Atom Biology General Molecule Reaction Tools Trial Virus

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"babel -... --..." Command - Generic Conversion Options
What are generic conversion options that I can use on "babel" commands for all input and output formats? "babel" commands supports a number of generic conversion options that applies all input and output formats as listed below: --addtotitle Append text to the current molecule title --addformula App... 2021-07-19, 715🔥, 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, 711🔥, 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, 690🔥, 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, 686🔥, 0💬

Ketcher JavaScript API
Where to find FAQ (Frequently Asked Questions) on Ketcher JavaScript API? Here is a list of tutorials to answer many frequently asked questions compiled by FYIcenter.com team on Ketcher JavaScript API. What Is Ketcher JavaScript API contentWindow.ketcher - Access "ketcher" Object ketcher.setMolecule... 2023-10-05, 675🔥, 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, 673🔥, 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, 667🔥, 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, 653🔥, 0💬

Difference between 3Dmol.js and 3Dmol-min.js
What is the difference between 3Dmol.js and 3Dmol-min.js? From code point of view, 3Dmol.js and 3Dmol-min.js are the same. But they are stored in different file formats: 1. 3Dmol-min.js is the minimized version of 3Dmol.js with all line breaks and other white spaces removed. 2. 3Dmol-min.js is 3 tim... 2022-12-24, 612🔥, 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, 585🔥, 0💬

Display 3-D Molecule Structure with 3Dmol.js
How to display a 3-D molecule structure with 3Dmol.js? If you have a 3-D molecule structure stored in SDF format, you can follow these steps to load and display it with the 3Dmol.js library. 1. Create an HTML file, Display-Molecule.html, with the following code. The molecule's SDF data is hidden in ... 2022-12-24, 562🔥, 0💬

Getting Started with 3Dmol.js
Where to find FAQ (Frequently Asked Questions) on Getting Started with 3Dmol.js? Here is a list of tutorials to answer many frequently asked questions compiled by FYIcenter.com team on Getting Started with 3Dmol.js. What Is 3Dmol.js Library Use the Online Version of 3Dmol.js Library Install 3Dmol.js... 2022-12-24, 553🔥, 0💬

generateImage() - Generate Image from Structure
How to generate image from a given chemical structure with the ketcher.generateImage() method? If you want to generate an image from the chemical structure in the Ketcher editor, you can export the structure in a specific format using a get*() method. Then call the ketcher.generateImage(structur e,o... 2023-12-14, 551🔥, 0💬

"pdb=..." - Load PDB Data in 3Dmol Viewer
How to load a protein structure with the PDB ID in the Online 3Dmol Viewer? You can use the pdb={PDB_ID} URL parameter to load protein data from https://www.rcsb.org/ in the Online 3Dmol Viewer. https://3dmol.org/viewer.html? pdb={PDB_ID}For example, enter the following URL in Web browser. You see t... 2023-01-06, 529🔥, 0💬

Download and Install Ketcher in Standalone Mode
How to Download and Install the latest version of Ketcher in standalone mode? Ketcher can be installed in 2 modes: Standalone and Remote. The Standalone mode incorporates Indigo backend services in the Ketcher build. It allows for Ketcher to work in browser with no server and even without the Intern... 2023-12-17, 520🔥, 0💬

OBF (Open Bioinformatics Foundation) Tools
Where to find molecule FAQ (Frequently Asked Questions)? I want to learn more about OBF (Open Bioinformatics Foundation) and its software tools. Here is a large collection of tutorials to answer many frequently asked questions compiled by FYIcenter.com team about OBF (Open Bioinformatics Foundation)... 2023-02-04, 502🔥, 0💬

ketcher.getSmiles() and ketcher.getSmarts()
How to export the chemical structure in SMILES and SMARTS formats from the Ketcher with the ketcher.getSmiles() and ketcher.getSmarts() methods? To export the chemical structure (molecule, reaction, or substructure pattern) in SMILES and SMARTS formats from the Ketcher, you can use the getSmiles() a... 2023-12-10, 497🔥, 0💬

Load Data by URL into Embedded 3Dmol Viewer
How to load data by URL into the Embedded 3Dmol Viewer? You can use "data-href" and "data-type" attributes on the DIV element to load molecule data from a URL into the Embedded 3Dmol Viewer. Here is an HTML code example, Embedded-Viewer-data-href.html ,that loads a Benzene molecule in SDF format wit... 2023-02-03, 465🔥, 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, 463🔥, 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, 434🔥, 0💬

What Is 3Dmol.js Library
What Is 3Dmol.js Library? 3Dmol.js is an object-oriented, WebGL based JavaScript library for online molecular visualization - No Java required! With 3Dmol.js, you can add beautifully rendered molecular visualizations to your web applications. Main features of 3Dmol.js are: support for pdb, sdf, mol2... 2022-12-24, 417🔥, 0💬

What Is Ketcher - Chemical Structure Editor in JavaScript
What Is Ketcher, Chemical Structure Editor in JavaScript? Ketcher is an open-source web-based chemical structure editor written in JavaScript. It can be used as an integrated online Web tool to draw chemical structures and reactions. Main features of Ketcher are: Fast and convenient editing - Ketche... 2023-12-17, 412🔥, 0💬

Build Ketcher Editor Web Page
How to build my own Ketcher editor Web Page? If you want to build your Web page and offer Ketcher as a Chemical Structure Editor in the middle of the page, you can follow this tutorial. 1. Follow the previous tutorial to install Ketcher on your Web server. 2. Create a new HTML document, editor.html,... 2023-10-05, 409🔥, 0💬

Display Protein Structure with 3Dmol.js
How to display a protein structure with 3Dmol.js? You can follow these steps to display a protein structure by loading an online PDB file. 1. Get URL of the online PDB file: https://files.rcsb.org/downloa d/1YCR.pdb2. Create an HTML file, View-PDB-Online.html, with the following code. The PDB file l... 2022-12-26, 405🔥, 0💬

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Atom Biology General Molecule Reaction Tools Trial Virus