- 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.
|
Figure 2: Screenshot of WODCA's graphical user
interface
- 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:
|
|
- 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.
|
|
- 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.
|
|
- 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 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).
- 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
- 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?
-
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. |
|
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. |
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. |
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. |
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. |
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. |
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.
-
-
|
|
- 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.
- 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.
|
|
- 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 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 is located below the WODCA console
(Figure 2). It is used to inform the
user about the action which is presently performed.
- Last change: 2000-07-03
-
Webmaster: matthias.pfoertner@chemie.uni-erlangen.de