{warning} If you are using JChem Oracle Cartridge, please take note, that JOC will not work with OJVM_UPDATE_171018 (2017 Oct) Oracle DB patch. For more details see here. JChem team is trying to find a workaround.
The nps.properties configuration file is automatically created during application start in the working directory. (PC-1086)
Export to PDF has been fixed. When WebBrowserWidget is in the Form view, the PDF export of the form no longer crashes. (PC-1016)
Locale language settings support and input values validators have been implemented. (PC-954)
Spontaneous disappearance of the Lists and Saved queries from the Left Panel has been fixed for IE 11. (PC-821)
New Charts integration has been introduced.
Charts does work in IE 11, however card view functionality is missing.
Fixed displaying markush structure hits (PC-773)
Connect now supports modifying multiple.schemas.auth with java option. (PC-888)
Plexus Connect respects absolute label for structure settings (PC-867)
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Binary fields (pictures) are displayed by Plexus Connect. (PC-548)
Plexus Connect now exports binary fields (images) in Excel export. (NPS-7543)
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Data displayed in both Connect grid and form view can be visualized using a new integrated component called Chart views. Please visit our documentation for further information Charts view
{warning} Known issue: Charts integration does not work in IE 11 (fixed since version 19.7.0)
Binary data, like images, are now possible to export. (NPS-7541)
Issues with JNLP file created by Plexus Connect has been fixed. (PC-442)
Fixed an issue when views were not synchronised after sorting on a child entity field (PC-524)
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{info} JCHEMPROPERTIES table upgrade is triggered on Oracle for both JChem Base and JChem Oracle Cartridge. If ORA-01502 appears, then perform rebuild of the system index of the JCHEMPROPERTIES table - alter index SYSxxxxxx rebuild; SYSxxxxxx will be name of the index found in the error message.
Bug in Plexus Connect version dialog has been fixed. (PC-332)
Added a possibility to clean up untitled enumerations stored in the schema, via Plexus' Admin Tools (PC-53)
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{info} JCHEMPROPERTIES table upgrade is triggered on Oracle for both JChem Base and JChem Oracle Cartridge. If ORA-01502 appears, then perform rebuild of the system index of the JCHEMPROPERTIES table - alter index SYSxxxxxx rebuild; SYSxxxxxx will be name of the index found in the error message.
Possibility to download logs through the admin panel has been restored. (PC-207)
Issue where sorting was not consistent with structure related queries has been fixed. (PC-204)
The .tab file format was replaced by .txt file format in export actions. (PC-189)
Support for encoding requiring UTF characters, i.e. in Japanese has been properly restored. (PC-195)
Possibilities of customizable area in Plexus Connect has been improved. New possibilities such as resizing, possibility to change background colours or possibility to insert pictures and links has been introduced. (PC-155)
Decimal part of the similarity search threshold is now visible. (PC-203)
Fixed possibility of change column width, while column reorder is on (PC-196)
Fronted shouldn't freeze anymore during record-to-record navigation (NPS-7470)
Customizable area on Dashboard allows admins to create space on dashboard with adjustable content like comments, short descriptions, warnings, references, links and etc. (PC-155)
Improvement in diagnosis of wrongly configured .ijs file. From now on, if the schema initialization fails because of missed information about database URL, than following error will appear:
Database URL must be provided.
{warning} Connection pooling library was upgraded. As a result, two properties in .ijs configuration file were replaced:
" custom.connection.pool.maxActive " is replaced with (renamed to) " custom.connection.pool.maxTotal " - meaning of the property and the value remains the same
" custom.connection.pool.whenExhaustedAction " is replaced with " custom.connection.pool.blockWhenExhausted " - meaning of the property is changed in accordance with the meaning in the upgraded library. If you are using this property please consult the library manual. (old version: [https://commons.apache.org/proper/commons-pool/api-1.6/org/apache/commons/pool/impl/GenericObjectPool.html#getWhenExhaustedAction(),](https://commons.apache.org/proper/commons-pool/api-1.6/org/apache/commons/pool/impl/GenericObjectPool.html#getWhenExhaustedAction(),) new version: https://commons.apache.org/proper/commons-pool/apidocs/org/apache/commons/pool2/impl/BaseGenericObjectPool.html#getBlockWhenExhausted--))
In a case where a configuration file will contain an old property, a user will be notified via an error message.
ERROR: Connecting to database failed: Your configuration file contains deprecated property specification
custom.connection.pool.maxActive/custom.connection.pool.whenExhaustedAction.
Please visit [Editing Schema Connection Settings](editing-schema-connection-settings.md) for further information how to fix the problem
{warning} Known issue: It is not possible to download logs through the admin panel (PC-207)
{info} JCHEMPROPERTIES table upgrade is triggered on Oracle for both JChem Base and JChem Oracle Cartridge. If ORA-01502 appears, then perform rebuild of the system index of the JCHEMPROPERTIES table - alter index SYSxxxxxx rebuild; SYSxxxxxx will be name of the index found in the error message.
Records are correctly synchronized after searching substructures (NPS-4394)
Fixed a problem with "Return to enumeration" functionality (PC-188)
{warning} Known issue: Firefox is unable to read response from image url. Structures do not load or display in Firefox at all. (PC-181)
Known issue: Japanese characters are not properly displayed. (PC-195)
{info} JCHEMPROPERTIES table upgrade is triggered on Oracle for both JChem Base and JChem Oracle Cartridge. If ORA-01502 appears, then perform rebuild of the system index of the JCHEMPROPERTIES table - alter index SYSxxxxxx rebuild; SYSxxxxxx will be name of the index found in the error message.
No changes.
{warning} Known issue: Firefox is unable to read response from image url. Structures do not load or display in Firefox at all. (PC-181)
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Added ability to insert new row in Grid View, even when there was previously no data in it (PC-66)
Less complex type of TableWidget in Plexus Suite Connect, which increase speed of rendering, but there are missing functionalities like rendering structures, changing size of columns or other advanced features. It also loads max. 30 records. Could be turn on in IJC's TableWidget settings. (NPS-6598) See the documentation here.
Now we are able to remove selected rows from enumerations in PS (PC-140)
Fixed issue - Plexus Connect was not able to load Pivot entity data. (PC-135)
Plexus now reflects frozen column functionality from IJC. IJC allows to define number of frozen columns which will not be moved when horizontal scrolling is used. (NPS-6918)
Plexus Connect 17.23.0 can now be deployed via Tomcat as before.
{warning} Known issue: Plexus Connect 17.22.0 will not successfully start when deployed via Tomcat. Embedded Jetty deployment has to be used instead.
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{warning} Minor known issue: Selection is not properly synchronised between forms, when a row is selected for new Delete Row functionality. (PC-65)
Added a possibility to delete rows in grid views
Now, it is possible to modify schemas with IJC, without a need to restart Plexus Suite servlet container (documentation)
Printing option has been introduced. (documentation)
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An error message appeared when the download process was cancelled during file export.
While selecting multiple widgets, black rectangles appeared in the forms.
While creating or editing a list, the "active cell" highlight moved to an adjacent cell when the column of check boxes was added or removed from a grid view.
Dashboard and views are not loaded properly when using Firefox or Internet Explorer.
When a histogram was created from a "date" type column, the values on the histogram's X-axis were numbers instead of dates.
When exporting a data set which was originally imported from Plexus Connect, the name of the downloaded file was not correct.
When auto-saving and user authentication were turned on, date type values were exported as numbers.
When user authentication is enabled, analysis documents can be renamed by editing the name in the header of an open document.
Data can be exported from Plexus Analysis in MRV, SDF, SMILES or tab-separated text format. An option has been added to export only selected rows or columns.
The pick list functionality can be now used in Plexus Connect. Currently only the 'field's existing values' and 'constant list of values' can be used. Please see the Pick list documentation for Instant JChem for the details.
The ascending/descending badge indicating the order of sorting was not displayed in form and table views.
Cherry picking ( i.e. , manual list creation) did not work in table views
Cherry picking ( i.e. , manual list creation) does not work in table views.
The ascending/descending badge indicating the order of sorting is not displayed in form and table views.
When user authentication is enabled, analysis documents will be saved automatically on the server for each user. When there is no user authentication, the analysis documents will not be saved.
Saved analysis documents of each user are listed on the starting page of Plexus Analysis. The list becomes available after logging in to the application. A saved analysis can be opened by double-clicking on one of the list items.
A saved analysis can be deleted from the list of saved files on the starting page by using the right-click menu of one of the list items.
When running a query, you can specify the domain of your search. You can decide to search in the entire database, in the current record set or among the records of a specific saved list.
From this version, it is possible to use a simple properties based configuration file in a custom location. Documentation
The coloring and positioning of widget selection highlight has been improved.
Cherry picking ( i.e. , manual list creation) does not work in table views.
The ascending/descending badge indicating the order of sorting is not displayed in form and table views.
Columns in grid views for which initial data loading was disabled were initially not fit to the table width in Internet Explorer 11.
In certain cases, incorrect structure search options were displayed on the search panel.
Linear trend lines can be fitted to data points in scatter plots to check the relationship between the X and Y properties or to fit a predictive model to the observed data.
Four parameter logistic function can be fitted to data points in scatter plots to determine the parameters (IC50, EC50, Hill slope...) of dose-response data sets.
From this version, it is possible to use logarithmic scale on the X- and Y-axis of scatter plots besides the standard linear scale.
When a chart becomes very small, axes, axis labels and grid lines are not displayed, so that data symbols (scatter plot points and histogram bars) can take up more space.
In smaller scatter plots where the legend would not fit in the available space on the right side of the chart, a "Legend" icon is displayed in the upper right corner of the chart. Moving the mouse cursor over this icon will display the full legend. Please note that the legend display has to be turned on in the scatter plot's pop-up menu in order to see the icon and the legend.
Too narrow database view headers became unusable because their height did not increase when the header became overcrowded.
After a query, the header of single-column table widgets was also marked with filter icon although this marker should be placed only in the filtered column header.
In order to make saved queries editable, Plexus Connect can load the query definition to the Search panel. When a saved query is used for searching, its definition is automatically loaded to the Search panel.
Binary Large Object, i.e. , BLOB fields, and text fields with Oracle text index can be queried with Plexus Connect.
From this version, it is possible to modify the Plexus Storage destination. Please note that as a result, the following information will be lost when you update to this version:
Text alignment in grid views and table widgets did not respect the settings defined in Instant JChem. From this version, text in table cells and headers is aligned according to the Instant JChem setting.
When a saved list has been selected to enter "cherry-picking" mode, columns were not displayed in grid views in certain cases.
Certain display settings which were adjusted in Instant JChem (such as border settings and the font size of widget titles) were not respected in Plexus Connect.
When you start an analysis by importing data, a name will be generated for the new analysis either from the name of the source file or from the name of the Plexus Connect database view from which the data has been imported.
The default cell size has been enlarged in structure columns.
Similarly to histograms, panning is limited in scatter plots as well from this version, so that some points will always remain visible in a chart.
Exporting data from a form which contained a structure field from a child table with one-to-many relationship threw an error and gave an empty file.
When a query returned no hits, the record chooser disappeared from the header of the database view, and the notification that there was no item to display was missing as well.
Plexus Analysis
New Features and Improvements
In histograms, bins can be selected by a left-click. Multiple bins can be selected by CTRL+click or SHIFT+click
The selection in a histogram is synchronized with the selection in the data sheet and in other charts.
Hovering over a histogram bin will highlight the bin and an information box will appear providing details about the current bin, like the total number of items and the number of selected items in the bin. The information box can be made hidden by the "Hide information box" context menu item.
Histograms can be zoomed and scaled as well as panned by rolling the mouse wheel and dragging the histogram, respectively. The original histogram can be reset from the context menu.
When the last search did not find any hit, saved lists did not load in form views.
"The query returned no hits" message was still displayed on the search panel while a new query was already running or when a saved list has been loaded.
In Internet Explorer, the vertical scroll bar was missing from the Lists panel when there were multiple saved lists on it.
Plexus Connect form and grid views and their data (current query/record set, sort order and active record) can be shared among users by generating URLs for the given form or grid.
From this version it is possible to gather information from the log files about each user logged into Plexus Suite.
IJC/Plexus can optionally use a shared pool of connections to a database for all IJC schemas that it opens from the same database schema.
After losing server connection and than reconnecting to the server again, the "Re-connected to the server" notification did not disappear and there was no way to close it either except by reloading the page.
Selecting a column containing images in a grid view threw several error messages and the application became frozen.
Using the "Any of" query operator on a child entity field during search failed and threw an error.
When either the "Last 7 days" or the "Last 14 days" search operator had been selected for searching in a date type field, and then the search operator was switched to "On", the text box of the search condition was filled with an incorrect value. From this version, switching to the "On" operator will open an empty value text box.
The "Fit to screen" option did not work in the case of the table widgets in Plexus Connect.
The vertical scroll bar was missing from the search panel when there were multiple search conditions on it.
Removing a search condition from the search panel changed the operator of other existing conditions.
During export in Plexus Connect, an error message was thrown when a structure field where the MIME type has not been set was bound to a text field or to a text column of a table. From this version Plexus Connect will export the value such fields as text.
Admin users could not download the Plexus Connect backend and frontend log files through the Plexus Connect GUI (from the System tab of Admin Tools dialog ( User account > Admin tools > System ).
At similarity search, the value in the similarity threshold text box was not displayed properly.
The "DefaultSortProperty", used for setting the default sort order in tables, was not taken into account in Plexus Connect.
Plexus Connect did not take in account the row height of a sheet widget cell set in Instant JChem, so longer texts were only partially visible.
Label widgets with an URL did not work.
In Plexus Connect, the "showTableheader" property did not work for the table widgets.
Plexus Connect did not take in account settings for table header heights.
Building blocks from the predefined collection could not be selected to be used either in scaffold-based or in reaction-based enumerations.
Plexus Connect stopped authenticating a user if he/she had no roles defined in a particular Instant JChem schema. From this version, Plexus keeps authenticating users to all schemas even if they do not have roles in some of those schemas. The user is then logged in to only those schemas where he/she has at least some roles.
New lists can be created and already existing lists can be edited manually using the form views as well.
A new business flag, "ADD_CALCULATED_COLUMN" has been created in Plexus Suite. In order to have the calculated column insertion feature available, this business flag has to be set to "true".
Please note that this feature requires a valid Plexus Design license regardless of the state of the ADD_CALCULATED_COLUMN buisiness flag.
Long text was not wrapped in grid cells.
Plexus Connect could not use multiple structure fields for searching even when there were more than one available in the given form.
The list of favorite views on the Plexus Connect dashboard contained those database views as well which had already been removed from the favorites.
Loading the dashboard with a large amount of grid and form views could take a long time.
The "calendar" button was missing from the date type search conditions on the search panel.
The blue line indicating synchornized database views was visible even when only one view was open or when the active form or grid was the only open view from a datatree.
In order to speed up file export into Microsoft Excel with chemical structures as images, image rendering is performed in multiple threads from this version.
New query conditions cannot be added by right-clicking on a field when the search panel is closed.
multiple.schemas.auth
property has to be set to true
. Please note that from this version the old property, ijc.single.auth
is not supported anymore.
Font sizes of text box widgets on forms did not adjust to the size of the widget.
In order to make file export smoother, starting the file download does not have to wait for the data export to finish.
The users did not get any feedback when sorting failed on the server-side due to a database issue.
The result of sorting of a large filtered data set was not correct.
$HOME/.chemaxon/plexus-suite/
(in UNIX systems) or %USERPROFILE%\chemaxon\plexus-suite\
(in Windows systems). Documentation
Synchronization of database views did not work when saved queries or saved lists were used.
The sorting state of database views were not synchronized when a form had been sorted by a master and detail table field, too.
When synchronized forms were open, the active record in the record navigator was not updated after the forms ahd been filtered.
The administrator can customize the landing page content from the Admin Tools > Dashboard Configuration dialog.
Permission for data editing in grid views and table widgets is controlled by the ROLE_EDIT_DATA user role.
The landing page of Plexus Connect has been imrpoved.
After logging in to Plexus Connect, the user can browse, search and open his or her form and grid views on the landing page.
The scaffold based and reaction based enumeration tools are available by using their respective button on the landing page.
The Plexus button in the upper left corner of the Plexus Connect application can be used to navigate back to the landing page.
When initial data loading was turned off for a schema, Plexus Connect used an empty search conditiion at the first search after opening a form.
Deleting a selected list did not remove the Load List button from the Lists panel.
Column headers had extra top and left borders in tab pane widgets.
Closing a database view while the data in it was still loading threw an error.
The checkboxes used for manual list editing appeared in grid views even when the selected list was not editable by the current user, i.e. , when the user was not the owner of that list.
Deleting a selected list did not remove the checkboxes from the active grid view.
You can calculate physico-chemical properties for an entire table of molecules. These properties are added as new columns to grid views owned by you.
Saved lists has been moved to a separate left-side panel in Plexus Connect.
On the Lists panel, new lists can be created from grid views by manually adding records to the list.
The content of a list can be modified in a grid view by manually adding and removing items to/from it.
When you log in to Plexus Suite, you will be navigated to a dashboard, where you can browse, search and open database views available for you.
Database views can be marked as "favourites" or removed from favourites by using the context menu when a view has been opened.
Lists of recently viewed and favourite views have been added to the dashboard. Both of these lists can be searched and used for opening a view.
New lists can be created with logical set operators - intersection, union, XOR and difference - by selecting two or more saved lists using the CTRL key.
Form and grid views belonging to the same data tree are synchornized by default, i.e. , they have the same record set as well as the same active record, and they are sorted in the same way.
The default synchronization of form and grid views can be turned off.
Relational data from a child table can be exported as well even when a one-to-many relationship is employed. The data from the parent table will be duplicted if fields are selected both from the parent and the child table.
The Property Viewer page, which summarizes the phyisico-chemical properties of single molecules, has been redesigned.
Widgets can be added to or removed from the Property Viewer page.
Chemical structures on the Property Viewer page can be enlarged by clicking on them.
{info} From version 15.8.3, Java 8 has become the officially supported Java version for Plexus Suite. From this point, previous Java versions (Java 6 and 7) are not supported anymore.
Histogram widgets on forms appeared without any data.
Scatter plots on an initially inactive tab of a tabbed pane widget were too small.
Navigating among the records in a form which contains charts threw an exception.
Fixed flushing of data load streams into individual widgets happening too often, which previously slowed down record-to-record navigation on widget-rich forms.
While a long running query is being executed, early search hits are returned as soon as they have been found, so the user can start browsing in the results set faster and does not have to wait until the search gets finished.
Long running queries have become cancellable by pressing the Stop Search button on the search panel while the query is in progress.
User-defined reactions can be saved in the user's own reaction library. These reactions can be annotated, edited or removed from the library by their owner.
The Clear all option of scaffold and reaction based enumerations has been extended with a confirmation step in order to prevent accidental removal of the enumeration settings.
Dialogs and context menus were not closed when the user navigated away from a page or when he/she got logged out from Plexus Suite.
Conditional formatting was not visible in sheet widget cells.
Background color of label widgets did not fill the whole cell of the widget only the area behind the label text.
In Safari, the Marvin JS editor did not open in the search panel when the user wanted to modify a query structure or when he/she wanted to run a structure search for a second time.
{info} From version 15.6.22, Java 8 is going to be the officially supported Java version for Plexus Suite. From this point, previous Java versions (Java 6 and 7) will not be supported anymore.
Excel export did not work correctly for enumerated tables.
Plexus Suite tried to authenticate the same user multiple times against the same authentication provider.
When the Multi line text renderer setting was used on a table column, conditional formatting was not visible in the cells of the column.
Errors were thrown when the active view had been closed and then the user tried to select new fields while the search panel was open.
Reaction Enumeration has been introduced into Plexus Suite.
Advanced search parameters have been introduced for the substructure and full structure search types.
When a query did not give any hits, the data did not disappear from grid views and table widgets.
The notification that the last query did not have any hits was missing from the search panel.
Plexus Suite did not work on Internet Explorer 11 due to browser incompatibility when "Compatibility mode for intranet" was switched on.
The "Sorted" icon disappeared from column headers when another database view was opened.
Plexus Suite threw error messages when a query without any hits ran on a form.
A new information panel was introduced that shows enumeration details for the scaffold based enumeration results.
A new icon is now available on the action bar that enables the users to get back to the scaffold based enumeration page from a generated virtual library and make some modifications in the settings.
Users were not able to log in to Plexus Suite when it was installed outside the root context under Tomcat.
The old name of a query or a list flashed briefly when it was changed.
When the user opened a database view more than once, the views were numbered only if they belonged to the current user.
The numbering of database views was wrong when the same view was opened more than once.
File import failed for several files.
The "Use in scaffold enumeration" function did not work for the first time when the user wanted to load a complete Markush library or a single scaffold molecule to the scaffold enumeration page.
The "Sort ascending" and "Sort descending" items were missing from the contextual menu of cells in a sheet widget.
Uploading files as R-group definitions in scaffold enumeration splits fragments into separate R-group structures.
Performance has been improved for tab pane widgets by not loading IDs and data for hidden widgets.
The application renders the content of each widget as soon as possible and does not wait until data has been loaded for every widget.
Data was missing from widgets on inactive tabs of forms.
Scaffold enumeration returned only one structure when the maximum number of structures was less than the estimated library size and the enumeration type was set to random.
When initial data loading was turned off for a schema, an exception was thrown when the user clicked on an empty structure widget.
Due to a security issue, users could log in to Plexus Suite even when they had no Instant JChem role assigned to them.
The performance of retrieving data for 1:N relationships has been improved.
The user can change the name of those database views (form or grid views) which are owned by him/her.
The list of text search operators has been modified and new operators have been introduced, such as does not contain , does not start with , does not end with .
Browser widget is supported in Plexus Suite.
The Import and Export buttons are now available under the Import-Export group button.
Minor improvements have been added to the search user interface.
Selected values and chemical structures can be added to new query conditions on the search panel in order to build complex queries more quickly and effectively.
Row height can be changed in grid views and in table widgets.
Chemical structures in the active widget or cell can be copied to the clipboard.
The performance of data retrieval has been improved for data trees with a many-to-one relationship where the source field is referring to a non-ID field.
A checking mechanism has been introduced to determine whether the current browser can support the proper running of Plexus Suite. If the criteria are not fulfilled, a notification is offered instead of the login dialog.
Text search has become case-insensitive in Plexus Suite.
The logging of eventual export issues has been improved.
Data loading has become more efficient in the case of Many-to-One relationships.
The user interface for running, editing and deleting saved queries and lists has been improved.
During file export, chemical file formats are offered only in those cases when the active form or table contains a structure field and either this structure field is part of the selection or there is no selection at all on the active database view. In every other case, only the non-chemical file formats can be used.
A user can connect in admin mode through the Instant JChem desktop application and he can make changes to the schema while the Plexus server is running.
The Building Blocks Collection is now available where well-defined lists of structures can be stored that are ready to be used in enumeration workflows.
Additional option for adding R-group definitions from the Building Blocks Collection (From collection).
Conditional formatting was not exported into Microsoft Excel ( * .xlsx ) files.
Multiline text was converted into single line text in a multiline text area widget.
Data from an "Any structures" type table could not be exported in .txt format.
The value text box of the "in list" and "not in list" search operators changed its size and sometimes disappeared completely.
In Internet Explorer and Firefox, the "calendar" button for opening the date picker was in the wrong position in text boxes and cells containing date type values.
Extra attributes belonging to R-group fragments are displayed in tables created by scaffold enumeration.
By default, the following business flags have become turned off: FILE_UPLOAD, COLUMN_REORDER, CELL_EDITING.
Data in tables and forms can be exported into a variety of file formats. It is possible to export every field from a table or a form, or select only certain fields for export.
Custom JavaScript files can be added to Plexus Suite to provide custom functionality for end users.
Date widget has become supported in Plexus Suite.
New query operators have been introduced to enable relative date search.
Saved lists have been introduced into Plexus Suite.
The "in list" and "not in list" query operators can be used to search for alphanumeric values which are members of a comma separated list.
Metadata is added to tables which were generated by scaffold enumeration.
Sheet widget is supported on form views designed in Instant JChem.
Alphanumeric values in table cells or in widgets can be copied to the clipboard with the CTRL+C keyboard shortcut.
In the hit list of a substructure search, the matching parts of the structures are highlighted by coloring, and the molecules are aligned to match the substructure query.
A notification tool has become available for users with administrator role, to send instant notifications to logged in users, or to write messages on the log-in dialog window.