Atom Biology General Molecule Reaction Tools Trial Virus

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editor.options() - Get Editor Options
How to get a list of options used by the Ketcher editor with the editor.options() method? If you want to get a list of options used by the Ketcher editor, you can use the editor.options() method on the Ketcher Editor interface. Here is an HTML document that shows you how to get a list of options cur... 2023-11-18, 947🔥, 0💬

Pre-defined Sequence Alignment Score Settings
How to Use Pre-defined Sequence Alignment Score Settings? Biopython provides 3 Pre-defined Sequence Alignment Score Settings: "blastn" and "megablast" for nucleotide alignments, and "blastp" for protein alignments. Here is an example on how to "blastp" score settings. fyicenter$ python &gt;&... 2023-08-03, 945🔥, 0💬

What Are Translation Tables
What Are Translation Tables? Translation tables, also called codon tables, are conversion tables that map 3-nucleobase combinations into amino acids to form protein sequences. It is known that all organisms do not use exactly the same translation table. But they vary from a standard translation tabl... 2023-03-17, 944🔥, 0💬

What Is BioJava
What is BioJava? BioJava is a open-source Java library for bioinformatics. BioJava versions and release dates are: BioJava 6.1.0 BioJava 6.0.0 BioJava 5.3.0 BioJava 5.2.0 BioJava 5.0.0 BioJava 4.2.9 BioJava 4.2.1 BioJava 4.2.0 BioJava legacy 1.9.1 Main modules of BioJava: The Core Module (biojava-co... 2023-04-26, 938🔥, 0💬

Retrieve Record Summary with Bio.Entrez.esummary()
How to Retrieve Record Summary with Bio.Entrez.esummary() function? Bio.Entrez.esummary() function allows you to retrieve summary information of a given record in a given NCBI Databas. It uses the Entrez Web services provided by www.ncbi.nlm.nih.gov. 1. Retrieve summary information from the "nlmcata... 2023-08-09, 935🔥, 0💬

Load Data from Another HTML Element
How to load molecule data from another HTML element into the Embedded 3Dmol Viewer? You can use "data-element" and "data-type" attributes on the DIV element to load molecule data another HTML element into the Embedded 3Dmol Viewer. Here is an HTML code example, Embedded-Viewer-data-element.h tml,tha... 2023-01-31, 934🔥, 0💬

UI Components of Online 3Dmol Viewer
What functions are supported by UI components on the Online 3Dmol Viewer? UI components on the Online 3Dmol Viewer support the following functions: 1. Model Data Input: Accessible through the "File/PDB/URL" menu item. You can load PDB protein data from the online PDB database, molecule compound data... 2023-09-07, 931🔥, 0💬

Motif Counts and Consensus with Bio.motifs
How to Get Motif Counts and Consensus with Bio.motifs Module? Motif counts represent how often each letter appears at each position in a motif sample set. Motif counts is also called PFM (Position Frequency Matrix). Motif consensus is the sequence of letters along the positions of the motif for whic... 2023-07-05, 929🔥, 0💬

Use BioJava with "Maven" Build Tool
How to Use BioJava with "Maven" Build Tool? If you want to install one or more BioJava Libraries with Maven, you can include BioJava libraries as dependencies in the Maven project file as shown in this tutorial. 1. Make sure that you have JDK installed. fyicenter$ javac -version javac 17.0.1 2. Make... 2023-04-25, 928🔥, 0💬

Ketcher File Structure for Reaction
What is the Ketcher file structure for a chemical reaction? The Ketcher file structure for a chemical reaction is an extension of the Ketcher file structure for a molecule. Additional molecule objects are added as reactants, reagents, solvents, and products of the reaction. A long arrow is also adde... 2024-02-18, 925🔥, 0💬

editor.struct().loops - Get Loop List
How to get a list of loops currently in the Ketcher editor with the editor.struct().loops property? If you want to get a list of loops currently in the Ketcher editor, you can use the editor.struct().loops property on the Ketcher Editor interface. Here is an HTML document that shows you how to get a... 2023-11-23, 925🔥, 0💬

What Is Biopython
What is BioJava? Biopython is a set of freely available tools for biological computation written in Python by an international team of developers. Biopython versions and release dates are: Biopython 1.80, November 18, 2022 Main features of Biopython: The ability to parse bioinformatics files into Py... 2023-02-04, 924🔥, 0💬

Fetch Sequences from NCBI with Bio.Blast.NCBIWWW.qblast()
How to Fetch Sequences from NCBI with Bio.Blast.NCBIWWW.qblast()? The function qblast() in the Bio.Blast.NCBIWWW module allows you to call the online version of BLAST to fetch DNA or protein sequences from https://blast.ncbi.nlm.nih.gov /Blast.cgi.Currently the qblast() function only works with 5 BL... 2023-05-09, 917🔥, 0💬

Failed to Load D4DF9EC9DD21B943E35F3D5696D5D2A1.cache.js
Why JSME editor is not showing after upgrade to the 2022-09-26 version? If you upgraded JSME to the 2022-09-26 version from an older version, the JSME editor may fail to show up in your browser. In the browser developer console, you will see that a required JSME JavaScript file, D4DF9EC9DD21B943E35F... 2023-04-13, 917🔥, 0💬

What Is OBF (Open Bioinformatics Foundation)
What Is OBF (Open Bioinformatics Foundation)? OBF (Open Bioinformatics Foundation) is a non-profit, volunteer-run group dedicated to promoting the practice and philosophy of Open Source software development and Open Science within the biological research community. Currently, OBF supports the follow... 2023-02-04, 917🔥, 0💬

Motif PSSM with Bio.motifs
How to Calculate Motif PSSM with Bio.motifs Module? PSSM (Position-Specific Scoring Matrix), also referred as PSWM (Position-Specific Weight Matrix) or LSM (Logodds Scoring Matrix), represents how well the frequency of each letter at each position matches with a given background frequency. PSSM can ... 2023-07-01, 916🔥, 0💬

Too Many Results from align() Function
Why there are So Many Results from the align() Function? If you are using the default score settings, you may get a very large number of possible alignments. Here is an example using the first and the third sequences from the PF05371_seed.faa file. fyicenter$ python &gt;&gt;&gt; from Bio... 2023-05-09, 914🔥, 0💬

JSApplet.Inchi.computeInchi() - Generate InChI
How to generate InChI and InChIKey with the JSApplet.Inchi.computeInchi() method? The latest version of JSME allows you to generate InChI and InChIKey from a given molecule in SDF format. Here are the steps you can follow to do this in JavaScript code: 1. Create an empty object called "JSApplet" and... 2023-01-18, 913🔥, 0💬

Single Sequence Record in FASTA Format
How to read a Single Sequence Record in FASTA Format? If you want to store additional information to a DNA or protein sequence, you can use the Bio.SeqRecord class, which contains the following properties: seq – The sequence itself as a Seq object. id – The primary ID used to identify the sequence. ... 2023-04-04, 910🔥, 0💬

What Is Ketcher File Format
What is Ketcher File Format? A Ketcher file is a JSON document that stores the entire content created in the Ketcher editor. It supports the following features: Supports molecule 3-D structures. Supports chemical reactions. Supports styled text labels. Supports S-Groups. Here is a simple example of ... 2024-02-11, 906🔥, 0💬

Create Motif With Biopython Bio.motifs Module
How to Create Motif With Biopython Bio.motifs Module? Biopython Bio.motifs Module allows you to create a motif object with a list of DNA or protein sequences. A motif object actually represents a sample set of sequences that matches a sequence motif pattern. 1. Create a motif object with a single se... 2023-07-11, 906🔥, 0💬

Multiple Selections with Embedded 3Dmol Viewer
How to create multiple selections apply different styles with Embedded 3Dmol Viewer? In order to create a separate selection, you need add a suffix code to the "data-select" attribute name as "data-select{code}". Then other selection related attributes can use the same suffix code to refer to the se... 2023-02-03, 898🔥, 0💬

Call getSmiles() and getSmarts() Parallelly
Why do getSmiles() and getSmarts() methods return the same result, if they are called in 2 parallel promises? There seems to be a bug in Ketcher v2.11.0 release. If you call getSmiles() and getSmarts() methods one after the other, you are creating 2 promises The first promise seems to be overriding ... 2024-01-24, 896🔥, 0💬

List NCBI Databases with Bio.Entrez.einfo()
How to List NCBI Databases with Bio.Entrez.einfo() function? Bio.Entrez.einfo() function allows you to list NCBI Databases and their related information. It uses the Entrez Web services provided by www.ncbi.nlm.nih.gov. 1. Get a list of NCBI databases. fyicenter$ python &gt;&gt;&gt; from... 2023-07-08, 894🔥, 0💬

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Atom Biology General Molecule Reaction Tools Trial Virus