Open Babel Tutorials
Where to find FAQ (Frequently Asked Questions) on Open Babel, Chemistry Toolbox? I want to learn more about Open Babel.
✍: FYIcenter.com
Here is a large collection of tutorials to answer many frequently asked questions
compiled by FYIcenter.com team on
Open Babel, Chemistry Toolbox:
What Is Open Babel, Chemistry Toolbox
Open Babel History and Releases
Open Babel Web Interface at cheminfo.org
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
Open Babel Installation Options on macOS
Install Open Babel Binary Package on macOS
Understanding "babel" Command Line Syntax
"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 ... -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
Substructure Search with Open Babel
"babel -s ..." Command - Substructure Search
Substructure Search with Wildcard Atom "*"
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
"babel -ofpt -xs" - Display Fingerprint Fragments
"babel" - FP2 Exhaustive Fingerprint Fragments
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
Stereochemistry with Open Babel
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
"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
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