Plexus Connect

New Features and Improvements

• The "Charting" business flag, which could be used to switch on and off the connection to Plexus Analysis has been renamed as "Plexus Analysis".

Bugfixes

• 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

New Features and Improvements

• 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.

Bugfixes

• 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.

Plexus Analysis

New Features and Improvements

• Rectangular areas can be selected in scatter plots with Shift+drag.

Plexus Connect

New Features and Improvements

• Users with data editing rights can insert new records into their Plexus Connect grid views to add new data to their database.

Bugfixes

• 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.

Plexus Analysis

• The first official release of Plexus Analysis

Please note that the release of Plexus Suite version 16.5.9 was skipped.

New Features and Improvements

• Plexus Connect grid views can be used to send data into Plexus Analysis and to initiate histogram generation in Analysis by using the Create histogram context menu item in the header of numerical columns.

Bugfixes

• 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.

Bugfixes

• 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.

Please note that the release of Plexus Suite version 16.4.18 was skipped.

Bugfixes

• Copy-pasting a list into the text box of the "in list"/"not in list" operators did not work in Internet Explorer.

Bugfixes

• 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.

Bugfixes

• Enumerated tables could not be exported into .xlsx file format.

Bugfixes

• When a list was loaded in a grid view, the number of rows rendered in the grid view did not match number of records saved in the selected list: depending on the row number in the previous state, there were either empty rows at the bottom of the grid or some records of the loaded list were not visible.

New Features and Improvements

• Buttons on the Lists panel (New List, Load List, logical list operations) will always remain in the visible part of the panel, so users do not have to scroll down to perform actions on their lists even when they have many of them.

Bugfixes

• 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 Features and Improvements

• For text and integer fields, the default search operator has become "equals" in Plexus Connect.

Bugfixes

• The Compliance Checker widget did not work on the Property Viewer page.

Please note that the release of Plexus Suite version 16.2.22 was skipped.

New Features and Improvements

• 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.

Bugfixes

• 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.

New Features and Improvements

• Users with administrator rights can download the server- and client side log files from the System tab of the Admin Tools dialog window available under the "User" menu.

Bugfixes

• Clicking on the name of an inactive database view opened the name editor right after the first click. From this version the name of a view can be edited only when the view is already active.

Bugfixes

• Saved queries and lists could not be deleted by using a keyboard shortcut.

New Features and Improvements

• Chemical structures in grid views and in the table widgets of form views can be edited.

Bugfixes

• 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.

Bugfixes

• Clicking on the Search and Stop Search buttons while a search was running was not handled properly.

New Features and Improvements

• 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.

New Features and Improvements:

• The default behavior of authentication when multiple schemas are registered has been modified to authenticate against only one schema. To change this behavior and authenticate against every registered schema, the recently introduced 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.

Bugfixes

• 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.

Known issue:

• Exporting from Plexus Connect into a Microsoft Excel file is very slow when structures are exported as images.

Bugfixes

• When initial data retrieval was turned off, loading a list in a grid view did not work properly and threw an error.

Known issue:

• Exporting from Plexus Connect into a Microsoft Excel file is very slow when structures are exported as images.

Known issue:

• Exporting from Plexus Connect into a Microsoft Excel file is very slow when structures are exported as images.

New Features and Improvements

• The default configuration directory of Plexus Suite has become $HOME/.chemaxon/plexus-suite/ (in UNIX systems) or %USERPROFILE%\chemaxon\plexus-suite\ (in Windows systems). Documentation

Bugfixes

• 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.

Known issue:

• Exporting from Plexus Connect into a Microsoft Excel file is very slow when structures are exported as images.

New Features and Improvements

• 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.

Bugfixes

• The firt login to Plexus Connect takes less time because the schemas specified in the .ijs files are initialized already during the Plexus server's start-up.

New Features and Improvements

• 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.

Bugfixes

• 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.

Bugfixes

• 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.

New Features and Improvements

• 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.

New Features and Improvements

• 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.

Bugfixes

• The scrollbar was missing from saved list panel of Plexus Connect.

New Features and Improvements

• 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.

Bugfixes

• The "in list" search operator of Plexus Connect did not automatically add commas between the items of a pasted list.

Please note that the release of Plexus Suite version 15.9.21 and 15.9.28 were skipped.

New Features and Improvements

• When the user edits data in a table cell, a redesigned tooltip and a red frame indicates if the data type does not match the column type or if a required value is missing from a cell.

New Features and Improvements

• 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.

New Features and Improvements

• Users can navigate among records with the UP and DOWN arrow keys on form views as well.

New Features and Improvements

• Users are logged out from Plexus Suite after a pre-defined period of inactivity. The time period is configurable (see the plexus.sessionExpirationTimeSec property in the CB/ws/ijc-ws-app/src/main/resources/nps.properties file) and the default value is one hour.

Bugfixes

• While processing an enumeration in Plexus Design, the new table got a randomly generated name, and the default name did not appear until the enumeration was ready.

Known issue

• While processing an enumeration in Plexus Design, the new table gets a randomly generated name, and the default name will not appear until the enumeration is ready.

Bugfixes

• Histogram widgets on forms appeared without any data.

• Scatter plots on an initially inactive tab of a tabbed pane widget were too small.

Known issue

• While processing an enumeration in Plexus Design, the new table gets a randomly generated name, and the default name will not appear until the enumeration is ready.

Bugfixes

• 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.

Bugfixes

• Scripts could not be attached to individual table cells.

Known issues

• Record navigation over charts throws an exception.

Please note that the release of Plexus Suite version 15.7.6 was skipped.

Bugfixes

• Context menu was missing from some widgets when initial data loading had been turned off.

New Features and Improvements

• 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.

• Full type enumeration has been renamed to Sequential.

Bugfixes

• When the user tried to access a Plexus workspace with a URL which had already become invalid (due to server restart, for instance), an error message appeared and it was not possible to open any other database view inside Plexus.

New Features and Improvements

• 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.

Bugfixes

• 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.

Bugfixes

• 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.

New Features and Improvements

• Similarity search has been introduced into Plexus Suite

Bugfixes

• Excel export did not work correctly for enumerated tables.

• Plexus Suite tried to authenticate the same user multiple times against the same authentication provider.

Bugfixes

• 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.

New Features and Improvements

• Reaction Enumeration has been introduced into Plexus Suite.

• Advanced search parameters have been introduced for the substructure and full structure search types.

Bugfixes

• 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.

New Features and Improvements

• 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.

Bugfixes

• 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.

New Featues and Improvements

• The latest settings used in a scaffold enumeration are saved for each user.

Bugfixes

• 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.

New Features and Improvements

• The order of buttons on the action bar (the toolbar on the left side of the application) has been made consistent.

Improvements

• 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.

Bugfixes

• 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.

Bugfixes

• 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.

Bugfixes

• During file import in Plexus Suite, binary database field was created for strings which were longer than 512. From this version, longer strings are supported as well, and it depends on the specific database maximal VARCHAR length if VARCHAR or CLOB database field will be created.

New Features and Improvements

• 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.

New Features and Improvements

• 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.

New Features and Improvements

• 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.

New Features and Improvements

• 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.

New Features and Improvements

• 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.

Bugfixes

• LDAP group -> Instant JChem roles assignment works despite Unprocessed Continuation Reference(s).

New Features and Improvements

• 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).

Bugfixes

• 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.

New Features and Improvements

• Helper text has been added to the export panel to indicate which fields will be added to the exported file.

Bugfixes

• 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.

New Features and Improvements

• 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.

Bugfixes

• Structure file formats, such as *.mrv or *.sdf, were not available for export at those forms where the structure field was not part of the root entity of the data tree.

New Features and Improvements

• 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.

New Features and Improvements

• 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.

New Features and Improvements

• 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.

Bugfixes

• On a Tomcat application server, due to the long polling request the session expired before the session timeout and before the login dialog was displayed on the client side.

New Features and Improvements

• First public release