Once MolDiA software is installed following the steps of the setup provided, execution of the software will
display the following Menu which contains the software main computation options.
To access the Wizard Beginners Tutorial, go to the menu
File |
Wizard.
The Welcome window (WINDOW W0) gives a brief description of the software goals and the molecular format required.
WINDOW W0
Then the WINDOW W1 is displayed. To effectuate the computation, it is possible to choose between two kind of analysis:
- The "S" analysis allows the comparison between molecules only in function of their 2D structure.
Structural descriptors will be constructed and the similarity computation will depend on the common substructures
between the molecule query and test.
- The "SP" analysis allows the comparison between molecules in function of the structure and the physicochemical
properties. The dual descriptors constructed will allow a more complex comparison between the molecules analyzed.
It is possible to choose only one option.
WINDOW W1
To personalize the analysis it is possible to use the
custom options. The structural and physicochemical
information belonging to the molecular descriptors contain inherent weights. The customization of the structural weights
is done by means of the WINDOW W2-1, in this window a list of meta-structures is proposed. It is posible to
ignore the structure setting the weight to zero, or to increase their contribution by setting the weight to two.
Default values are the same for all the structures and are automatically set to one. The customization of the
physicochemical property weights is done by means of the WINDOW W2-2. In this window a limited set of properties and
characteristics is proposed to be customized. The same procedure described before is applied to set the property weights.
For more details about the custom screens go to the
Advanced Features section of this tutorial.
WINDOW W2-1 and WINDOW W2-2
Once the kind of analysis is chosen and the structural and property weights modified (or not), we access to the
WINDOW W3 which gives the cardinality of the comparison.
Four posibilities are given:
- The 1-1 Analysis, which compute a similarity comparison between two molecules called "the query" and "the test".
- The 1-N Analysis, which compute a similarity comparison between one query molecule and a group of N test molecules.
- The N-N Analysis, where a diversity measure is computed between all the N molecules of a database (all the molecules
will act as the query structure alternately).
- The N-M Analysis, where a diversity measure is computed between all the N molecules of a query database and all
the M molecules of a test database.
WINDOW W3
Once the choice is done, we can upload the molecular files to be analyzed, as shown on WINDOW W4-1 and W4-2.
Only MOL files will be displayed. Pay attention to the number of query molecules, which could be restricted in
the 1-1 and 1-N analysis. The right and left arrows easy the copy of molecules from one window to another.
WINDOW W4-1 and WINDOW W4-2
The next step is the molecular analysis which can be run from WINDOW W5. On a first moment the tool extracts and
load the molecular informations of query and test molecules on the interface. Then comes the time-consuming step, which is the
construction of the descriptors for the computation of similarity or diversity between the molecules loaded.
Computation times, will depend of the number, size and complexity of the molecules to be analyzed.
WINDOW W5
When the computation is finished, the "See Results" button will appear and gives access to the WINDOW W6.
This window will allow the customization of the final computation and presentation of similarity or diversity indices.
Three diferent indices (Tanimoto, Sympson and Cosine) can be computed simultaneously or individually.
It is also possible to choose to show or not the descriptor vector of the analyzed molecules.
The final results will be presented in form of hyperlinks which will give access to the XML result files.
WINDOW W6
To open the XML result or descriptor-vector files, it is posible to use a text or XML editor. The XML files can be
also saved as TXT files or imported using Excel or other tool for posterior treatment and analysis (ranking,
plotting, statistics, etc). To visualize the content of the XML file it is enough to open the file in a web browser
(e.g. IE). The automatic visualization of the file is assured by the presence of a XSL file. This file is
automically copied to the results directory and allow the user to visualize the molecules and the informations
computed by MolDiA in a clear and easy way.
Some visualization requirements:
- To ensure the molecular visualization when loading the XML file on a web browser it is necesary to have the
MDL Chime plugin, as well as the
JMOL JAVA engine.
- To avoid "broken links" of the molecular information inside the result files is important to assure that
the molecules which have been part of the calculus will remain at their original localisation. The absence
of the molecular files can generate an error message of the MDL Chime plugin or JMOL applet in IE which will
avoid visualisation of the file.
A brief survey of some results files (WINDOW W7-2 and WINDOW W7-3) as well as descriptor-vector files (WINDOW W7-1),
visualized using Internet Explorer 7.0 is given below.
WINDOW W7-1, WINDOW W7-2 and WINDOW W7-3
