Open Babel Documentation and Resources

Q

Where can I find Open Babel documentations and resources?

✍: FYIcenter.com

A

Here is a list of links to Open Babel documentations and resources.

Open Babel Command Manuals and Tutorials - http://openbabel.org/wiki/Category:Guides

Open Babel v2.3.1 Documentation - "Open Babel, or how I learned to love the chemistry file format" at http://openbabel.org/docs/current/

Open Babel API Documentation - http://openbabel.org/api/2.3/

Open Babel Code Repository at sourceforge.net - https://sourceforge.net/projects/openbabel/

Open Babel Code Repository at github.com - https://github.com/openbabel/openbabel

Open Babel User Forum - http://forums.openbabel.org

Open Babel Web User Interface - http://www.cheminfo.org/Chemistry/Cheminformatics/FormatConverter

Open Babel: An open chemical toolbox - ”Journal of Cheminformatics“ technical paper at https://jcheminf.biomedcentral.com/articles/10.1186/1758-2946-3-33

Fingerprints - Screening and Similarity - Description of Structural keys, Fingerprints and Similarity Measures at https://daylight.com/dayhtml/doc/theory/theory.finger.html

Molecular fingerprints library - List of Molecular Fingerprint Algorithms at http://www.scbdd.com/chemdes/list-fingerprints/

⇒ Running Open Babel on CentOS

⇐ Open Babel History and Releases

⇑ Introduction to Open Babel

⇑⇑ Open Babel Tutorials

2021-01-09, 547👍, 0💬

"babel -o fpt ..." Command - Similarity Search
How to use "babel -o fpt ..." command to do similarity search? You can use the "fpt" output file format with the "babel" command to do similarity search using the following syntax: babel input_section -o fpt When you run the above commands, Open Babel will perform the following: Take the first molec... 2020-12-15, 748👍, 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, 703👍, 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, 621👍, 0💬

"babel -s ..." Command - Substructure Search
How to use "babel -s ..." command to do substructure search? You can do substructure search using the "-s ..." option of the "babel" command with the following syntax: babel input_section output_section -s smarts_string The smarts_string specifies a SMARTS string that represents a molecule pattern. ... 2020-06-08, 555👍, 0💬

What Are SMARTS Expressions
What are SMARTS expressions? SMARTS expressions are divided into 3 types: 1. Atom Expressions - An expression that can be evaluated to an atom pattern using atom operations on atoms and atom expressions. An atom expression must be enclosed in square brackets, if it is not a single simple atom symbol... 2020-06-08, 553👍, 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, 550👍, 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, 548👍, 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, 529👍, 0💬

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