== CRYSTALEYE ==
=== Installation ===
You will first need to download and install the following:
* A Java JDK (version 1.5 or later)
* Mercurial - http://mercurial.selenic.com/wiki/Download
* Maven 2 - http://maven.apache.org/download.html
1. Navigate to the directory you wish to download the CrystalEye code to and issue
hg clone http://bitbucket.org/ned24/crystaleye
this will create a 'crystaleye' dir.
2. Issue the following command from inside the 'crystaleye' dir:
this will create a 'target' folder which contains (amongst other things)
3. Copy crystaleye.jar to the place that you'll run it from.
=== Updating ===
* If you want to update your CrystalEye code, execute the following commands
from your CrystalEye code directory:
* Then you can do the steps 2 & 3 from the Installation section to install your
=== Execution ===
* In the root of the 'crystaleye' directory that you cloned is a file called
'crystaleye.properties.example'. Copy this to your preferred location on your
machine and rename it to 'crystaleye.properties'. If you are only going to be
using the crawlers and CIF2CML parts of CrystalEye then you only need to set the
cif.dir and web.dir properties. If you are using anything else, then you will
need to also set web.dir.url.
* To execute the CrystalEye code you need to issue a command of the type
java -jar <path-to-your-crystaleye-jar> -p <path-to-your-properties-file>
* If you use the above command (with your machine specific paths put in) then all
of the processes in CrystalEye will be run after one another, these are:
-fetch : finds and downloads CIFs from publishers websites
-cif2cml : converts CIFs to CML
-cml2foo : creates 2D images of the structures and breaks them up into
-webpage : creates the CrystalEye website around the structures that have been
-rss : creates a number of RSS feeds to publish the structures in your CrystalEye
-doilist : keeps an index of all DOIs that have been downloaded
-smiles : keeps an index of all SMILES contained within the structures.
-cellparams : keeps an index of all the cell parameters of the structures.
-bondlengths : keeps indexes of all the bond lengths found within the structures
and creates histograms of the data.
* If you just want to run one at a time, then you can append the name of the
processor as observed in the list above. For instance, the following command
would just run the web-crawlers
java -jar <path-to-jar> -p <path-to-props> -fetch
Or you could run the crawlers and CIF2CML processing with
java -jar <path-to-jar> -p <path-to-props> -fetch -cif2cml