Screening Assistant 2

Frequently (or not...) Asked Questions

Last edited: 08/11/2011
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.

Table of Contents

General questions - top

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...

Installation instructions.

Platform / Software - top

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 ?

Check this out.

Can I run more than one instance of SA2 ?

Nope (although there might be a trick which I haven't tested yet).

MySQL - top

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.

Input / Output - top

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.

SDF import - top

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.

Properties / Fingeprints - top

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! :)

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