Last edited: 08/11/2011
By: VLG
Sourceforge: SA2 website
Help: SA2 forums
Documentation index
This page group all questions that have been frequently asked about various aspects of SA2. Together with the Goot-to-know section, there is a fairly good chance that you will find answer to simple questions / issues related to SA2.
Which OS / architecture are supported by SA2
Although SA2 is writen in JAVA, it also relies on non-portable applications such as MySQL or the IUPAC InChI program. You can read the list of successfully tested OS / architectures in the Installation instructions.
Which version of MySQL server do I need ?
Well, at least the 5.0. We havent tested previous versions, and guess that they might not be compatible. See the Installation instructions.
Which version of JAVA do I need ?
1.5 at least. Installation instructions.
I can't connect to my newly installed MySQL server... Why is that so ?
The most probable reasons for this are:
Check all these things first, and then... Call IT people, because either your network is not properly configured to be reached by your computer, or MySQL is not properly configured. :)
I can connect to the MySQL server, but I can't create new databases...
Where is SA2 installed?
Where you have unzipped the archive.
Properties file
Located in the installation directory in the following path: $SA/sa/sa.properties, this file contains some parameters that can be changed to tune SA2. Only a few are currently available though:
Parameter | Description | Default value | Possible values |
---|---|---|---|
sa.debug.log | The verbosity of logging (View->IDE Log) | FINE | FINE, FINER, FINEST (the most verbose log level) |
sa.import.maxAtoms | Maximum number of heavy atoms allowed in SA2 | 100 | Up to you. |
sa.ui.plot.dotsize | Size of the dots in the various plot windows | 4 | Up to you. |
sa.ui.plot.circle | Plot molecules as circle instead of square. Slow down the plot process but is a bit more sexy. | 0 | 0 (squares) or 1 (circles). |
What is the SA2 user directory and where can I find it ?
The user directory of SA2 is basically where the application will put various configuration files. The user directory can be found in the following places:
Alternatively, in the top Menu bar of the application, Help->About will give you the information.
How can I increase the memory allocated to SA2 upon startup ?
Can I run more than one instance of SA2 ?
Nope (although there might be a trick which I haven't tested yet).
Do I have to tune MySQL if I plan to setup a large database ?
Definitely yes. The best thing to do would be to talk to a computer scientist guy. Otherwise, you can have a look at this section for a first start.
Which input format are supported by SA2 ?
To import your molecules (their actual structures), only SDF files are supported. To import properties, SDF and delimited text files are currently supported.
Which output format are supported by SA2 ?
You can export your molecules using either the SDF format, or the CSV format (if you export properties...).
Can I export a particular set of properties only ? (without the structure)
Yes. To be documented, but it's very easy to achieve even without documentation.
Can I export a particular library only ?
Yes. To be documented, but it's very easy to achieve even without documentation.
Can I export fingerprints ?
Yes, just select it the same way you select properties for export. It will be written in binary format.
Do you change my molecule in any ways when I import a new dataset ?
Not currently. See here.
Molecules having more that 100 atoms are systematically skipped... Why ?
Several reasons for this:
Note that you can change this threeshold in the properties file of SA2, by changing the value of the sa.import.maxAtoms property.
Can I change the category of my property table?
Not yet. Too bad indeed, some days, we will implement drag and drop facilities.
Can I store my own fingerprint and perform similarity search using it ?
Yes and Yes, BUT you will not be able to perform a similarity search on a molecule that does not exists in the database. Think about it... Or read here.
Can I store properties if I don't have the structure of my molecules
No way! :)