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Frequently (or not...) Asked Questions

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Table of Contents

• General questions     
• Platform / software general questions   -   memory, configuration...
• MySQL
• Input / Output format
• SDF Import
• Properties / Fingeprints

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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:

• You forgot to create a new user
• The URL / user name / password is invalid
• The computer hosting your server is behind a firewall
• Your network is down (ah!)

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...

• Have you created a new user with the appropriate rights after installing the server ?
• Do you have the appropriate right (writing) on the directory that contain your databases?

Installation instructions.

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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:

• Windows XP: C:\Documents and Settings\username\Application Data\.sa
• Windows Vista/Seven: C:\Users\username\AppData\Roaming\.sa
• Mac OS X: /Users/username/Library/Application Support/sa
• Linux: /home/username/.sa

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).

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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.

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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.

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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:

• Computing HTS flags (SMART substructure searches) on such complex molecules can be very long!
• Computing descriptors or fingerprints on such huge molecules can be very long!
• Computing descriptors or fingerprints on such huge molecules does not really make sense
• Displaying these molecules in 2D does not make sense either, is long and will freeze your GUI

Note that you can change this threeshold in the properties file of SA2, by changing the value of the sa.import.maxAtoms property.

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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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