Open Babel Tutorials

Q

Where to find FAQ (Frequently Asked Questions) on Open Babel, Chemistry Toolbox? I want to learn more about Open Babel.

✍: FYIcenter.com

A

Here is a large collection of tutorials to answer many frequently asked questions compiled by FYIcenter.com team on Open Babel, Chemistry Toolbox:

Introduction to Open Babel

What Is Open Babel, Chemistry Toolbox

Open Babel History and Releases

Open Babel Web Interface at cheminfo.org

openbabel.cheminfo.org/v1/convert - Web API

Open Babel Documentation and Resources

Running Open Babel on CentOS

Open Babel Installation Options on CentOS

"DNF/YUM search" - Open Babel Binary Packages

"DNF/YUM install" - Open Babel Binary Packages

Search Open Babel RPM Packages for CentOS

Install Open Babel Library RPM Package for CentOS

Install Open Babel CLI RPM Package for CentOS

Install Open Babel from Source Code on CentOS

Running Open Babel on macOS

Open Babel Installation Options on macOS

Install Open Babel Binary Package on macOS

Open Babel File Location on macOS

Open Babel Command Files on macOS

Running Open Babel on Windows

Install Open Babel Binary Package on Windows

Run Open Babel GUI on Windows

Structure Display Command on Open Babel GUI

Understanding "babel" Command Line Syntax

What Is "babel" Command

"babel" Command - Input Data Source and Format

"babel" Command - Output Data Destination and Format

"babel" Command - Use "-o ..." as Output Delimiter

"babel" Command - From STDIN To STDOUT

"babel -... --..." Command - Generic Conversion Options

"babel" Command Option Argument Syntax

"babel ... -f # -l #" - Split Large Molecule File

"babel -h" Command - Add Hydrogens to Molecule Data

"babel -d" Command - Delete Hydrogens from Molecule Data

"babel --append ..." Command - Calculate Molecule Properties

List of File Formats Supported by Open Babel

"babel -a..." Command - Extra Input Reading Options

"babel -x..." Command - Extra Output Writing Options

"babel" vs. "obabel" Commands

"babel ... -o svg" - Generating SVG Pictures

"babel -o svg" Command - SVG Generation Options

"obabel ... -o svg" Command - Generate SVG from SMILES

"babel ... -o svg -xi" - Show Atom Indices in SVG

"babel ... -o svg -xS" - Ball/Stick Depiction in SVG

"babel ... -o svg -xX" - Hide Implicit H in SVG

"babel ... -o svg -xC" - Hide Terminal C in SVG

"babel -i sdf -o svg" - Custom Atom Positions

"babel ... -o svg" - Two "svg" Tag Levels

"obabel ... -o svg -xP300" - Scale SVG Image

Scaling SVG Images using "viewBox" Attribute

"babel ... -o svg -xP300" Bug - width="px" height="px"

"babel ... -o svg -xd -xP300" Bug - Option -d takes a parameter

"-o svg -xd -d" Bug in Open Babel 3.1.1

Substructure Search with Open Babel

"babel -s ..." Command - Substructure Search

Substructure Search with Wildcard Atom "*"

Substructure Search with Wildcard Bond "~"

What Are SMARTS Expressions

Substructure Search with SMARTS Expressions

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

Using Fastsearch Fingerprint Index

"babel ... -o fs" - Generate Fastsearch Index

"babel -i fs ..." - Fingerprint Index Based Search

"babel -i fs ... -s ... -at n" - Top n Similarity Search

"babel -i fs ... -s ... -at score_range" - Similarity Search

"Difficulty opening ..." Error Using Fastsearch Index

"babel -i fs ... -s SMILES" - Substructure Search with Index

"babel -i fs ... -s query_file" - Substructure Search

"babel -i fs ... -s query_file" - Exact Match Search

Stereochemistry with Open Babel

What Is Stereochemistry

Read Stereoinformation from Input

Stereo Perception Performed by Open Babel

Write Stereoinformation to Output

Wedge/Hash Bond Changed by Open Babel

R/S (Right/Left) Hand Stereo Centers

Custom Wedge/Hash with SVG output

Hash Bond with Solid Line

Other Open Babel Commands

List of Open Babel Commands

"obchiral" - Print Chirality Information

"obconformer" - Generate Best Conformer

"obenergy" - Calculate Molecule Energy

"obfit" - Superimpose Two Molecules

"obgen" - Generate Molecule 3D Structures

"obgrep" - Search Molecules using SMARTS

"obminimize" - Optimize Geometry/Energy of Molecule

"obprobe" - Create Electrostatic Probe Grid

"obrotamer" - Generate Random Rotational Isomers

"obrotate" - Rotate Dihedral Angles with SMARTS

⇒ Introduction to Open Babel

2020-05-21, 1921👍, 0💬