Atom Biology General Molecule Reaction Tools Trial Virus

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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, 1116🔥, 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, 1111🔥, 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, 1105🔥, 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, 1105🔥, 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, 1105🔥, 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, 1103🔥, 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, 1097🔥, 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, 1093🔥, 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, 1093🔥, 0💬

Install Online 3Dmol Viewer on Linux
How to install Online 3Dmol Viewer on my local Linux computer? The easiest way to use the Online 3Dmol Viewer is through the hosted server at https://3dmol.org/viewer.html . But if you want to have full control of the Online 3Dmol Viewer and faster response time, you can host it yourself on a Linux ... 2023-09-10, 1090🔥, 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, 1089🔥, 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, 1089🔥, 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, 1086🔥, 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, 1074🔥, 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, 1072🔥, 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, 1067🔥, 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, 1060🔥, 0💬

3Dmol.js Bug - data-ui=true Impacts on Selection
Why is the default style done after removing data-ui="true" in the embedded 3Dmol viewer? There seems to be code bug in the 3Dmol.js library. Here is an HTML code example, Embedded-Viewer-data-ui-Bug.ht ml,that contains 2 embedded viewers: one with data-ui="true" and the other without data-ui="true"... 2023-09-10, 1059🔥, 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, 1059🔥, 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, 1052🔥, 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, 1049🔥, 0💬

"DNF/YUM install" - Open Babel Binary Packages
How to install Open Babel binary packages with DNF/YUM commands on CentOS systems? If you are running CentOS 8, you can follow this tutorial to install Open Babel binary packages: 1. Install "openbabel" package: fyicenter$ sudo sdf install openbabel Installed: openbabel-3.1.1-14.el8.x86_64 openbabel... 2023-01-24, 1046🔥, 0💬

Motif ICM Logo with WebLogo Tools
How to Create Motif ICM Logo with WebLogo Tools? Motif ICM Logo is a graphical representation of the ICM (Information Content Matrix). Motif ICM Logo is also referred as Multiple Sequence Alignment Logo, Sequence Conservation Logo, or Sequence Logo. You can use the WebLogo tool provided by US Berkel... 2023-04-26, 1043🔥, 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, 1035🔥, 0💬

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Atom Biology General Molecule Reaction Tools Trial Virus