Atom Biology General Molecule Reaction Tools Trial Virus

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Install Open Babel CLI RPM Package for CentOS
How to download and install Open Babel CLI (Command Line Interface) RPM package for CentOS computers? Open Babel CLI RPM package offers a number of pre-build command line tools for you convert and manipulate molecule data from one format to another format using Open Babel library. You can follow thi... 2020-10-10, 952🔥, 0💬

"babel ... -f # -l #" - Split Large Molecule File
How to split a file with a large number of molecules? You can split a file with a large number of molecules into smaller files by extracting a chunk of molecules to the output using the "-f #" and "-l #" options. The "-f #" option specifies the index of the first molecule to be extracted. The "-l #"... 2020-09-30, 2425🔥, 0💬

Using Fastsearch Fingerprint Index
Where to find FAQ (Frequently Asked Questions) on Using Fastsearch Fingerprint Index with Open Babel? Here is a list of tutorials to answer many frequently asked questions compiled by FYIcenter.com team on Using Fastsearch Fingerprint Index with Open Babel. "babel ... -o fs" - Generate Fastsearch In... 2020-09-30, 738🔥, 0💬

Open Babel Installation Options on macOS
What are the options for installing Open Babel on macOS computers? There are a number of options for installing Open Babel on macOS computers: 1. Install Open Babel with a pre-compiled binary package. Open Babel 2.3.1 macOS binary package is available. This is the easiest option to install Open Babe... 2020-09-15, 2418🔥, 0💬

Running Open Babel on macOS
Where to find FAQ (Frequently Asked Questions) on running Open Babel on macOS? Here is a list of tutorials to answer many frequently asked questions compiled by FYIcenter.com team on running Open Babel on macOS. Open Babel Installation Options on macOS Install Open Babel Binary Package on macOS Open... 2020-09-15, 1672🔥, 0💬

What Is Open Babel, Chemistry Toolbox
What Is Open Babel, Chemistry Toolbox? Open Babel, is a chemical toolbox designed to speak the many languages of chemical data. It's an open, collaborative project allowing anyone to search, convert, analyze, or store data from molecular modeling, chemistry, solid-state materials, biochemistry, or r... 2020-09-15, 1064🔥, 0💬

Open Babel History and Releases
When Open Babel was first developed? And how many Open Babel releases are there? The original Babel was written by Pat Walters and Matt Stahl in 2001, based on the "convert" program by Ajay Shah. The original Babel is a remarkable chemistry file conversion tool. Pat Walters and Matt Stahl rewrote Ba... 2020-09-15, 816🔥, 0💬

What Is "babel" Command
What Is "babel" Command? How to get command line help for Open Babel? "babel" Command is the command to invoke Open Babel different functionalities by specifying different command options. You can use "babel -H" command to get help information on Open Babel command: fyicenter$ babel -H Open Babel co... 2020-09-15, 781🔥, 0💬

"babel ... -o fs" - Generate Fastsearch Index
What is Open Babel Fastsearch Index file? How to generate it with the "babel" command? Fastsearch index file is an Open Babel specific binary file that stores pre-calculated fingerprints and their indexes for multiple molecules. Fastsearch index file can improve similarity search significantly faste... 2020-08-25, 790🔥, 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, 780🔥, 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, 753🔥, 0💬

"babel -i fs ... -s ... -at n" - Top n Similarity Search
How to perform a top 10 similarity search using the fastsearch index file with the "babel" command? If you want to perform a top n similarity search using the fastsearch index file, you can use the following "babel" command syntax: babel -i fs index_file output_section -s query_molecule -at n -aa In... 2020-08-25, 710🔥, 0💬

"babel -i fs ... -s ... -at score_range" - Similarity Search
How to perform a similarity search in a given score range using the fastsearch index file with the "babel" command? If you want to perform a similarity search in a specific score range using the fastsearch index file, you can use the following "babel" command syntax: babel -i fs index_file output_se... 2020-08-25, 683🔥, 0💬

JSME Molecule Editor User Interface
Where to find FAQ (Frequently Asked Questions) on JSME Molecule Editor User Interface? Here is a list of tutorials to answer many frequently asked questions compiled by FYIcenter.com team on JSME Molecule Editor User Interface. JSME User Interface Menu Icons Show InChI and InChIKey on JSME Build Mol... 2020-08-03, 978🔥, 1💬

Scaling SVG Images using "viewBox" Attribute
What is the meaning of the &lt;svg viewBox="..." ...&gt; attribute? I want to understand how it is used to scale up the image. The &lt;svg viewBox="..." ...&gt; attribute defines view box properties which work together to scale and translate a SVG image. View Port Properties - Specif... 2020-08-03, 3464🔥, 1💬

"babel ... -o svg -xP300" Bug - width="px" height="px"
Why "babel ... -o svg -xP300" command is not able scale a molecule SVG image? The "babel ... -o svg -xP300" command has a code bug that results incorrect attributes, width="px" height="px", in the top level "svg" element. in both Open 2.3 and 2.4 releases. However, "obabel ... -o svg -xP300" command... 2020-07-22, 1266🔥, 0💬

"babel ... -o svg -xX" - Hide Implicit H in SVG
How to hide those H symbols (Hydrogen symbols) implicitly added to non-carbon terminal atoms in SVG with the "babel" command? If you want to hide those Hydrogen symbols implicitly added to non-carbon terminal atoms in SVG format, you can use the "-o svg -xX" option with the "babel" command. Here is ... 2020-07-22, 1252🔥, 0💬

"obabel ... -o svg -xP300" - Scale SVG Image
How to scale and center a molecule SVG image in a given square area? The default behavior of Open Babel 2.4 is different than 2.3 regarding scaling and centering SVG images. With Open Babel 2.4, the molecule SVG image is defaulted in the center of 200x200 square. With Open Babel 2.3, the molecule SV... 2020-07-22, 1006🔥, 0💬

"babel ... -o svg -xC" - Hide Terminal C in SVG
How to hide those C symbols for terminal carbon atoms in SVG with the "babel" command? If you want to hide those C symbols for terminal carbon atoms in SVG format, you can use the "-o svg -xC" option with the "babel" command. Here is how the "-xC" option is described in Open Babel help document: "C ... 2020-07-22, 798🔥, 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, 752🔥, 0💬

"babel ... -o svg -xd -xP300" Bug - Option -d takes a parameter
Why "babel ... -o svg -xd -xP300" command is giving the "Option -d takes a parameter" error in Open Babel 2.4? It seems to be another code bug in the "babel" command in Open Babel 2.4 release. "-xd" option for "svg" output format should not require any parameters according the help document: "d - do... 2020-07-15, 733🔥, 0💬

"babel ... -o svg -xS" - Ball/Stick Depiction in SVG
How to generate a ball and stick depiction of a molecule in SVG with the "babel" command? If you want to a ball and stick depiction of a molecule in SVG format, you can use the "-o svg -xS" option with the "babel" command. For example, the following command generate a ball and stick depiction of of ... 2020-07-15, 850🔥, 0💬

"babel -h" Command - Add Hydrogens to Molecule Data
How to add hydrogen atoms to molecule data during data conversion? Most molecules contains many hydrogen atoms. When molecules are written in many data formats, those hydrogen atoms are removed. We normally can read molecule structure without hydrogen atoms. But if you want to add those removed hydr... 2020-07-15, 3049🔥, 0💬

List of File Formats Supported by Open Babel
How to get a list of File Formats Supported by Open Babel? You can use "babel -L formats" command to get a list of File Formats Supported by Open Babel: fyicenter$ babel -L formats abinit -- ABINIT Output Format [Read-only] acr -- ACR format [Read-only] adf -- ADF cartesian input format [Write-only]... 2020-07-15, 1298🔥, 0💬

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Atom Biology General Molecule Reaction Tools Trial Virus