Atom Biology General Molecule Reaction Tools Trial Virus

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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, 1162🔥, 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, 1154🔥, 0💬

Biopython - Tools for Biological Computation
Where to find FAQ (Frequently Asked Questions) on Biopython - Tools for Biological Computation? Here is a list of tutorials to answer many frequently asked questions compiled by FYIcenter.com team on Biopython - Tools for Biological Computation. What Is Biopython Install Biopython Play with the Bio.... 2023-02-04, 1154🔥, 0💬

Read Sequence Alignments with Bio.AlignIO
How to Read Sequence Alignments with Bio.AlignIO package? Bio.AlignIO module allows you to read and write Sequence Alignments as MultipleSeqAlignment objects. Enter the following sequence alignment file, PF05371_seed.faa, in FASTA format. &gt;COATB_BPIKE/30-81 AEPNAATNYATEAMDSLKTQAIDLISQTWP VVTTV... 2023-09-05, 1153🔥, 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, 1151🔥, 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, 1151🔥, 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, 1148🔥, 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, 1146🔥, 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, 1143🔥, 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, 1140🔥, 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, 1134🔥, 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, 1129🔥, 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, 1129🔥, 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, 1127🔥, 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, 1115🔥, 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, 1115🔥, 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, 1107🔥, 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, 1106🔥, 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, 1105🔥, 0💬

About OBF (Open Bioinformatics Foundation)
Where to find FAQ (Frequently Asked Questions) in understanding what is OBF (Open Bioinformatics Foundation)? Here is a list of tutorials to answer many frequently asked questions compiled by FYIcenter.com team in understanding what is OBF (Open Bioinformatics Foundation). What Is OBF (Open Bioinfor... 2023-02-04, 1101🔥, 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, 1100🔥, 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, 1096🔥, 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, 1096🔥, 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, 1085🔥, 0💬

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Atom Biology General Molecule Reaction Tools Trial Virus