Atom Biology General Molecule Reaction Tools Trial Virus

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"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, 1352🔥, 0💬

"labelres={...}" - residue Label Properties
How to turn on and specify residue label properties using the "labelres={...}" URL parameter in the Online 3Dmol Viewer? You can use the labelres={key:value;key:value; ...}URL parameter to turn on residue labels with given properties. For example, the following URL turns on residue labels with defau... 2023-09-07, 1349🔥, 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, 1339🔥, 0💬

"Difficulty opening ..." Error Using Fastsearch Index
Why am I getting this "Difficulty opening ..." error using Fastsearch Index files? When you are using a fastsearch index file as the input, you must keep the original molecule data files in the original location, because the index file has references to the original data files. If those original dat... 2020-08-25, 1334🔥, 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, 1334🔥, 0💬

What Is Ketcher Editor Interface
What is Ketcher Editor interface? Ketcher Editor interface is part of the Ketcher JavaScript API that allows you to interact with Ketcher editor UI elements. To access Ketcher Editor interface, you need to access the "ketcher" object as a property of the content "window" object of the "iframe" where... 2023-12-08, 1330🔥, 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, 1330🔥, 0💬

Pairwise Sequence Alignment Score Settings
How to change Pairwise Sequence Alignment Score Settings? Bio.Align.PairwiseAligner().al ign()uses a set of Alignment Score Settings to control how each possible alignment score is calculated. It then returns only those alignments that have the highest score. Here are the Alignment Score Settings th... 2023-05-09, 1326🔥, 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, 1326🔥, 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, 1322🔥, 0💬

Scan Prosite Database with Bio.ExPASy.ScanProsite.scan()
How to Scan Prosite Database with Bio.ExPASy.ScanProsite.scan() function? Bio.ExPASy.ScanProsite.scan() function allows to scan the Prosite database with a given sequence. Here is an example on how to Scan Prosite Database. fyicenter$ python &gt;&gt;&gt; from Bio.ExPASy import ScanProsit... 2023-09-05, 1319🔥, 0💬

"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, 1315🔥, 0💬

"style={...}:..." - Specify Style Attributes
How to Specify Style Attributes using the "style={...}:...,..." URL parameter in the Online 3Dmol Viewer? Style Attributes can be specified as a comma separated list of "key~value" tokens. For example, the following URL provided 3 style attributes for the "carton" style: https://3dmol.org/viewer.htm.. . 2023-09-07, 1311🔥, 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, 1311🔥, 0💬

"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, 1309🔥, 0💬

"babel -i fs ..." - Fingerprint Index Based Search
How to perform a Fingerprint Index Based Search with the "babel" command? You can perform a Fingerprint Index Based Search with the "babel" command using the "-i fs" option to specify the fingerprint index file as the input. For more information, read the help document on fastsearch index file forma... 2020-08-25, 1308🔥, 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, 1301🔥, 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, 1296🔥, 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, 1296🔥, 0💬

Install 3Dmol.js Library Locally
How to install the 3Dmol.js library locally on my own Web server? If you want use a local copy of the 3Dmol.js library, you can follow these steps. 1. Download a copy of the 3Dmol.js library: fyicenter$ curl https://3Dmol.csb.pitt.edu/bui ld/3Dmol-min.js&gt; 3Dmol-min.js 2. Create an HTML file, ... 2022-12-24, 1295🔥, 0💬

"cid={PubChem_CID}" - Load Molecule from PubMed
How to load a molecule structure with the CID in the Online 3Dmol Viewer? You can use the cid={PubChem_CID} URL parameter to load a molecule structure from https://pubchem.ncbi.nlm.nih.g ov/in the Online 3Dmol Viewer. https://3dmol.org/viewer.html? cid={PubChem_CID}For example, enter the following U... 2023-09-07, 1290🔥, 0💬

Call getInchi() and generateInchIKey() Methods
How to generate the InChI and InChIKey with the ketcher.getInchi() and ketcher.generateInchIKey() methods? InChI (International Chemical Identifier) and InChIKey (InChI Key) are identifiers of molecule structures, originally developed by Initially developed by the International Union of Pure and App... 2023-12-14, 1284🔥, 0💬

"url={URL}" - Load Molecule from URL
How to load a molecule structure with a given URL in the Online 3Dmol Viewer? You can use the url={URL} URL parameter to load a molecule structure from a given URL in the Online 3Dmol Viewer. https://3dmol.org/viewer.html? url={URL}&amp;type={Type}The type={Type} parameter is needed to specify t... 2023-09-07, 1280🔥, 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, 1276🔥, 0💬

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Atom Biology General Molecule Reaction Tools Trial Virus