All change

After three years at a AstraZeneca I decided it was time for a change. So instead of Manchester I opted for Santa Fe, New Mexico. I've been here for nearly two weeks now and in terms of culture, food and weather it couldn't be more different to Manchester. Thankfully, I'm loving every minute of it. In no small part that is thanks to my new employer - OpenEye. I've had a week at work so far and am immersing myself in the startup like culture that OpenEye has.

I'm speaking at CUP XIII next month on some of my work from AstraZeneca entitled, "Keepalive with OEChem 24x7x365". Given I work for a software company now I expect (though I won't promise) to actually post more to this blog.

Eclipse with C++/OEChem

The final post in this series, allowing you to develop your OpenEye applications using Eclipse.

First off you will need to ensure the CDT plugin is installed, or download Eclipse for C++ developers.

Now we are set to go. Create a new C++ Project (Executable > Hello World). Edit/Add C++ files to the source folder. Next we need to inform the project about OpenEye.

• Open your project properties (Project > Properties).
• Pick C/C++ Build > Settings
• Edit [ All Configurations ] (by default Debug and Release)
• Set include paths (-I) under GCC C++ Compiler > Directories > Include paths
• Add $OE_DIR/toolkits/include
• Set library paths (-L) under GCC C++ Linker > Libraries > Library search path
• Add $OE_DIR/toolkits/lib
• Set specific libraries (-l) under GCC C++ Linker > Libraries > Libraries
• Add oeplatform, oesystem, oechem, m, z, pthread
• You can set further Makefile details from this panel (optimisation etc)

If you have multiple versions of the toolkit you can create a configuration for each one.

Between C++/Java/Python you should be able to code away happily within Eclipse.

Eclipse with Java/OEChem

Following up from a previous post, here I present the settings required to get Eclipse running with the OEChem Java wrapper.

Make sure you have Eclipse and and working OpenEye installation setup and running first.

1. Create a regular Java Project
2. Configure your build path to add:
3. a) Under sources add a linked source $OE_DIR/java/libs
4. b) Under libraries add external jars, $OE_DIR/java/*.jar (add them all)
5. Run your OEChem program, if you get license errors edit the run configuration; under environment add OE_LICENSE, with $OE_DIR/etc/oe_license.txt; OE_HOME with $OE_DIR and OEJAVA with $OE_DIR/java

Obviously substitute $OE_DIR with your actual absolute file path.

Now Eclipse's CDT can be used to use the C++ toolkit direct, so I'll post that - once I've started to use it!

Eclipse with Python/OEChem

Eclipse is an excellent IDE. Alas it doesn't have support for Python - fear not the PyDev plugin comes to the rescue. (Installation information here).

While that now works like a charm, if you have an OpenEye license to hand (academics see this post) if would be great to use the Python toolkit through Eclipse.

Follow these steps to make your Python project OEChem ready:

Window > Preferences > Pydev > Interpreter - Python.
To Libraries add your $OE_DIR/python folder.
To Environment add OE_LICENSE and OE_DIR, with their respective locations.
Create a new PyDev project and it should have OE capability by default.

Java users don't worry, I'll cover OEChem/Java in my next post.

Python training

Forgot to mention in my last post. If you are after Python/OEChem training and are not coming to EuroCUP, there is an alternative. Andrew Dalke is offering Python training for Cheminformatics. OEChem is just one part of this course, Django, SQL, R are also covered.

I've spoken to a previous attendee and he recommended it.

See Andrew's website for more details.

EuroCUP III

I'm off to OpenEye's third annual EuroCUP next month. I've not been to a vendor organised conference before, so am looking forward to it.

Although I've previously posted about the free academic license; I wish I'd taken advantage of mine more. Alas time didn't permit. That's now changed and I've learning Python as quick as I can to take full advantage of the Python/OEChem training session offered at EuroCUP.

I can jump straight into OEChem via Java, but the Python wrapper lends itself better for web-based applications. I've no plans (yet) to use the C++ toolkit directly.

I've used Eclipse as my editor of preference and will post how to configure it to use the Java & Python wrappers. Any C++ users feel free to contribute!