Atom Biology General Molecule Reaction Tools Trial Virus

<< < … 2 3 4 5 6 7 8 9 10 11 12 … > >>   ∑:312  Sort:Date

"babel ... -o svg -xi" - Show Atom Indices in SVG
How to show atom indices in a molecule SVG picture? I want to see in what order each atom is listed in the SMILES string. The SMILES string list each atom a molecule is a specific sequence. You can use the "-xi" option when generating the SVG file to show the index of each atom corresponding to the ... 2021-02-04, 1480🔥, 0💬

editor.setOptions() - Set Editor Options
How to get a list of options used by the Ketcher editor with the editor.setOptions() method? If you want to update one or more options used by the Ketcher editor, you can use the editor.setOptions() method on the Ketcher Editor interface. Here is an HTML document that shows you how to update some op... 2023-11-18, 1479🔥, 0💬

$3Dmol.download('cid:...', ...) - Download CID Molecule
How to download molecule by CID with the $3Dmol.download() method? The syntax to download molecule by CID with the $3Dmol.download() method is shown below: $3Dmol.download("cid:{CID}", viewer, options, callback) -&gt; {$3Dmol.GLModel} viewer - The $3Dmol.GLViewer instance where the downloaded pr... 2023-01-11, 1478🔥, 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, 1474🔥, 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, 1474🔥, 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, 1471🔥, 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, 1469🔥, 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, 1466🔥, 0💬

"babel -a..." Command - Extra Input Reading Options
How to pass extra options for "babel" to read input data of a specific format? If you want to pass extra options for "babel" to read input data of a specific format, you need to use one or more "-a..." options in the "babel" command line as shown in the following syntax: babel input_section output_s... 2020-07-15, 1465🔥, 0💬

Search for Related Items in NCBI with Bio.Entrez.elink()
How to Search for Related Items in NCBI with Bio.Entrez.elink() function? Bio.Entrez.elink() function allows you to find related items in a NCBI database for a given record. It uses the Entrez Web services provided by www.ncbi.nlm.nih.gov. Here is an example on how to find related items with the Bio... 2023-08-25, 1450🔥, 0💬

Ketcher Indigo Interface
Where to find FAQ (Frequently Asked Questions) on Ketcher Indigo Interface? Here is a list of tutorials to answer many frequently asked questions compiled by FYIcenter.com team on Ketcher Indigo Interface. What Is Ketcher Indigo Interface indigo.calculate() - Calculates Chemical Properties indigo.ge... 2023-11-13, 1447🔥, 0💬

Play with the ls_orchid.fasta File
How to download and process ls_orchid.fasta file? ls_orchid.fasta file is an example of DNA sequence file in FASTA format provided in the Biopython source code package. You can also download it and use it to test Biopython library. 1. Download ls_orchid.fasta. fyicenter$ curl https://raw.githubuserc... 2023-07-08, 1447🔥, 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, 1444🔥, 0💬

Open Babel Web Interface at cheminfo.org
Is there any Web interface available for Open Babel? I want to try it before installing it on my local computer. You can try Open Babel on the Web interface provided by cheminfo.org. 1. Go to http://www.cheminfo.org/Chemis try/Cheminformatics/FormatConv erter/index.html. You see the Web interface tha... 2023-01-24, 1443🔥, 0💬

"style=..." - Specify Display Style in 3Dmol Viewer
How to specify display style in the Online 3Dmol Viewer? You can use the style={line|cross|cartoon|stic k|sphere}URL parameter to specify the display style for the selected substructures in the Online 3Dmol Viewer. https://3dmol.org/viewer.html? ...style={line|cross|cartoon|s tick|sphere}For example,... 2023-01-06, 1440🔥, 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, 1429🔥, 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, 1428🔥, 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, 1423🔥, 0💬

Missing 3Dmol-min.js on Local 3Dmol Server
Why is my local 3Dmol server redirecting to browser to https://get.webgl.org/? If you access your local 3Dmol server with a browser, and you see the https://get.webgl.org/ Website displayed, it's most likely missing the 3Dmol-min.js file on the server. This may happen if 3Dmol server was not install... 2023-02-19, 1418🔥, 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, 1412🔥, 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, 1411🔥, 0💬

"babel" Command - Use "-o ..." as Output Delimiter
How to use "-o ..." flag as a delimiter to separate output file from input files in a "babel" command? The "-o ..." flag is optional, since "babel" command can implicitly determine the output data format from the file extension of output file name. However, it is important to use the "-o ..." flag a... 2021-07-19, 1406🔥, 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, 1405🔥, 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, 1396🔥, 0💬

<< < … 2 3 4 5 6 7 8 9 10 11 12 … > >>   ∑:312  Sort:Date

Atom Biology General Molecule Reaction Tools Trial Virus