Cheminformatics Tutorials - Herong's Tutorial Examples - v2.01, by Herong Yang
"obabel ... -f # -l #" - Split Large Molecule File
This section provides tutorial examples on how to extract a chunk of molecules from a large molecule file with Open Babel 'obabel' command option arguments.
If you have a large molecule file with thousands of molecules, you can use Open Babel "obabel" command to extract a chunk of molecules to the output using the "-f #" and "-l #" options.
The "-f #" option specifies the index of the first molecule to be extracted.
The "-l #" option specifies the index of the last molecule to be extracted.
For example, the following "obabel" command extract 100 molecules from a large file starting at molecule # 101.
herong$ obabel molecules.sdf -O molecules-chunk.sdf -f 101 -l 200 100 molecules converted
For example, the following "obabel" command extract the first molecule from a large file:
herong$ obabel molecules.sdf -O molecule-first.sdf -f 1 -l 1 1 molecule converted
Table of Contents
SMILES (Simplified Molecular-Input Line-Entry System)
Open Babel: The Open Source Chemistry Toolbox
►Using Open Babel Command: "obabel"
"obabel -i ..." - Input Data Format and Source
"obabel -o ... -O" - Output Data Format and Destination
"obabel -... --..." - Generic Conversion Options
"obabel" Command Option Argument Syntax
"obabel ... --gen2D" - Calculated 2D Coordinates
►"obabel ... -f # -l #" - Split Large Molecule File
"obabel -h/-d" - Add/Remove Hydrogens in Molecule Data
"obabel --append ..." - Calculate Molecule Properties
"obabel -L formats" - List of File Formats Supported
"obabel -a..." - Extra Options for Input Reading
"obabel -x..." - Extra Options for Output Writing
"obabel" vs. "babel" Open Babel Commands
Generating SVG Pictures with Open Babel
Substructure Search with Open Babel
Similarity Search with Open Babel
Fingerprint Index for Fastsearch with Open Babel
Stereochemistry with Open Babel
Command Line Tools Provided by Open Babel
RDKit: Open-Source Cheminformatics Software
rdkit.Chem.rdchem - The Core Module
rdkit.Chem.rdmolfiles - Molecular File Module
rdkit.Chem.rdDepictor - Compute 2D Coordinates
rdkit.Chem.Draw - Handle Molecule Images
Molecule Substructure Search with RDKit
rdkit.Chem.rdmolops - Molecule Operations
Daylight Fingerprint Generator in RDKit
Morgan Fingerprint Generator in RDKit
RDKit Performance on Substructure Search
Introduction to Molecular Fingerprints
OCSR (Optical Chemical Structure Recognition)
AlphaFold - Protein Structure Prediction