OSRA 2.0.0 released

22 May 2013

OSRA 2.0.0 was released with significantly improved recognition rates, recognition of Iodine, wavy bonds and a completely modified confidence function.

We have uploaded a new version of our wrapper with three new options to the test toolshed.

New Orphan Packages

20 May 2013

Numpy can be compiled against the atlas and lapack libraries to gain much better performance. Today we updated our package for numpy to make use of that.

• http://testtoolshed.g2.bx.psu.edu/view/bgruening/package_atlas_3_10
• http://testtoolshed.g2.bx.psu.edu/view/bgruening/package_lapack_3_4
• http://testtoolshed.g2.bx.psu.edu/view/bgruening/package_numpy_1_7

Additional, the GraphicsMagick dependency from OSRA was extracted into an own package.

• http://testtoolshed.g2.bx.psu.edu/view/bgruening/package_graphicsmagick_1_3

One Click Installation of CTB

12 May 2013

It's done! Thanks to the awesome work of the Galaxy Team, in particular Greg Von Kuster, hours of debugging and many features requests we finally have a One Click Installation of ChemicalToolBoX through the Tool Shed. Search for chemicaltoolbox on the test toolshed and click install, voila!

To the command line enthusiasts: We have a script for you!

$ ./scripts/api/install_tools.py --api  <Your Galaxy API Key> \
 -l http://localhost:8080 --url http://testtoolshed.g2.bx.psu.edu/ \
 -o bgruening -r 7e98219aa915  --name chemicaltoolbox \
 --tool-deps --repository-deps \
 --panel-section-name ChemicalToolBoX

RDKit 2013-03 released

26 April 2013

RDKit 2013-03 was released a few hours ago with many new features and bugfixes.

If you wish to use it in galaxy I uploaded a orphan-tool-dependency defintion to the test toolshed.

Natural product likeness scorer

13 April 2013

From the natural product likeness scorer paper:

The natural product likeness scorer implemented by Peter Ertl [1] was originally devised to screen large compound libraries for natural product likeness in drug designing studies. His work is re-implemented using open source and open data to validate natural product likeness of theoretical metabolite structures in computer assisted structure elucidation.

And its now included in ChemicalToolBoX.

It's Java based. So fire up your Java Virtual Machine on your server and install it via the toolshed.

DOI: 10.1021/ci700286x

Opsin integration

12 April 2013

Opsin is a Chemical Name to Structure converter and stands for Open Parser for Systematic IUPAC nomenclature. Opsin can generate SMILES, InChI and CML files and is from now on included in ChemicalToolBoX.

It is written in Java and if you have a Java Virtual Machine on your server you can install it via the toolshed.

DOI: 10.1021/ci100384d

Fingerptints, Fingerprints!

02 April 2013

We now have support for 10 different fingerprints with all addional options. So you can specify the number of bits or the used path length.

Available are:

• Open Babel FP2 fingerprints
• Open Babel FP3 fingerprints
• Open Babel FP4 fingerprints
• Open Babel MACCS fingerprints
• RDKit topological fingerprint
• RDKit topological Torsion fingerprints
• RDKit Morgan fingerprints
• RDKit Atom Pair fingerprints
• RDKit MACCS fingerprints
• RDKit substructure fingerprints

CTB: Bug & Feature Tracker

25 March 2013

ChemicalToolBoX has now its own bug and feature tracker. I decided to use trello because trello is just awesome and galaxy is using it also.

Create your feature request and bug reports!

Divide & Conquer (mutiprocessing)

02 March 2013

Galaxy has some initial support for build-in multiprocessing. In the datatype definition you can define merge() and split() functions to devide & conquer your input datasets. After processing every splitted file all results will be merged automatically.

I commited today an extended definition of SMILES, InChI and SDF datatypes and enabled the multiprocessing feature in a few tools, like QED and Converters. Depending on your galaxy configuration and the available computer cores your calculations can be X times faster now.

During processing 50.000.000 SMILES I found a small bug in the concatination routine of galaxy. Using cat to merge 1000 of files seems not to be suitable, because the shell has a commandline limit defined in ARG_MAX:

$ getconf ARG_MAX
$ 2097152

The solution is to use python's shutil module and iterate over all splitted files.

for fsrc in split_files:
   shutil.copyfileobj( open( fsrc, 'rb' ), fdst )

That solution is not slower than cat, pythonic and it works for a unlimited amount of files. Patch and Pull request is submitted as #141.