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

Q

How to use "babel --append ..." command to calculate Molecule Properties?

✍: FYIcenter.com

A

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 used to calculate new properties from the input molecule data, and append them to the "title" field of output molecules.

Properties that can be calculated from molecule data are listed below with their code names:

  • abonds - Number of aromatic bonds
  • atoms - Number of atoms
  • bonds - Number of bonds
  • cansmi - Canonical SMILES
  • cansmiNS - Canonical SMILES without isotopes or stereo
  • dbonds - Number of double bonds
  • formula - Chemical formula
  • HBA1 - Number of Hydrogen Bond Acceptors 1 (JoelLib)
  • HBA2 - Number of Hydrogen Bond Acceptors 2 (JoelLib)
  • HBD - Number of Hydrogen Bond Donors (JoelLib)
  • InChI - IUPAC InChI identifier
  • InChIKey - InChIKey
  • L5 - Lipinski Rule of Five
  • logP - octanol/water partition coefficient
  • MR - molar refractivity
  • MW - Molecular Weight filter
  • nF - Number of Fluorine Atoms
  • sbonds - Number of single bonds
  • tbonds - Number of triple bonds
  • TPSA - topological polar surface area

Here are some examples of calculating molecule properties using "babel --append ..." commands

fyicenter$ obabel "-:c1cc(ccc1CC(C(=O)O)N)O" -o smiles --append "MW"
c1cc(ccc1CC(C(=O)O)N)O  181.189
1 molecule converted

fyicenter$ obabel "-:c1cc(ccc1CC(C(=O)O)N)O" -o smiles --append "MR"
c1cc(ccc1CC(C(=O)O)N)O  47.5242
1 molecule converted

fyicenter$ obabel "-:c1cc(ccc1CC(C(=O)O)N)O" -o smiles --append "LogP"
c1cc(ccc1CC(C(=O)O)N)O  1.0469
1 molecule converted

fyicenter$ obabel "-:c1cc(ccc1CC(C(=O)O)N)O" -o smiles --append "TPSA"
c1cc(ccc1CC(C(=O)O)N)O  83.55
1 molecule converted

fyicenter$ obabel "-:c1cc(ccc1CC(C(=O)O)N)O" -o smiles --append "MW MR LogP TPSA"
c1cc(ccc1CC(C(=O)O)N)O  181.189 47.5242 1.0469 83.55
1 molecule converted

 

⇒ List of File Formats Supported by Open Babel

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

⇑ Understanding "babel" Command Line Syntax

⇑⇑ Open Babel Tutorials

2020-12-26, 374👍, 0💬