Atom Biology General Molecule Reaction Tools Trial Virus

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"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, 1541🔥, 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, 1539🔥, 0💬

What Is Embedded 3Dmol Viewer
What Is Embedded 3Dmol Viewer? Embedded 3Dmol Viewer is a built-in 3Dmol viewer in the 3Dmol.js library. You can assign the Embedded 3Dmol Viewer to a DIV element in your HTML document using a special "class=viewer_3Dmoljs" attribute. Molecule data, display styles and other options can be specified ... 2023-01-30, 1530🔥, 0💬

Hash Bond with Solid Line
Why Hash Bond with a Solid Line used by Open Babel? Sometimes, when a hash bond is located on a ring structure, Open Babel adds a solid line to the hash bond. Here is an example SDF/Mol file, Hash-with-Solid-Line.sdf, that has 4 stereo centers on a ring structure. Hash-with-Solid-Line FYICenter.com ... 2022-07-26, 1529🔥, 0💬

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, 1527🔥, 0💬

Read Stereoinformation from Input
How stereoinformation is being read from input data by Open Babel? Most molecule data files store stereoinformation in 3 ways: 0D, 2D, and 3D. 0D: Stereoinformation in 0 dimension is defined by parity (or chirality) at atom level. 2D: Stereoinformation in 2 dimension is defined by bond style as wedg... 2022-11-16, 1525🔥, 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, 1513🔥, 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, 1513🔥, 0💬

URL to Start Online 3Dmol Viewer
What Is URL to Start the Online 3Dmol Viewer? You can use the following URL to the the Online 3Dmol Viewer: https://3dmol.csb.pitt.edu/vie wer.htmlThe 3Dmol Viewer will display a blank window with a menu icon. Click the menu icon, you can see 3 options to load the molecule data into the viewer: Sele... 2023-09-07, 1511🔥, 0💬

Use the Online Version of 3Dmol.js Library
How to use the online version of the 3Dmol.js Library to draw a graphical object? I don't want to install the library locally. Yes, you can follow these steps to the online version of the 3Dmol.js library to draw graphical objects. The online version is located at https://3Dmol.csb.pitt.edu/bui ld/3D... 2022-12-24, 1509🔥, 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, 1501🔥, 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, 1499🔥, 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, 1497🔥, 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, 1496🔥, 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, 1495🔥, 0💬

Running Open Babel on CentOS
Where to find FAQ (Frequently Asked Questions) on running Open Babel on CentOS? Here is a list of tutorials to answer many frequently asked questions compiled by FYIcenter.com team on running Open Babel on CentOS. Open Babel Installation Options on CentOS "DNF/YUM search" - No Open Babel Binary Pack... 2020-10-20, 1494🔥, 0💬

"style={...};{...}" - Specify Multiple Styles
How to Specify Multiple Styles using the "style={...};{...}" URL parameter in the Online 3Dmol Viewer? If you want overlay the selected structure in multiple styles, you can provide a semicolons separated list of styles. For example, the following URL displays the protein structure overlaid in 2 sty... 2023-09-07, 1489🔥, 0💬

"select=resi:..." - Select Protein Residues by Numbers
How to select Protein Residues by Numbers using the "select=resi:..." URL parameter in the Online 3Dmol Viewer? There are different ways to select Protein Residues by Numbers: select=resi:{number} - Select single residues. select=resi:{number-number} - Select multiple residues in a range. select=res... 2023-09-07, 1478🔥, 0💬

Using Fastsearch Fingerprint Index
Where to find FAQ (Frequently Asked Questions) on Using Fastsearch Fingerprint Index with Open Babel? Here is a list of tutorials to answer many frequently asked questions compiled by FYIcenter.com team on Using Fastsearch Fingerprint Index with Open Babel. "babel ... -o fs" - Generate Fastsearch In... 2020-09-30, 1478🔥, 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, 1469🔥, 0💬

"babel ... -o svg -xd -xP300" Bug - Option -d takes a parameter
Why "babel ... -o svg -xd -xP300" command is giving the "Option -d takes a parameter" error in Open Babel 2.4? It seems to be another code bug in the "babel" command in Open Babel 2.4 release. "-xd" option for "svg" output format should not require any parameters according the help document: "d - do... 2020-07-15, 1468🔥, 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, 1464🔥, 0💬

Play with Embedded 3Dmol Viewer
Where can I play with the Embedded 3Dmol Viewer? You can play with the Embedded 3Dmol Viewer below. Because there is a code bug in the 3Dmol.js library, you need to select "cid" to load a PDB protein, or select "pdb" to load a CID molecule.   x=1; Leave a message in the comment area, if you have any... 2022-12-26, 1462🔥, 0💬

"surface={...}" - Specify Surface Properties
How to turn on and specify surface properties using the "surface={...}" URL parameter in the Online 3Dmol Viewer? You can use the surface={key:value;key:value;. ..}URL parameter to turn on the Van der Waals surface with given properties. For example, the following URL turns on the Van der Waals surf... 2023-09-07, 1461🔥, 0💬

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Atom Biology General Molecule Reaction Tools Trial Virus