Depth-First

Run Babel Anywhere Java Runs with JBabel

By Richard L. Apodaca

A recent series of D-F articles have discussed the use of NestedVM to compile cheminformatics programs written in C/C++ to pure java binaries that can be run on any system with a JVM. More specifically, an attempt to compile OpenBabel's babel program to bytecode was only partially successful. With the help of Geoff Hutchison, the problem was resolved. This article introduces JBabel, a platform-independent, pure Java implementation of OpenBabel's babel program.

A Little About JBabel

JBabel was compiled from the Open Babel 2.1.1 source release and can be downloaded from SourceForge. The same jarfile was successfully tested on Linux, Windows and Mac OS X. You can verify JBabel works on your platform with the following command:

java -jar jbabel-20071209.jar -Hsmi
smi  SMILES format
A linear text format which can describe the connectivity
and chirality of a molecule
Write Options e.g. -xt
  n no molecule name
  t molecule name only
  r radicals lower case eg ethyl is Cc

This version of JBabel was compiled with support for three formats:

  • SMILES (smi). Non-canonical SMILES.
  • MDL (mol). Molfiles and SD Files.
  • Canonical SMILES (can). Canonical SMILES implementation donated by eMolecules.

I'll discuss exactly how support for these formats was added in a subsequent post. More formats will be added in the future. For now, let's just try JBabel out.

Testing JBabel

One way to use JBabel is interactively from the command line - just leave out an input or output file parameter. For example, if you wanted to get the eMolecules canonical SMILES for sertraline, you might do something like this (be sure to use two returns to begin processing):

java -jar jbabel-20071209.jar -ismi -ocan
CN[C@H]1CC[C@H](C2=CC=CC=C12)C3=CC(=C(C=C3)Cl)Cl

CN[C@H]1CC[C@H](c2ccc(Cl)c(Cl)c2)c2ccccc12
1 molecule converted
34 audit log messages

This canonical SMILES can be converted into a molfile with the following:

$ java -jar jbabel-20071209.jar -ismi -omol
CN[C@H]1CC[C@H](c2ccc(Cl)c(Cl)c2)c2ccccc12


 OpenBabel12090723182D

 22 24  0  0  0  0  0  0  0  0999 V2000
    0.0000    0.0000    0.0000 C   0  0  0  0  0

...

To convert using input and output files, we could use a medium-sized dataset such as the PubChem benzodiazepine dataset prepared for Rubidium:

java -jar jbabel-20071209.jar -imol pubchem_benzodiazepine_20071110.sdf -ocan pubchem_benzodiazepine_20071110.smi
==============================
*** Open Babel Warning  in ReadMolecule
  WARNING: Problems reading a MDL file
Cannot read title line

2117 molecules converted

This test, which parses 2117 records, required four minutes forty-five seconds on my system. For comparison, the natively compiled binary did the same thing in about thirteen seconds. Clearly, the JBabel performance hit is substantial.

Uses

Although it's very unlikely that JBabel will ever be useful in performance-critical situations, its portability makes it attractive for other uses. Examples include:

  • application development in heterogeneous computing environments;
  • use on systems in which native compilation may be difficult, such as those with unusual configurations or operating systems;
  • cases in which native binaries work poorly or not at all, such as in applets and Java applications;
  • situations in which performance is a minor consideration, such as in end-user applications that process only a few molecules at a time, or during application prototyping

Conclusions

This article has described JBabel, the first portable binary version of OpenBabel's babel molecular file format interconversion program. The next article in this series will describe in detail the steps that were used to compile it.