new HTM... 2023-10-11, 1688🔥, 0💬

"obchiral" - Print Chirality Information
What Is "obchiral" command? How to use it to Print Chirality Information? "obchiral" command is a command line tool provided in the Open Babel package that allows you to calculate and print molecule chirality information. Here is the user manual of the "obchiral" command. NAME obchiral -- print mole... 2020-11-22, 1686🔥, 0💬

"babel" Command - Output Data Destination and Format
How to specify Output Data Destination and Format for a "babel" command? "babel" command arguments and options are organized into 3 sections as shown in the following syntax to convert chemical data from input to output with specified options. babel input_section output_section option_section You us... 2021-07-19, 1684🔥, 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, 1680🔥, 0💬

"babel ... -o svg" - Two "svg" Tag Levels
Why am getting two "svg" tag levels in SVG source code generated by the "babel" command? If you are using Open Babel 2.4.1 or higher, you will notice that there are two "svg" tag levels in SVG source code generated by the "babel" command. The main reason for using two "svg" tag levels for including ... 2020-07-22, 1677🔥, 0💬

"babel -x..." Command - Extra Output Writing Options
How to pass extra options for "babel" to write output data of a specific format? If you want to pass extra options for "babel" to write output data of a specific format, you need to use one or more "-x..." options in the "babel" command line as shown in the following syntax: babel input_section outp... 2020-07-15, 1676🔥, 0💬

Write Stereoinformation to Output
How stereoinformation is being written to output data by Open Babel? Stereoinformation is being written to output data based on stereo centers maintained by Open Babel according the following rules: 1. 3D Stereoinformation - By default, 3D coordinates are copied over from input data to output data w... 2023-08-17, 1672🔥, 0💬

"babel" Command - Input Data Source and Format
How to specify Input Data Source and Format for a "babel" command? "babel" command arguments and options are organized into 3 sections as shown in the following syntax to convert chemical data from input to output with specified options. babel input_section output_section option_section You use inpu... 2021-07-19, 1663🔥, 0💬

"babel ... -o svg" - Generating SVG Pictures
Where to find FAQ (Frequently Asked Questions) on using Open Babel to generate SVG Pictures from molecule input data? Here is a list of tutorials to answer many frequently asked questions compiled by FYIcenter.com team on using Open Babel to generate SVG Pictures from molecule input data. "babel -o ... 2021-07-19, 1660🔥, 0💬

"babel" - FP2 Fingerprint Fragment Ends at Ring
What happens if a ring is in the molecule FP2 fragment path? In the Open Babel FP2 fingerprint algorithm, if a ring is in the fragment path, the path will end when the atom meets the same atom again in the path. In other words, the same atom in a ring should not appear twice in the same fragment pat... 2020-12-02, 1655🔥, 0💬

Stereo Perception Performed by Open Babel
What is stereo perception performed by Open Babel? Stereo perception performed by Open Babel is the process of constructing stereo centers with stereoinformation received from input data. Stereo perception is performed in the following order of precedence: 1. Constructing stereo centers with 3D ster... 2022-11-16, 1650🔥, 0💬

"babel" Command - From STDIN To STDOUT
Can I use "babel" to convert chemical data from "stdin" to "stdout" without input and output files? Yes, you can use "babel" to convert chemical data from "stdin" to "stdout" without input and output files. Just use "-i ..." and "-o" flags to specify input data format and output data format. For exa... 2021-07-19, 1647🔥, 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, 1638🔥, 0💬

"obgrep" - Search Molecules using SMARTS
What Is "obgrep" command? How to use it to Search Molecules using SMARTS strings? "obgrep" command is a command line tool provided in the Open Babel package that allows you to Search Molecules using SMARTS strings. "obgrep" command does the same job as the "babel ... -s ..." with more options. Here ... 2020-11-11, 1633🔥, 0💬

"babel -i fs ... -s ... -at score_range" - Similarity Search
How to perform a similarity search in a given score range using the fastsearch index file with the "babel" command? If you want to perform a similarity search in a specific score range using the fastsearch index file, you can use the following "babel" command syntax: babel -i fs index_file output_se... 2020-08-25, 1631🔥, 0💬

"babel -i fs ... -s SMILES" - Substructure Search with Index
How to perform a substructure search using the fastsearch index file with the "babel" command? If you want to perform a substructure search using the fastsearch index file, you can use the following "babel" command syntax: babel -i fs index_file output_section -s SMILES In the above command: "-i fs ... 2020-05-25, 1606🔥, 0💬

"babel -d" Command - Delete Hydrogens from Molecule Data
How to delete hydrogen atoms from molecule data during data conversion? If hydrogen atoms of a molecule are included in the input data source, you can use the "babel" generic option "-d" remove those hydrogen atoms during the molecule data conversion process. Here is an example of using the "-d" opt... 2020-07-15, 1603🔥, 0💬

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, 1592🔥, 0💬

"babel -i fs ... -s query_file" - Substructure Search
Why am I getting no results with "babel -i fs ... -s query_file" command? It should perform a substructure search in a fastsearch index file. According to the "babel -H fs" help document, you can perform a substructure search in a fastsearch index file with the query molecule stored in a file in any... 2020-05-25, 1585🔥, 0💬

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Atom Biology General Molecule Reaction Tools Trial Virus