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The Graphical User Interface

WODCA's Main Window

WODCA's main window appears after calling the start script wodca.sh from a UNIX shell. The WODCA main window consists of certain window elements. The following scheme shows the arrangement of each window element, e.g., the menu bar, the information area, the structure display, the WODCA console, and the message line. An assignment of each window element to its name is given in Figure 1.

Figure 1: Arrangement of the window elements in WODCA's main window

Figure 2 shows the entire graphical user interface of WODCA at the beginning of a synthesis planning process. A target compound - shown in the structure display area - has already been loaded into WODCA. The information area indicates that the Fluka catalog comprising 16,769 chemical compounds has been loaded (Catalog icon) and that the similarity search "Ring Substitution Positions" (WODCA console) has been applied to the target compound and five potential starting materials have been found (Match List icon). Additionally, the name and the molecular weight of the target compound are displayed. The console gives additional output about the hits found in the similarity search such as the names of the compounds and the message line displays an informative text during a similarity search.
Info

If you are currently reading the online manual of WODCA you can use the hyperlinks on the picture in Figure 2. Just click with the left mouse button on a window element of your interest and follow the link to obtain directly an explanation. Use the back button of your WWW browser to get back to this place.

The disconnection menuThe target information displayThe message lineThe display menuThe name of the similarity search appliedThe WODCA consoleThe synthesis iconThe match list iconThe catalog iconThe structure displayThe help menuThe tools menuThe options menuThe evaluation menuThe searches menuThe export menuThe file menuThe information areaThe menu barWODCA main window

Figure 2: Screenshot of WODCA's graphical user interface

WODCA's Menu Bar

The menu bar is located in the upper line of the main window. It contains nine menu entries.


File menu

The File menu contains read and write commands for chemical compounds and match lists. Furthermore, it enables access to different catalogs of chemicals.
Description of the File menu

The File menu contains a Load command, a Save command, and a history function for the last five chemical compounds which were loaded or saved. The last option in the File menu is the Exit command. It is used to terminate WODCA.
The File menu is used to load a molecule, a catalog of chemicals, or a match list. After clicking with the left mouse button on the Load entry a cascaded menu with the following three entries Molecule..., Catalog..., and Match List... appears:

How to Load a Chemical Compound into WODCA

To load a molecule either choose Molecule... from the cascaded File menu or use the context menu in WODCA's Structure Display. A new dialog box for navigation to the directory of your choice appears (see Figure 3).

Figure 3: Dialog box to load a molecule into WODCA

The left side of the window in Figure 3 shows a listbox of Directories with all the subdirectories within WODCA's working directory. If you want to navigate to a parent directory, double click on the two dots »..« in the Directories listbox. To open a directory, double click on the corresponding directory name in the Directories listbox. The contents of an directory is shown in a listbox of Files on the right side of the window. Select a suitable molecule file from the Files listbox and click on the OK button with the left mouse button.
Info

If you had already read the selected molecule file previously, a new window appears to determine which structure from the CTX data file should be loaded. In this case, click on the First button.

How to Load a Catalog of Chemical Compounds into WODCA

To load a catalog of chemicals, either choose Catalog... from the cascaded menu of the File menu or directly click with the left mouse button on the catalog icon in WODCA's Information Area. A new dialog box with the entire set of installed catalogs appears (Figure 4). Select a catalog of your choice and press the Load button. The catalog icon switches immediately to the new catalog selected.

Figure 4: Dialog box to load a catalog of chemicals into WODCA

Info

It is also possible to save a molecule which has already been loaded as a CTX file. To do that you have to click on the Save entry in the File menu. A cascaded menu with the following two entries Molecule... and Match List... appears. With Molecule... a single molecule can be saved, with Match List... an entire match list.

How to Save a Chemical Compound in WODCA

To save a molecule choose Molecule... from the cascaded menu. A new window appears as shown in Figure 5. The same dialog box appears if you use the context menu in WODCA's structure display. Go to a directory of your choice and click into the Selection field. Enter a file name for the compound you want to save and press the OK button. It is recommended to add the file suffix .ctx to a molecule file name, e.g. compound.ctx.

Figure 5: Dialog box to save a molecule

Export menu

The Export menu manages the interaction between WODCA and the external programs of the CACTVS system. Some Export menu entries appear also in the context menu of WODCA's Structure Display and Strategic Bonds Window. The Export menu can be torn off to give a permanent window.
What Can be Done with the Export Menu?

The following tasks can be carried out with the Export menu:
  • Transfer of a molecule to the CACTVS editor to edit the chemical structure.

  • Transfer of a match list to the CACTVS browser to look at the structures found in a similarity search and to display some properties like catalog index number, CAS number, package information, or the purity of the compounds.

Searches menu

The Searches menu offers some key features of WODCA for the application in synthesis design: similarity searches and substructure searches in catalogs of chemicals. The Searches menu can be torn off to give a permanent window.
Description of the Searches menu


  • Identical Structure checks whether the query compound is contained in the loaded catalog of chemicals or not.
  • The Similar Compounds... entry is used to start a similarity search with a query structure to search for similar compounds in a catalog of chemicals. After clicking on this menu entry with the left mouse button a new window for the application of a similarity search is shown.
  • The menu field Other contains a cascaded menu with search methods like Name Search..., CAS Number Search..., (Gross) Formula search..., Atom Count Search..., and Index Range Search... .
  • The option Match List Operations in the Searches menu opens a cascaded menu.
    The first entry List Matches is used to output the match list to the WODCA console. The second entry Remove Dublicates removes duplicate structures from the match list.

Disconnection menu

The Disconnection menu provides important tools for the retrosynthetic analysis of a target compound. It allows the selection of a disconnection strategy and the evaluation of strategic bonds. The Disconnection menu can be torn off to give a permanent window.
Description of the Disconnection menu


  • A single click on the menu command Strategic Bonds ... opens a dialog box for the evaluation und disconnection of strategic bonds. The use of this dialog box is explained in the chapter Strategic Bonds.
  • The manual definition of strategic bonds can be performed in a dialog box which is opened by a single mouse click on the menu command Manual Definition ... .

Display menu

The Display menu is seldom used. One of the few uses is given when one wants to verify some WODCA proposals concerning the evaluation of strategic bonds or the calculation of physicochemical properties.
When Do I Need the Display Menu?

The Display menu controls the display of chemical structures in WODCA's Structure Display. It is used to configure the Display Mode. If the Display Mode is set to Atom Labels, WODCA shows no atom symbols but only atom labels. Atom labels are necessary for the manual definition of strategic bonds or for the evaluation of atom or bond properties. The following two formulea in Figure 6 show a target compound displayed with atom labels (left one) and with atom symbols (right one): The default value for the Display Mode is set to Atom Symbols.

Figure 6: A molecule displayed with Atom Labels and with Atom Symbols

Evaluation menu
The Evaluation menu is used to calculate physicochemical properties of atoms and bonds within the target compound. Furthermore, it enables the display of special bonds which are part of functional groups within the target compound. The calculation of physicochemical properties and the perception of functional groups are important methods used internally in the WODCA program for the proposal of strategic bonds and for the generation of suitable synthesis precursors. The Evaluation menu can be torn off to give a permanent window.
Info

Normally, WODCA executes physicochemical calculations in the background, e.g. during the rating of strategic bonds. But the Evaluation menu makes the result of these calculations more visible to the user. The results are displayed in WODCA's console (see Figure 7). During the evaluation of atom properties, bond properties, or functional groups WODCA's structure display is switched automatically to the display mode Atom Labels. The evaluation of match lists has not yet been implemented in WODCA.

Figure 7: Output given to the WODCA console after the analysis of the target compound shown in Figure 6. It is demonstrated the calculation of the »Difference in Pi-Electronegativity« for each bond on the aromatic ring system (1) and the perception of ether bonds (2).

Calculation of Physicochemical Properties for Atoms and Bonds in WODCA

The calculation of physicochemical properties is based on published empirical methods developed in the research group of Prof. Gasteiger. WODCA has implemented a subset of these descriptors completely contained in the program system PETRA.

Description of the Evaluation Submenus

Atom Properties

The entry Atom Properties in the Evaluation menu opens a cascaded menu for the selection of an atom property to be calculated. The atom property is calculated for the presently loaded compound shown in WODCA's structure display. Depending on the settings in the Options menu the calculation is performed for all atoms, all atoms without hydrogen, all atoms without carbon, or all carbon and hydrogen atoms.
The meaning of the abbreviations is given in the following:
A_ENPI: -electronegativity of the atoms
A_ENSIG: -electronegativity of the atoms
A_QPI: -charge on the atoms
A_QSIG: -charge on the atoms
A_QTOT: total charge on the atoms
A_POLARIZ: effective atom polarizability
The output is sent directly to the WODCA console. In case of selecting the entry All Atom Properties it is possible to write the output to a text file into WODCA's working directory. The file name is derived automatically from the name of the compound. If the compound is not named, the file allAtProp.noname is created.



Bond Properties

The option Bond Properties in the Evaluation menu opens a cascaded menu for the selection of a bond property to be calculated. The bond property is calculated for the compound actually loaded shown in WODCA's structure display. Depending on the settings in the Options menu the calculation is performed for all bonds, all bonds except CH, or only bonds directly leading to an aromatic system (alpha aromatic bonds).
The meaning of the abbreviations is given in the following:
B_DENPI: difference in -electronegativity
B_DENSIG: difference in -electronegativity
B_DQPI: difference in -charge
B_DQSIG: difference in -charge
B_DQTOT: difference in total charge
B_POLARIZ: average effective atom polarizability
B_SQIT: sum of -charges shifted across a bond in all iterations
B_SDELOC: delocalization stabilization of both a negative and a positive charge
B_PDELOC: delocalization stabilization of a positive charge
B_NDELOC: delocalization stabilization of a negative charge
I-EFFECT: derived quantity for the I-effect of substituents on benzene rings
M-EFFECT: derived quantity for the M-effect of substituents on benzene rings
The output is sent directly to the WODCA console. In case of selecting the entry All Bond Properties it is possible to write the output to a text file into WODCA's working directory. The file name is derived automatically from the name of the compound. If the compound is not named, the file allBdProp.noname is created.



Functional Groups

The option Functional Groups in the Evaluation menu opens a cascaded menu for the selection of a functional group to be perceived. The list of functional groups perceived by WODCA is not yet complete and will be extended gradually. The output is sent directly to the WODCA console.

Options menu

The Options menu is used as a control center for some global WODCA settings. It is divided into seven parts. The meaning of each part is described in the following. The Options menu can be torn off to give a permanent window.
Which Settings Can Be Controlled with the Options Menu?


  • Atom Calculation Mode

The Atom Calculation Mode allows one to determine for which atoms physicochemical properties are to be calculated. For example, if you are not interested in physicochemical properties of hydrogen atoms you should activate the switch No H Atoms. This saves computation time and makes the output in the WODCA console more readable.

  • Bond Calculation Mode

The Bond Calculation Mode allows one to determine for which bonds physicochemical properties are to be calculated. Thus, if you are only interested in physicochemical properties of bonds to aromatic ring systems you should select the switch Alpha Aromatic Bonds.

  • Property Output Mode

With this switch one can choose whether the results of a calculation should be written to a file in WODCA's working directory or should be displayed in the WODCA console. In the former case the file name is derived automatically from the name of the compound, e.g. allBdProp.name_of_compound or allAtProp.name_of_compound. The file format is ASCII. Thus, it can be viewed with any text processor.

  • FGI Mode

The FGI Mode controls if a functional group interchange is restricted to functional groups on an aromatic ring system or to functional groups in the entire molecule.

  • Export Mode

If you have performed a similarity search within WODCA and you transfer the match list to the CACTVS match list browser this switch controls if the contents of the CACTVS match list browser will be overwritten or the match list will be appended to the former contents.

  • Operation Mode

The Operation Mode of WODCA can be set either to Expert or or to Novice. In Novice mode WODCA displays a help panel if a similarity search with the similarity criterion substitution pattern is selected. The help panel is shown in Figure 8, (1). Furthermore, some WODCA windows (e.g. the dialog box for the manual definition of strategic bonds (2) or the window for the modification of precursors (3)) contain additional information if the system is running in Novice mode (see Figure 8, red boxes). Another feature of the Novice mode is that WODCA automatically finishes all external programs of the CACTVS system if a WODCA session is terminated by the user.

  • Similarity Searches

The switch Only Unique Matches in the Options menu influences the result of a similarity search. The catalogs of chemicals often contain the same compound in different qualities. For example, the Fluka catalog contains eleven different entries for acetone in different purities and isotopic substitution. If Only Unique Matches is activated, WODCA neglects the purity of a compound during a search and shows only one representative instead of all entries of a compound in a match list.

Figure 8: Effects of WODCA's novice mode on some dialog boxes: Dialog box (1) is only visible in Novice mode. Additional information is displayed in dialog box (2) and (3).

Tools menu
The Tools menu provides a convenient way to start programs from the CACTVS system
Info

The Tools menu is used to start the external CACTVS programs which are necessary for use within WODCA , e.g. the molecule editor, the match list browser, the synthesis planner, or the tool for substructure searches. The Tools menu can be torn off to give a permanent window.
The Configure ... option opens a dialog box where the names of the start scripts of the CACTVS programs have to be entered. If the paths to the CACTVS programs are not set in the user environment (see Adaptation of WODCA) the absolute paths of the start scripts have to be given in this dialog box.

Help menu
If you need some help, you will probably find it here.
Info

The Context-Sensitive Help is not implemented yet. The Online Help starts Netscape Navigator and automatically loads the WODCA Home Page with the online manual. The About... entry shows a message box with some product information.

Information Area and Structure Display

Two adjacent window areas with different tasks are below the menu bar (see also Figure 2). The left one is called the information area. The right one displays the chemical structure of the query and is called the structure display.

WODCA's Information Area

The information area is divided into an upper icon bar and a lower information bar.
Description of the Icon Bar

The icon bar contains three icons for information purposes and for a fast access to different functions of the WODCA system.
  • The Catalog icon indicates whether a catalog of chemicals is loaded into WODCA or not (see also Figure 2). It gives the name of the catalog and shows the total number of compounds in the catalog (e.g. the FLUKA catalog presently contains 16769 compounds). A single mouse click with the left mouse button on the Catalog icon opens a dialog box for the selection of a catalog of chemicals.

  • The Match List icon indicates the number of hits received from a similarity search applied to a query structure (here: 1). Additionally, it gives the name of the similarity search (e.g. Largest Molecule).
    To view a match list click with the left mouse button on the Match List icon.
    Alternatively, the match list can be exported to the CACTVS Structure Browser via the Export menu. Whether the contents of the CACTVS Structure Browser will be overwritten or not depends on the setting of the switch Export Mode in WODCA's Options menu.
  • The Synthesis icon displays the status of the synthesis tree. It indicates whether the external CACTVS Synthesis Planner is running or not. Additionally, the number of synthesis level is displayed.
Description of the Information Panel

The lower information panel displays the name of the target compound and its molecular weight.
The molecular weight is automatically calculated during the loading of a chemical compound.
The chemical name has to be entered by the context menu in WODCA's structure display.

WODCA's Structure Display

Each chemical compound loaded into WODCA is shown in WODCA's structure display. The molecule can be a target structure for a synthesis planning study, a precursor derived from a target structure, or a starting material for the beginning of a synthesis.
It is possible to import a chemical structure from the CACTVS Molecule Editor into WODCA by using the editor's File menu and selecting the Export command.
The Context Menu of the Structure Display

The structure display contains a context menu. The context menu appears as long as the right mouse button is pressed.
  • Define New Target ... starts the external molecule editor from the CACTVS system.
  • Load Target ... corresponds to the command Load Molecule from the File menu.
  • Edit Target ... starts the external molecule editor with the target compound currently loaded.
  • Save Target ... corresponds to the command Save Molecule from the File menu.
  • Enter Name ... opens a dialog box to define the name of the current compound.
  • Start New Synthesis Plan ... starts the external synthesis planner with the present target compound displayed on top of the synthesis tree.
  • Recalculate 2D-Coordinates is useful only in some cases: Sometimes the structure display shows bad coordinates for the current compound. After clicking on this menu entry, WODCA recalculates the 2D-coordinates of the current ensemble and displays the structure with better coordinates.
  • Refresh Structure Display is seldom used: If the WODCA main window is resized or the name of a compound is edited, WODCA automatically refreshes the structure display. It is possible to enforce the structure display update by this command.

The Console

The WODCA console is located in the bottom part of the main window (see Figure 2 and Figure 7). It is a scrollable region to provide the user with additional information about the results of a similarity search, the evaluation of strategic bonds, the calculation of physicochemical properties, or the perception of functional groups. The console can also be used for manual intervention.

The Message Line

The message line is located below the WODCA console (Figure 2). It is used to inform the user about the action which is presently performed.

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Last change: 2000-07-03
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