[Briefer than I would have liked as MSWord crashed and so did the document recovery.]
I explained that I blogged everything now as Open. Imagine what I wrote and Word wiped out.
This blog is mainly for my own memory. It’s not guaranteed accurate. Note all software mentioned is Open. Use Wikipedia to find the non PMR stuff.
Prerequisites:
Most software is on Bitbucket under mercurial source control (yes, look them up – they are friendly).Easy to download with
hg clone
which populates a directory. Use Eclipse, Netbeans or IntelliJ to explore(they’re friendly too after a little while). Blog me if you need help. If you want to build and install use Maven (look it up) from commandline (note there are scientists who do not know what a comandline is – please help them – it is the easiest way to do this stuff). And guess where to look it up…
JUMBO (just JUMBO):
If you are a developer, install in order. If you are not then skip this – it’s all packaged for you.
- euclid a set of maths libraries: https://bitbucket.org/wwmm/euclid ; then
mvn test install
on the commandline
- schema2 CML schema: http://xml-cml.org/schema/schema24/index.php ; not bedtime reading; `It’s long,’ said the Knight, `but very, very beautiful.
- cmlxom basic CML: https://bitbucket.org/wwmm/cifxom ; then
mvn test install
- jumbo6 lost of molecular stuff, geometry, connections tables, etc: https://bitbucket.org/wwmm/jumbo6 ; then
mvn test install
This gives the basic CML toolkit. It is all packaged in a single maven Jar file. Just use maven and sleep soundly
JUMBOConverters:
Convert lots of legacy / foreign file formats to CML. Needed for CIF, Chemdraw, spectra and lots of compchem. Again, skip if not a dev.
- jumbo-converters everything in one go: https://bitbucket.org/wwmm/jumbo-converters ; then
mvn test install
There are 26 sub-projects ranging from CIF , Chemdraw, many molecules, spectra, reactions, many many compchem.
If you use Eclipse import it manages them beautifully. Now you have the jumbo-converters package which is used in Quixote, etc. But you can also skip and rely on the packaged jar.
Dictionaries:
Still intensively under development. Inspect if you like raw stuff, else skip
- dictionaries a bit of dictionary soup: https://bitbucket.org/petermr/dictionary ; then
Conventions:
Still intensively under development. Skip…
- convention for different CML conventions: https://bitbucket.org/jat45/cmllite
Chempound:
You will need this if you want to run Chempound unless you use the Quixote stuff below. Skip…
-
chempound build a chempound repository: https://bitbucket.org/ chempound/chempound-aggregator
mvn test install
There are about 28 packages. If you use Eclipse import it manages them beautifully
Sam Adams built this. It’s impressive code. Worth reading for an idea how to manage repository import using SWORD, etc.
Quixote:
You will need this if running a Quixote repository
- quixote and chempound: https://bitbucket.org/chempound/quixote-repository
- quixote-utils: https://bitbucket.org/sea36/quixote-utils
UPDATE: Docs from Jorge Estrada: https://bitbucket.org/jestrada/quixote-docs
More later