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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, 191👍, 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 specifing different command options. You can use "babel -H" command to get help information on Open Babel command: fyicenter$ babel -H Open Babel con...
2020-09-15, 191👍, 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 convesion tool. Pat Walters and Matt Stahl rewrote Bab...
2020-09-15, 188👍, 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, 187👍, 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 orginal molecule data files in the original location, because the index file has references to the original data files. If those original data...
2020-08-25, 214👍, 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, 208👍, 0💬

"babel -i fs ... -s ... -at n" - Top n Similarity Search
How to perform a top 10 similary search using the fastsearch index file with the "babel" command? If you want to perform a top n similary 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 the...
2020-08-25, 203👍, 0💬

"babel -i fs ... -s ... -at score_range" - Similarity Search
How to perform a similary search in a given score range using the fastsearch index file with the "babel" command? If you want to perform a similary 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_sectio...
2020-08-25, 202👍, 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 similarty search significantly faster...
2020-08-25, 200👍, 0💬

PyMol Screen Layout
What information is displayed in each area on PyMol Screen? Once PyMol is started, you should see two windows displayed: External GUI - A Graphical User Interface window with the following areas: 1. Output message area - An area where output messages are displayed. Initially, the output area display...
2020-08-03, 259👍, 1💬

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 InChi Key on JSME Build Mo...
2020-08-03, 243👍, 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, 285👍, 1💬

💬 2020-08-03 chelseaclark: The success of any ion channel research program involves complex decisions that require specific expertise to address the comple...

"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, 318👍, 0💬

"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, 269👍, 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 documebnt: "C...
2020-07-22, 260👍, 0💬

"obabel ... -o svg -xP300" - Scale SVG Image
How to scale and center a molecule SVG image in a given squar area? The default behavior of Open Babel 2.4 is different than 2.3 reguarding scalling 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 S...
2020-07-22, 244👍, 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, 242👍, 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, 228👍, 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, 247👍, 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, 242👍, 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, 239👍, 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, 193👍, 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, 191👍, 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, 182👍, 0💬

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