Atom Biology General Molecule Tools Trial Virus

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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, 777👍, 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, 624👍, 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, 597👍, 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, 611👍, 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, 606👍, 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, 593👍, 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, 571👍, 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, 564👍, 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, 780👍, 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, 2542👍, 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, 1095👍, 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, 832👍, 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, 811👍, 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, 666👍, 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, 618👍, 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, 613👍, 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, 652👍, 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, 1709👍, 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, 823👍, 0💬

"babel -x..." Command - Extra Output Writing Options
How to pass extra options for "babel" to write output data of a specific format? If you want to pass extra options for "babel" to write output data of a specific format, you need to use one or more "-x..." options in the "babel" command line as shown in the following syntax: babel input_section outp... 2020-07-15, 632👍, 0💬

"babel -d" Command - Delete Hydrogens from Molecule Data
How to delete hydrogen atoms from molecule data during data conversion? If hydrogen atoms of a molecule are included in the input data source, you can use the "babel" generic option "-d" remove those hydrogen atoms during the molecule data conversion process. Here is an example of using the "-d" opt... 2020-07-15, 595👍, 0💬

"babel -a..." Command - Extra Input Reading Options
How to pass extra options for "babel" to read input data of a specific format? If you want to pass extra options for "babel" to read input data of a specific format, you need to use one or more "-a..." options in the "babel" command line as shown in the following syntax: babel input_section output_s... 2020-07-15, 579👍, 0💬

Substructure Search with Wildcard Bond "~"
How to use Wildcard Bond in a substructure search using "babel" commands? You can use "~" in a SMARTS string as a wildcard bond to represent "ANY" bond in a substructure search using "babel" commands. Here are some examples of substructure matching with a wildcard bond "~" in the molecule pattern: f... 2020-06-08, 973👍, 0💬

Substructure Search with Wildcard Atom "*"
How to use Wildcard Atom in a substructure search using "babel" commands? You can use "*" in a SMARTS string as a wildcard atom to represent "ANY" atom in a substructure search using "babel" commands. Here are some examples of substructure matching with a wildcard atom "*" in the molecule pattern: f... 2020-06-08, 854👍, 0💬

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Atom Biology General Molecule Tools Trial Virus