"obabel --append ..." - Calculate Molecule Properties

Cheminformatics Tutorials - Herong's Tutorial Examples

∟"obabel --append ..." - Calculate Molecule Properties

This section provides a tutorial example on how to calculate molecule properties and append them to the 'title' field using Open Babel 'obabel' command.

If you are interested in molecule properties, you can use the Open Babel "obabel ... --append ..." command to calculate some of them.

The calculated property values will be appended 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 "obabel --append ..." commands

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

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

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

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

herong$ 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

herong$ obabel "-:c1cc(ccc1CC(C(=O)O)N)O" -o sdf --gen2D \
   --append "MW MR LogP TPSA"

  181.189 47.5242 1.0469 83.55
   OpenBabel09172113502D

   13 13  0  0  1  0  0  0  0  0999 V2000
      0.8660   -0.5000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
      0.8660   -1.5000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
      0.0000   -2.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
     -0.8660   -1.5000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
     -0.8660   -0.5000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
      0.0000   -0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
     -0.0000    1.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
      0.8660    1.5000    0.0000 C   0  0  3  0  0  0  0  0  0  0  0  0
      1.7321    1.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
      1.7321    0.0000    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
      2.5981    1.5000    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
      0.8660    2.5000    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
      0.0000   -3.0000    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1  6  2  0  0  0  0
    1  2  1  0  0  0  0
    2  3  2  0  0  0  0
    3  4  1  0  0  0  0
    3 13  1  0  0  0  0
    4  5  2  0  0  0  0
    5  6  1  0  0  0  0
    6  7  1  0  0  0  0
    7  8  1  0  0  0  0
    8  9  1  0  0  0  0
    8 12  1  0  0  0  0
    9 10  2  0  0  0  0
    9 11  1  0  0  0  0
  M  END
  $$$$
  1 molecule converted

The "--append ..." option of the "obabel" command can be used to copy existing molecule properties from the input data source, and append them to the "title" field of output molecules.