Atom General Molecule Tools Trial

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"babel" vs. "obabel" Commands
What are the differences between "babel" and "obabel" commands? "babel" and "obabel" commands are two commands of the same Open Babel chemical data conversion program with slightly different command line syntaxes. You can see the syntax differences between "babel" and "obabel" commands by running th... 2021-07-19, 308👍, 0💬

"obabel ... -o svg" Command - Generate SVG from SMILES
How to generate a molecule SVG picture from a SMILES string? The easiest way to generate a molecule SVG picture from a SMILES string is to use the the "babel ... -o svg" command. For example, the following command generate a SVG picture of the tyrosine molecule from a SMILES string: fyicenter$ obabe... 2021-07-19, 301👍, 0💬

"babel ... -o svg" - Generating SVG Pictures
Where to find FAQ (Frequently Asked Questions) on using Open Babel to generate SVG Pictures from molecule input data? Here is a list of tutorials to answer many frequently asked questions compiled by FYIcenter.com team on using Open Babel to generate SVG Pictures from molecule input data. "babel -o ... 2021-07-19, 289👍, 0💬

"babel -... --..." Command - Generic Conversion Options
What are generic conversion options that I can use on "babel" commands for all input and output formats? "babel" commands supports a number of generic conversion options that applies all input and output formats as listed below: --addtotitle Append text to the current molecule title --addformula App... 2021-07-19, 287👍, 0💬

"babel" Command - Use "-o ..." as Output Delimiter
How to use "-o ..." flag as a delimiter to separate output file from input files in a "babel" command? The "-o ..." flag is otional, since "babel" command can implicitly determine the output data format from the file extension of output file name. However, it is important to use the "-o ..." flag as... 2021-07-19, 283👍, 0💬

"babel" Command - Output Data Destination and Format
How to specify Output Data Destination and Format for a "babel" command? "babel" command arguments and options are organized into 3 sections as shown in the following syntax to convert chemical data from input to output with specified options. babel input_section output_section option_section You us... 2021-07-19, 282👍, 0💬

"babel -o svg" Command - SVG Generation Options
What options can I use when generating SVG pictures from molecule input data? You can see a list of options supported by Open Babel when generating SVG pictures from molecule input data by running the "babel -H svg" command: fyicenter$ babel -V Open Babel 2.4.1 fyicenter$ babel -H svg svg SVG 2D dep... 2021-07-19, 279👍, 0💬

"babel" Command - Input Data Source and Format
How to specify Input Data Source and Format for a "babel" command? "babel" command arguments and options are organized into 3 sections as shown in the following syntax to convert chemical data from input to output with specified options. babel input_section output_section option_section You use inpu... 2021-07-19, 274👍, 0💬

"babel" Command - From STDIN To STDOUT
Can I use "babel" to convert chemical data from "stdin" to "stdout" without input and output files? Yes, you can use "babel" to convert chemical data from "stdin" to "stdout" without input and output files. Just use "-i ..." and "-o" flags to specify input data format and output data format. For exa... 2021-07-19, 267👍, 0💬

Run Open Babel GUI on Windows
How to run OpenBabelGUI on Windows computers? Open Babel GUI is the graphical user interface for Open Babel. You can use Open Babel GUI to open a molecule file in any supported format and convert it to any other format. Here is how to Open Babel GUI on Windows. 1. Search for "Open Babel GUI" in "Sta... 2021-03-07, 439👍, 0💬

Install Open Babel Binary Package on Windows
How to Install Open Babel binary package on Windows computers? The easiest option to install Open Babel on Windows computers is to install the Open Babel pre-compiled binary package as shown in this tutorial.: 1. Go to GitHub Website for Open Babel 3.0.0. 2. Click to download "OpenBabel-3.0.0.exe" f... 2021-02-17, 410👍, 0💬

Running Open Babel on Windows
Where to find FAQ (Frequently Asked Questions) on running Open Babel on Windows? Here is a list of tutorials to answer many frequently asked questions compiled by FYIcenter.com team on running Open Babel on Windows. Install Open Babel Binary Package on Windows Run Open Babel GUI on Windows Structure... 2021-02-17, 386👍, 0💬

"babel ... -o svg -xi" - Show Atom Indices in SVG
How to show atom indices in a molecule SVG picture? I want to see in what order each atom is listed in the SMILES string. The SMILES string list each atom a molecule is a specific sequence. You can use the "-xi" option when generating the SVG file to show the index of each atom corresponding to the ... 2021-02-04, 391👍, 0💬

Substructure Search with SMARTS Expressions
How to use SMARTS expressions in a substructure search using "babel" commands? You can use SMARTS expressions in the "-s ..." option in "babel" commands to filter molecules that match given SMARTS expressions. Here are some examples: # C, C and O connected with single bonds fyicenter$ obabel "-:c1cc... 2021-01-09, 337👍, 0💬

Open Babel Documentation and Resources
Where can I find Open Babel documentations and resources? Here is a list of links to Open Babel documentations and resources. Open Babel Command Manuals and Tutorials - http://openbabel.org/wiki/Cate gory:GuidesOpen Babel v2.3.1 Documentation - "Open Babel, or how I learned to love the chemistry fil... 2021-01-09, 315👍, 0💬

"babel --append ..." Command - Calculate Molecule Properties
How to use "babel --append ..." command to calculate Molecule Properties? The "--append ..." option of the "babel" command can be used to copy existing molecule properties from the input data source, and append them to the "title" field of output molecules. But the "--append ..." option can also be ... 2020-12-26, 335👍, 0💬

"babel" Command Option Argument Syntax
How to write "babel" command option argument properly? What's the difference between "-isdf" and "-i sdf"? There is no difference between "-isdf" and "-i sdf". Both are valid "babel" option "-i" with an argument of "sdf". If a "babel" command option takes an argument, you can specify the argument in... 2020-12-26, 332👍, 0💬

Similarity Search with Open Babel
Where to find FAQ (Frequently Asked Questions) on Similarity Search with Open Babel? Here is a list of tutorials to answer many frequently asked questions compiled by FYIcenter.com team on Similarity Search with Open Babel. "babel -o fpt ..." Command - Similarity Search Fingerprint Types Supported i... 2020-12-22, 305👍, 0💬

Fingerprint Types Supported in Open Babel
What Fingerprint Types are Supported in Open Babel? You can get a list of fingerprint types supported in Open Babel by running the "babel -L fingerprints" command: fyicenter$ babel -L fingerprints FP2 Indexes linear fragments up to 7 atoms. FP3 SMARTS patterns specified in the file patterns.txt FP4 ... 2020-12-15, 322👍, 0💬

"babel -o fpt ..." Command - Similarity Search
How to use "babel -o fpt ..." command to do similarity search? You can do similarity search using the "-o fpt ..." option of the "babel" command with the following syntax: babel input_section -o fpt When you run the above commands, Open Babel will perform the following: Take the first molecule from ... 2020-12-15, 311👍, 0💬

"babel -ofpt -xs" - Display Fingerprint Fragments
How to Display Fingerprint Fragments usig "babel" command? I want to know how many fragments are used when taking the fingerprint of a given molecule. You can using ""-ofpt -xs" options of the "babel" command to Display Fingerprint Fragment information. Here are some examples of molecule fingerprint... 2020-12-02, 322👍, 0💬

Substructure Search with Fingerprints
Can I do Substructure Search with fingerprints using Open Babel? Yes, you can do Substructure Search with fingerprints using Open Babel. All you have to do is to take substructure as the query molecule and run a similarity search using the fingerprint output option "-o fpt ". When Open Babel calcula... 2020-12-02, 307👍, 0💬

"babel" - FP2 Exhaustive Fingerprint Fragments
How to exhaust all possible Open Babel FP2 Fingerprint Fragments in a molecule? The easiest way to exhaust all possible Open Babel FP2 Fingerprint Fragments in a molecule to following this algorithm: Loop through all atoms (except H) in the molecule. Set each atom as the root of a bond-atom tree. An... 2020-12-02, 307👍, 0💬

Generate Fingerprint of Single Molecule
How to generate the fingerprint of a single molecule? I want to see the fingerprint value. If you want see the fingerprint value of a single molecule, you can just specify the molecule as the only input molecule to the "babel ... -o fpt " command. Open Babel will output its fingerprint in hexadecima... 2020-12-02, 300👍, 0💬

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Atom General Molecule Tools Trial