Similarity Search with Open Babel

Q

Where to find FAQ (Frequently Asked Questions) on Similarity Search with Open Babel?

✍: FYIcenter.com

A

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 in Open Babel

Substructure Search with Fingerprints

Generate Fingerprint of Single Molecule

What Is Tanimoto coefficient

"babel -ofpt -xs" - Display Fingerprint Fragments

"babel" - FP2 Exhaustive Fingerprint Fragments

"babel" - FP2 Fingerprint Fragment Ends at Ring

"babel -H fpt" - Fingerprint Help Information

⇒ "babel -o fpt ..." Command - Similarity Search

⇐ Substructure Search with SMARTS Expressions

⇑⇑ Open Babel Tutorials

2020-12-22, 410👍, 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, 442👍, 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, 433👍, 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, 432👍, 0💬

"babel -ofpt -xs" - Display Fingerprint Fragments
How to Display Fingerprint Fragments using "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 fingerprin... 2020-12-02, 420👍, 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, 416👍, 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, 408👍, 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, 408👍, 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, 394👍, 0💬

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