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Compute physico-chemical properties (version 3.1.1+galaxy0)
Valid file types are: SDF, MOL, MOL2, CML, InChI, SMILES, and PDB

What this tool does

Computes several physico-chemical properties for a set of molecules.

The following physico-chemical properties and descriptors are computed for each molecule:

  • number of hydrogen-bond donor and acceptor groups
  • number of rotatable bonds
  • logP
  • number of rings
  • number of heavy atoms
  • molecular weight
  • total Polar Surface Area
  • molecular refractivity
  • Canonical SMILES
  • InChI string
  • InChI-Key
  • Spectrophores(TM)


3D coordinates of the molecules have to be provided.

Hint the generation of Spectrophores(TM) requires the previous addition of explicit hydrogen atoms and the proper definition of 3D coordinates. The user is directed towards the corresponding tools if accurate Spectrophores(TM) descriptors are required.


Either a SD-file containing several computed physico-chemical properties stored as metadata or a tabular file with the metadata stored in columns.


N M O'Boyle, C Morley and G R Hutchison - Pybel: a Python wrapper for the OpenBabel cheminformatics toolkit

Silicos - Spectrophores™ is a registered tool implemented in the open-source OpenBabel.

Open Babel