Atom Biology General Molecule Reaction Tools Trial Virus

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$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... 2023-09-10, 939🔥, 0💬

Use Bio.SearchIO Module to Parse BLAST XML Result
How to Use Bio.SearchIO Module to Parse BLAST XML Result? The Bio.SearchIO module allows to parse sequence search result from different result format. 1. Try the following code to query the "nt" database under the "blastn" program with a given DNA sequence, which is reverse translated from a protein... 2023-05-09, 939🔥, 0💬

Play with the Bio.Seq Module
How to import the Bio.Seq module and use its functions? Here are some examples on how to import the Bio.Seq module and use its functions. 1. Import the Bio.Seq module and create a Bio.Seq object. fyicenter$ python &gt;&gt;&gt; from Bio.Seq import Seq &gt;&gt;&gt; my_seq = Seq... 2023-02-04, 938🔥, 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, 936🔥, 0💬

Parse PDB Entry with Bio.PDB.MMCIFParser.parser Module
How to Parse PDB Entry with Bio.PDB.MMCIFParser.parser.get _structure()function? Bio.PDB.MMCIFParser.parser.get _structure()function allows you to parse and any PDB (Protein Database) data files. 1. Download a PDB file in PDB format. fyicenter$ curl http://files.rcsb.org/view/1fa t.pdb&gt; 1fat.... 2023-05-09, 935🔥, 0💬

Single Sequence Record in GenBank Format
How to read a Single Sequence Record in GenBank Format? The GenBank format for DNA or protein sequences contains more properties and a better structure that FASTA format. You can follow these steps to download GenBank file example and create a Bio.SeqRecord object. 1. Download an example of a Sequen... 2023-04-04, 933🔥, 0💬

One Molecule with Disconnected Parts
Can I specify a single molecule object with multiple disconnected parts in a Ketcher file? Yes, you can specify a single molecule object with multiple disconnected parts in a Ketcher file. Here is a simple example of Ketcher file with a single "molecule" object of a 4-carbon chain. But the bond betw... 2024-01-31, 931🔥, 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, 931🔥, 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, 931🔥, 0💬

Bond Type Codes in Ketcher File
What are bond type codes supported by Ketcher file? Ketcher file supports the following bond type codes: Single bond - "type": 1 Double bond - "type": 2 Triple Bond - "type": 3 Any bond - "type": 8 Aromatic bond - "type": 4 Single/double bond - "type": 5 Single/aromatic bond - "type": 6 Double/aroma... 2024-02-18, 930🔥, 0💬

editor.struct().atoms - Get Atom List
How to get a list of atoms currently in the Ketcher editor with the editor.struct().atoms property? If you want to get a list of atoms currently in the Ketcher editor, you can use the editor.struct().atoms property on the Ketcher Editor interface. Here is an HTML document that shows you how to get a... 2023-12-01, 930🔥, 0💬

editor.struct().bonds - Get Bond List
How to get a list of bonds currently in the Ketcher editor with the editor.struct().bonds property? If you want to get a list of bonds currently in the Ketcher editor, you can use the editor.struct().bonds property on the Ketcher Editor interface. Here is an HTML document that shows you how to get a... 2023-12-01, 925🔥, 0💬

What Is Sequence Motif Analysis
What is Sequence Motif Analysis? In biology, a sequence motif is a nucleotide or amino-acid sequence pattern that is widespread and usually assumed to be related to biological function of the macromolecule. For example, an N-glycosylation site motif can be defined as Asn, followed by anything but Pr... 2023-07-11, 924🔥, 0💬

BioJava - Java Bioinformatics Toolkit
Where to find FAQ (Frequently Asked Questions) on BioJava - Java toolkit for computational molecular biology? Here is a list of tutorials to answer many frequently asked questions compiled by FYIcenter.com team on BioJava - Java toolkit for computational molecular biology. What Is BioJava BioJava Li... 2023-04-26, 917🔥, 0💬

Search History with Bio.Entrez for Subsequent Calls
How to Use Search History with Bio.Entrez for Subsequent Calls? If use Bio.Entrez.esearch() and found a large number of matches, you can use the history feature to retrieve matched records in multiple sequence Bio.Entrez.efetch() calls. 1. Turn on the history feature in the esearch() call with the u... 2023-09-10, 906🔥, 0💬

HOWTO Documents at BioPerl.org
What tutorials are provided at BioPerl.org? BioPerl.org provides the following tutorials in the format of HOWTO documents: Beginners HOWTO - Introduction to BioPerl for biologists. Features and Annotations HOWTO - Reading and writing detailed data associated with sequences. BlastPlus HOWTO - Create,... 2023-03-07, 904🔥, 0💬

Search for Motif Matches with Bio.motifs
How to Search for Matches in a Target Sequence again a motif with Bio.motifs? Bio.motifs module offers two options to search for segments that match a motif in a target sequence. 1. Use the motif instances to search for exact matches. fyicenter$ python &gt;&gt;&gt; from Bio.Seq import Se... 2023-06-19, 899🔥, 0💬

BioPerl - Perl Bioinformatics Toolkit
Where to find FAQ (Frequently Asked Questions) on BioPerl - Perl toolkit for computational molecular biology? Here is a list of tutorials to answer many frequently asked questions compiled by FYIcenter.com team on BioPerl - Perl toolkit for computational molecular biology. What Is BioPerl BioPerl Mo... 2023-04-17, 889🔥, 0💬

$3Dmol Namespace and Static Methods
What is the GLViewer Class? $3Dmol is the top namespace of the $3Dmol.js library. It contains a sub-namespace, several classes and some static methods as listed below. Sub-namespaces : $3Dmol.GLDraw - Lower level utilities for creating WebGL shape geometries Classes : $3Dmol.GLModel - A group of rel... 2023-09-10, 888🔥, 0💬

Molecule with Substituted Functional Group
How to specify a S-Group (Substituted Functional Group) in a molecule structure in Ketcher file format? There are 2 options to specify a S-Group (Substituted Functional Group) in a molecule structure: 1. Specify S-Group without Group Substructure: Just replace the atom symbol at the s-group attachin... 2024-02-28, 886🔥, 0💬

Call getSmiles() and getSmarts() Chained
How to call getSmiles() and getSmarts() methods in 2 promises one chained to the other? Another way to avoid the bug mentioned in the previous tutorial is to call ketcher.getSmiles() and ketcher.getSmarts() methods in 2 chained promises. Chained promises use fulfilled and rejected handlers of the pr... 2024-01-15, 883🔥, 0💬

Read FASTA File with FastaReaderTeat.java
How to read a FASTA fie with FastaReaderTeat.java? If you compiled the example program, FastaReaderTeat.java, with Maven as shown in the previous tutorial, you can follow these steps to read a FASTA file. 1. Prepare a FASTA file, example.fasta. fyicenter$ cd bio fyicenter$ vi example.fasta &gt;s... 2023-04-17, 880🔥, 0💬

Get Help Documentation with Biopython
How to Get Help Documentation with Biopython? Biopython has help documentations built in the library. You can use the help() to read them. Read help documentation on Biopython library. fyicenter$ python &gt;&gt;&gt; import Bio &gt;&gt;&gt; help(Bio) Help on package Bio: NAME ... 2023-07-29, 874🔥, 0💬

Compare Motifs Using PSSM with Bio.motifs
How to Compare Motifs Using PSSM with Bio.motifs? If you know PSSMs of two motifs, you can compare them using the PSSM's dist_pearson() function. It returns a position offset for the best alignment and a distance between the two motifs. 1. Create a shorter motif from a given PCM without actual insta... 2023-06-19, 874🔥, 0💬

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Atom Biology General Molecule Reaction Tools Trial Virus