Parameter Client

Parameter Client - an applet that providesan interface to different programs that calculate molecular parameters.

Molecules can be input in SMILES or SDFformat. 2D and 3D SDF files are distinguished. SMILES can be input with thehelp of JME molecular editor. If the 3D atom coordinates are needed forparameter calculation, they are obtained with the help of CORINA, provided byJ.Gasteiger and his group.

At the presenttime Parameter Client provides an interface for DRAGON, developed by R.Todeschini(Milano, Italy) and ETState - program for the calculation of electrotopologicalstate molecular indices, developed by V.Tanchuk and I.Tetko (Kiev, Ukraine).

Look and Feels menu commands allowto choose the preferable interface of the Parameter Client.

Helpcontents - opens the Help Contents window and puts it on the Help Desktop

Task Desktop
shows one or several instances of the TaskWizard, to prepare and send new tasks.

Separator- allows to choose a separator for saved results. The table fields will beseparated by the selected symbol.

Saveas HTML - allows to save the results as an HTML file. Caution - the resultingHTML file may be too big.

HTMLfile options - allows to specify different parameters of the exported HTML file(font, font color, caption etc.)

Missing values - allows to specify how the missing values are treated at export (Save As TXT command). You can choose empty column, default value 999 or any user defined value.

Edit menu commands

Copy as text -copies the results as text into Clipboard.

Copy Selection -copies the selected rows into Clipboard in text format. This feature is usefulwhen the data are too bulky.

Copy as HTML -copies the results into Clipboard in HTML format. (Warning: the resulting HTMLdata may be too big).

View menu

allows to switchbetween the Results(Table), Error and Warning messages.

2) Parameter page - the page for theselection of molecular parameters. All parameter that can be calculated byParameter Client are displayed here. They are divided into group, which aredisplayed in the list at the left side of the page. The user can select thewhole group (Group menu) as well as the individual indices (Index menu). Theselection can be saved by File/Save As... command and loaded by File/Opencommand(application mode) or Upload/Show commands(applet mode). Custom Index command and page are used to select parameters that have custom names (parameters which like ET-state indices have the names, generated by calculating program).

3) Molecules page - allows to input themolecules and specify their type. The molecules can be:

a. input with the help of JME molecular editor by Peter Ertl -File / JME Editor command

b. Loaded from a file - File/Load command. In applet mode the file will be loaded to File Desktop and can be selected later by File/Select File command.

d. In applet mode the small files (up to 32K) can be loaded with the help of Clipboard Assistant command.

Before sending task the format of molecules must beproperly selected in the 'Molecule File Type' list. Please note that there aretwo types of SDF files that should not be mixed

a. 2D SDF files - molecules after the MDLISISDraw, suitable only as illustrations for chemical articles. There are only2D coordinates, that make good looking picture when printed. Most hydrogenatoms are skipped. Actually they are not suitable for any calculation, but manycompanies store them in such format in the MDL ISISBase. Nevertheless, suchmolecules may be used in our program if the user specifies their type properly.Parameter Client sends them first to CORINA, a program by J.Gasteiger and hiscoworkers []. CORINA adds missing hydrogens and calculates real 3D coordinates.After that any molecular parameters (even those that require 3D structures) canbe calculated. All this is done automatically without users interference.

b. 3D SDF files. These molecules can andwill be used without any restrictions. So, be careful specifying such format.You must be sure that there are no missing hydrogens and that 3D coordinatesare calculated (or measured) properly.

If the user provides molecules in the SMILES format andorders the parameters that require 3D structure, the 3D structure will becalculated by CORINA.

Clone Task button - creates a new task identical to the current one. The selected parameters and molecules are copie into the new task. This button alows to start the same task several times.

File desktop is used as storage of uploaded files in applet mode. The files uploaded by File/Load command at Molecules page of Task Wizard are received and stored here. Later they can be selected by File/Select File command. This method allows the user to use the same uploaded molecules several times (for several tasks).

Parameter Client Help