T71-2023 Notification regarding BIOVIA Pipeline Pilot 2024

Description

Areas Affected

Risk Level

Jira Issue ID

The Java run time environment included with Pipeline Pilot is upgraded to Temurin-11.0.20+8.

PPC: Server Infrastructure

Medium

PPC-11004

Apache is updated to version 2.4.57. Also, the httpd dependency apr is updated to version 1.7.3.

PPC: Server Infrastructure

Medium

PPC-11106

Python is updated to version 3.9.16.

PPC: Integration

Medium

PPC-11023

The Perl installation used for the Perl (on Server) component is updated to Perl 5.36.0. For more information, see https://www.perl.org/.

PPC: Integration

Medium

PPC-10944

The ODBC drivers for Oracle, SQLServer, and MySQL are updated: Oracle is 8.00.02.2713, SQL Server is 8.00.02.1196, and MySQL is 8.00.02.218.

PPP: Server Infrastructure, PPP: Integration

Medium

PPP-50076

Chromium Embedded is updated to the latest version as of September 2023.

PPP: Native Client

Medium

PPP-50877

libssh is updated to the latest available version, 0.10.4.

PPC: Server Infrastructure

Low

PPC-11005

The internal SQLite driver used for various tasks within Pipeline Pilot is updated to the latest version.

PPC: Server Infrastructure

Low

PPC-11269

OpenSSL is updated to the latest 3.0 release as of September 2023.

PPC: Server Infrastructure

Low

PPC-11312

The lz4 compression library is updated to the latest version as of September 2023.

PPC: Server Infrastructure

Low

PPC-9218

IMPORTANT! This change requires active administrator involvement.

By default, all new and existing Pipeline Pilot server users no longer have the Platform/PipelinePilot/Logon permission which allowed access to the Pipeline Pilot Professional Client. There is a new Pipeline Pilot administration group, Platform/Authors, which grants the Pipeline Pilot Professional Client logon permission. Groups are administered in the Pipeline Pilot Admin Portal > Security > Groups page.

For upgraded servers, existing members of the Platform/Administrators and Platform/PowerUsers groups are automatically included as members of Platform/Authors. For other users that require access to the Pipeline Pilot Professional Client, the Pipeline Pilot administrator must add those users to the Platform/Authors group. The administrator can also manage this permission through the use of “external claims” (for instance, Microsoft Active Directory domain groups or Linux local groups) defined within the group specification. For more information, see the Pipeline Pilot Admin Guide.

Note: The Platform/Authors group provides a clear distinction for protocol and component authors and controls default access to example protocols and components that are targeted specifically for authors. For instance, these protocols and components are inappropriate for Web Port users and could be confusing, and are therefore excluded from their clients. A user who is a member of the Platform/Authors group will have access to all the authoring examples, whichever client environment they are using.

PPC: Server Infrastructure, PPP: Native Client

High

PPP-50652

The Pipeline Pilot server can now support OpenSSL FIPS mode for both the embedded Apache HTTPd service and Pipeline Pilot-based uses of OpenSSL. You must contact BIOVIA Support to enable FIPS mode. When FIPS is enabled, the following Pipeline Pilot features, which are not compliant with FIPS, do not work:

·         Http based Microsoft NTLM authentication: The protocol requires the DES, MD4, and MD5 algorithms which are not available in FIPS mode.

·         Https connections to remote servers using the Http Connector (or other component-based Https connections) using Https TLS 1.0 and 1.1 protocols: These are older https protocols that are not supported in OpenSSL FIPS mode. TLS 1.2 and 1.3 are still functional. Additionally, the Pilotscript FileChecksum() function now allows you to specify the algorithm as an optional parameter.

PPC: Server Infrastructure, PPC: Security

Medium

PPC-11261

The Pipeline Pilot Apache service now supports brotli (RFC 7932) as an available decompression method when a web client connects to the server with Https and specifies Accept-Encoding: br. This is in addition to content encodings gzip and deflate which are already supported. Per https://bugs.chromium.org/p/chromium/issues/detail?id=452335, Brotli is only supported for https connections to avoid problems with proxy servers.

PPC: Server Infrastructure

Medium

PPC-8552

Https protocols TLS 1.0 and 1.1 are no longer supported for incoming https connections to the Pipeline Pilot server. Options for these protocol in the TLS/SSL Security Level in the Admin portal are removed. If you have older clients that require TLS 1.0 or 1.1, update your client framework to support TLS 1.2 or higher. This is usually due to using a client based on .NET framework 4.0 or earlier or Java version 7 or earlier. For these cases, update to at least .NET Framework 4.5 or Java version 8, and consult the documentation to ensure that you properly enable TLS 1.2 and/or TLS 1.3. For other clients, consult the documentation for that client for information on updating your https protocol or TLS version for https connections.

PPC: Server Infrastructure

Low

PPC-11012

Pipeline Pilot-defined users are now locked out after a certain number of failed sign in attempts. By default, accounts are locked out for 3 minutes after 5 failed attempts within 60 seconds. You can change these settings in the Security Configuration page in the Pipeline Pilot Admin Portal. Setting any of the three values to 0 will disable this feature. This feature does not affect external authentication methods such as Local, Domain, 3DPassport, and Foundation Hub.

PPC: Security

Low

PPC-11002

The Pipeline Pilot Admin Portal now displays a prominent yellow and then red banner when the license or SSL/TLS certificates are nearing expiration. By default the yellow banner appears with expiration is within 28 days, and red when it is within 14 days. You can adjust the days from the Pipeline Pilot Admin Portal Setup > Server Configuration page.

PPP: Server Infrastructure

Low

PPP-50250

New options in the Pipeline Pilot Admin Portal Setup > Server Configuration page control the number of days before displaying yellow and red license or SSL/TLS certificate expiration alerts in the Pipeline Pilot Professional Client and the Pipeline Pilot Admin Portal.

PPP: Server Infrastructure

Low

PPP-50256

You can no longer run protocols using a link that contains an embedded session or user credential.

PPP: Web Services

Medium

PPP-49107

Brotli (HTTP response header Content-Encoding: br) is now supported for all client HTTPS connections from the Http Connector and readers that support URL connections (for example, the Text Reader and XML Reader.) For more information see https://brotli.org/.

PPC: Web Application, PPC: Server Infrastructure, PPC: Web Services, PPC: Core Collection

Low

PPC-8553

Http Connector and other components that read URLs Pipeline Pilot is updated to use OpenSSL 3.0. Connections based on the older TLS 1.0 or TLS 1.1 protocols are now disabled by default. This impacts all outgoing connections from Http Connector components and other components that can read from remote URLs, such as the standard reader components. To enable use of TLS 1.0 and 1.1 for these components, use one of the following:

·         Use the latest Http Connector component, and set the Additional Options > Connection Options parameter to "Allow TLS 1.0 and 1.1". This allows the connection for that specific component, while disabling the protocol for connections from other components

·         In the Admin Portal, set Setup > Server Configuration > Allow outgoing TLS 1.0 and 1.1 Connections to Yes. This allows the outgoing connections from any component.

PPP: Integration

Low

PPP-49657

The scheduler system is extended to support the triggering of protocol execution upon the receipt of a JMS message for a specified topic, from a configured JMS broker. See more details in the application packaging guide.

PPP: Server Infrastructure

Low

PPP-49948

As a result of the enhancement PPP-49948, Pipeline Pilot may now be configured as a consumer of messages from the 3DX Platform, and to run a protocol to process such messages. This capability facilitates the sharing and synchronization of data between the 3DX Platform and enterprise systems in different environments, for example between the 3DX Cloud environment and on-prem ERP.

PPP: Server Infrastructure

Low

PPP-49597

The file management routines for SSH are updated from SCP calls to SFTP.

PPC: Integration

Low

PPC-11043

The Cache Writer component is updated to support Shared caches, which are accessible only to members of a specific Pipeline Pilot group. The "All users" cache scope has been renamed to "Shared". When this scope type is selected, the protocol author can specify a group name to restrict access to members of that group. See the component and parameter help for the Cache Writer for more information.

PPP: Core Collection

Low

PPP-32804

Interactive charting example protocols are updated to use the newer Highcharts-based reporting charts.

PPP: Core Collection

Low

PPP-49198

The formatting for dates in Highchart axes is improved.

PPP: Core Collection

Low

PPP-49752

A Sign Out Button component is added to the Reporting Collection. This component closes the current user session, and redirects the user to the Home Page, or to a specified location. There are parameters for linking from other elements, controlling the button actions, and defining the button style.

PPP: Web Application

Low

PPP-49329

The Prepare Data component now has data sampling options to only use the first N or a random selection of data records from large data sets. This ensures the user interface remains responsive when working with large data sets.

PPP: Web Application

Low

PPP-49833

When using the Prepare Data Component, you can now add a cleaning step for a specific property by selecting a cell in the data table and clicking the 'Add Step for" button. Cleaning actions that are not suitable for the current property will be greyed out.

PPP: Web Application

Low

PPP-49892

The Prepare Data component is updated. The main display of the table provides an improved view of the data when launching the application.

PPP: Web Application

Low

PPP-49969

The Prepare Data component now has a right panel showing a summary of the properties. This includes the name, type, range and the percentage of missing values. Missing values are highlighted as empty strings or data records without the property present.

PPP: Web Application

Low

PPP-49970

The interface and parameter help for the 3DX Service Connector component are updated to improve usability.

PPP: Server Infrastructure, PPP: Integration, PPP: Documentation

Low

PPP-49732

The Http Connector component's streaming mode, which is enabled when Response Is Binary is set to true, is now properly supported by the Binary Writer component. Very large files or responses from Http Requests (> 2GB) can be written by the Binary Writer when following the instructions in the parameter help for the Http Connector's Response Is Binary parameter.

PPP: Core Collection

Low

PPP-50526

Support for NTLMv1 in Http Authentication is removed from Pipeline Pilot. NTLMv1 is no longer secure. In a previous release, NTLMv1 was disabled by default, with an option for administrators to enable it. This option is removed. The updated NTLMv2 authentication method is still available. This update should only affect very old remote servers (pre-Windows 2000).

PPC: Server Infrastructure

Low

PPC-11009

The GET /jobs/ web service API now supports an optional query string parameter, $jobstate, which supports a value of "running" or "all". If not specified, the default is "all". When set to "running", only currently running jobIDs are returned by the call. For example, with GET /jobs/?$jobstate=running, only actively running jobIDs are returned, and initializing jobs that have not yet entered the running state are not included.

PPP: Web Services

Low

PPP-49324

You can now right-click a job and choose to Save All Job Results, which saves all non-html result files from the job.

PPP: Native Client

Low

PPP-47560

Component display names that are automatically generated from component parameter information are no longer limited to 30 characters. The limit is now 256 characters, which is the same as directly edited display names.

PPP: Native Client

Low

PPP-49330

The behavior when clicking to activate different Protocol Database Explorer tabs in the Professional Client is updated. The behavior is now the same as when pressing the Tab key to cycle through the User, Protocols, and Components tabs:

·         Existing search text (including an empty search) is copied from the last active explorer tab.

·         The search is applied, displaying the quick search results for the copied text.

·         The folder expansion state within the tab is preserved. Note that the search text will not be copied or applied to or from the Network Tab.

PPP: Native Client

Low

PPP-49337

The performance of the Keep Properties dialog is increased significantly for cases where data records contain large numbers of properties.

PPP: Native Client

Low

PPP-50014

The discarded properties list in the Keep Properties dialog is now sorted alphabetic with numbers. For example, instead of foo1, foo10, foo11, foo2, the properties are sorted as foo1, foo2, foo10, foo11.

PPP: Native Client

Low

PPP-50018

The visibility of the License Expiration warning in the Pipeline Pilot Professional Client is improved. Previously, when the license was close to expiration, the outline color of the key icon changed to red, which was easy to miss. Now, the background color of the icon panel in client's status bar changes to yellow or red depending on how many days before expiration.

PPP: Native Client

Low

PPP-50253

The Web Port interface is updated for usability. Navigation is improved in a collapsible side panel, and protocol help is now viewable while setting parameters.

PPP: Web Application

Medium

PPP-48758

The help tab in Web Port has been moved and can now be viewed while viewing the protocol's form. Small buttons have been added to display both protocol-level and parameter-specific help text in the new help tab. In all cases, HTML is now rendered correctly.

PPP: Web Application

Low

PPP-33159

The Web Port documentation has been updated to reflect the user experience changes in this release of the application.

PPP: Documentation

Low

PPP-50369

The Web Port interface now displays the protocol help text in a resizable and closable tab below the protocol parameters, which allows you to see the help and parameters simultaneously.

PPP: Web Application

Low

PPP-50468

When customizing Web Port, the ability to add a custom caption using  TEMPLATE_LOGO_CAPTION has been removed. Custom logos will also appear within a smaller space in the new Web Port side bar, so for best results, custom logos should fit within 32 by 32 pixels.

PPP: Web Application

Low

PPP-50600

A new method, plp_send_message_to_client(message), is added to the Python Script component, which allows users to send messages to the Pipeline Pilot Professional Client from their Python code.

PPP: Integration

Low

PPP-49574

The node object has an additional function to indicate whether the node is to be treated as an array, even if it has only a single child.

setArrayItemFlag() in Perl, Python, and Java.

SetArrayItemFlag() in .NET.

PilotScript syntax is updated to achieve the same result.

The Data to JSON and JSON Writer components have a new parameter, Array Handling of Single Nodes, to guide the interpretation of a data nodes property with a unique name. The option selected in that the parameter method determines the method used to assess whether the JSON representation of a data node is a scalar or array object.

The Data Record Tree Viewer component now indicates whether a node is marked as an array object, regardless of the number of child objects.

PPP: Core Collection

Low

PPP-35368

The PilotScript FileChecksum() function is updated to include an optional parameter to specify the algorithm. Choices include md5, sha1, sha224, sha256, sha384, and sha512. If not specified, md5 is used.

PPP: Integration

Low

PPP-50628

.NET Client SDK: nalpp_2_0.dll is no longer supported. It is based on the outdated .NET 2.0 framework, which does not support the minimum Https protocols TLS 1.2 or 1.3.

PPP: Client SDK

Low

PPP-49827

Added a new example protocol for the Reporting Collection, Generic Word Report Example, that demonstrates how to create a report in Word.

PPP: Packaging

Low

PPP-29576

A new example protocol demonstrating how to use the XY chart with multiple data series, where the number of data series is not known beforehand.

PPP: Packaging

Low

PPP-34106

A new example protocol demonstrates sending emails via Python.

PPP: Integration

Low

PPP-47787

The Send Messages to Client via Python Script example protocol demonstrates sending messages to the client via the Python Script Component.

PPP: Integration

Low

PPP-49667

A new example protocol demonstrates built-in Pipeline Pilot error handling capabilities.

PPP: Integration

Low

PPP-50274

A new example protocol demonstrates outputting multiple plots using Python Jupyter Notebook.

PPP: Integration

Low

PPP-50279

A new example demonstrates some of the basics to using the Python Jupyter Notebook component within Pipeline Pilot.

PPP: Integration

Low

PPP-50304

Description

Areas Affected

Risk Level

Jira Issue ID

R versions 4.0.x, 4.1.x, 4.2.x, and 4.3.x are now supported in Pipeline Pilot.

PSM: R Statistics

Low

PSM-2479

Description

Areas Affected

Risk Level

Jira Issue ID

BLAST+ is upgraded to version 2.12.0.

PBIO: Analysis

Medium

PBIO-6682

Updated biology collections to work with Pipeline Pilot infrastructure changes.

PBIO: Analysis

Medium

PBIO-6740

Open Targets online components are updated.

PBIO: Online Components

Low

PBIO-6546

Updated the list of biology third-party tools.

PBIO: Documentation

Low

PBIO-6717

Updated biology collections to work with Pipeline Pilot infrastructure changes.

PBIO: Infrastructure

Low

PBIO-6722

Entrez E-utilities components are updated.

PBIO: Online Components

Low

PBIO-6726

EBI online components are updated.

PBIO: Online Components

Low

PBIO-6727

GWAS Catalog and Reactome online components are updated.

PBIO: Online Components

Low

PBIO-6728

HMMER3 is upgraded to version 3.3.2 on Linux.

PBIO: Annotators

Low

PBIO-6731

EBI and NCBI online components are updated.

PBIO: Online Components

Low

PBIO-6747

Bowtie 2 is upgraded to version 2.5.1.

PBIO: Analysis

Low

PBIO-6729

"Humanize Antibody Sequences" has been added to Prototypes for predicting sequence mutations to humanize antibodies.

PBIO: Annotators

Low

PBIO-6733

The Pipeline Pilot Chemistry Collection and SDK, BIOVIA Draw and Pipette Sketcher now support enhanced stereochemistry for cis-trans double bonds. You can assign these bonds to relative absolute, AND, and OR geometric stereogroups, in a similar way to assigning tetrahedral stereo atoms to relative stereogroups. The new enhanced stereogroups of cis-trans double bonds are stored in molfiles V3000 stereo collections, and are taken into account in molecular depictions, stereoisomer enumeration, and substructure and exact searches.

PCHE: Chemistry Depiction, PCHE: File Formats

Medium

PCHE-8790

Changed the Peptide seC HELM Monomer and AA Sec SCSR Template structure in Biovia global configuration files, with the addition of the side chain leaving group.  Changed the Peptide Pyl, dPyl HELM Monomer and AA Pyl, pyl SCSR Template structure in Biovia global configuration files, with the addition of the side chain leaving group.  The structures are the same as in Biovia Draw.

PCHE: Hub Monomer Libraries

Medium

PCHE-9015

Added X and N to dropdown for RNA in monomer review tool; Added N to list of allowed analogs for RNA bases in the monomer review rules; Clear analog for RNA monomers with N analog when they are loaded in the sketcher. This causes them to appear in the same way as X monomers in the monomer search.

PCHE: Pipette

Low

PCHE-8573

Updated help text for the Pipeline Pilot components. "Note: This reader cannot read ChemDraw files with nested groups. It is recommended to flatten the nested groups in ChemDraw before saving it for reading."

PCHE: File Formats

Low

PCHE-8736

Added support for Microsoft Edge Chromium based WebView2 control used by Insight For Excel. This replaces IE-11 based WebBrowser component.

PCHE: Sketchers

Low

PCHE-8742

Improved support of monomers with multi-atom leaving groups in Perceive Sequence from Structure component

PCHE: Biologics, PCHE: Chemical Perception

Low

PCHE-8747

Improved the RepositionStereoBonds action in Standardize Molecule to perceive and fix cases where the three plane-defining atoms are on the same side of the tetrahedral center.

PCHE: Chemical Perception

Low

PCHE-8778

Added a mechanism to define number of rings, number of heteroatoms, ring size, aromaticity and homology group constraints for replacement of ring assemblies. It requires the definition of DAT Sgroups attached to any atom in the ring assembly for which you want to impose replacement constraints. These DAT Sgroups can be defined using Pipette Sketcher or BIOVIA Draw.

PCHE: Enumeration

Low

PCHE-8813

The configuration files are versioned with the timestamp in the file names and a summary pdf file as an archive for versioned centralized libraries. The history and timestamp (version) of residuals can be viewed from the version of configuration files. Reload of older version of monomers/templates can be done by create centralized libraries from the archived configuration files.

PCHE: Hub Monomer Libraries

Low

PCHE-8822

Added a function in Molecule object: MoveTetrahedralStereoWedge(fromBond, toBond, atom) to move the wedge from one bond (fromBond) to another bond (toBond) for a tetrahedral stereo atom (atom). The parity of the stereo is not changed by this move. Added a function in Bond object: SwapAtoms() to swap the designation of atom1 and atom2 for a bond. 

PCHE: Molecular API

Low

PCHE-8828

Added parameter to control sending messages to PP client to Matched Molecular Pairs enumeration component

PCHE: Enumeration

Low

PCHE-8832

Added two protocols 'Export All Libraries' and 'Import All Libraries' in the Web Port. 

PCHE: Hub Monomer Libraries

Low

PCHE-8845

Added a counter for number of heteroatoms to Molecular Property Counts. A heteroatom is defined as any heavy atom different from Carbon.

PCHE: Property Calculators

Low

PCHE-8861

All-Purpose drawing tool is provided for Traditional Mode in Pipette.

PCHE: Pipette

Low

PCHE-8882

Grouped templates such as Cyclo heptane, Aromatic and Cyclopentane are provided for Traditional mode in Pipette.

PCHE: Pipette

Low

PCHE-8905

Clicking on atom to edit is provided for Traditional Mode in Pipette.

PCHE: Pipette

Low

PCHE-8917

Keyboard shortcuts are provided for Traditional Mode in Pipette.

PCHE: Pipette

Low

PCHE-8919

Added information about the meaning of the NEMAKeyFlag to the Molecule to NEMA component help text.

PCHE: Documentation

Low

PCHE-8933

Implemented a new component, Replace Chain Assemblies, to replaces each chain assembly in the input molecule with chain assemblies and ring linkers collected from several datasets. Parameters in the Chain Assemblies Criteria group are used to select the type of chain assemblies to use as replacements. Replacements can be done changing one chain assembly at a time, or changing pairs of chain assemblies. 

PCHE: Enumeration

Low

PCHE-8940

Added archiving capability to the configuration files with date and time stamp (universal timestamp to millisecond) added to the file names of the three configuration files. When generating configuration files from a centralized library, an archiving copy of the files is generated in the same user defined folder. Administrator can copy/move the new set of configuration files to the Global HELM folder while the user folder has the archiving sets of configuration files with timestamps.

PCHE: Hub Monomer Libraries

Low

PCHE-8952

Added downloadable pdf file in a separate tab of the HTML reports to

·         protocols generating the configuration files from a library

·         protocols converting library from one type to another (HELM to SCSR and SCSR to HELM)

PCHE: Hub Monomer Libraries

Low

PCHE-8953

Added a 'View and Copy Configuration Files" protocol in the Webport, with the following functionality:

·         Visualized the three configuration files in the Webport

·         Create zip files for each config file and put them in the run folder to be downloaded from Webport

·         Can copy the config files to a folder which is accessible to the user, and also selecting whether to add a timestamp to the copied file name.

PCHE: Hub Monomer Libraries

Low

PCHE-8954

Added wild card search capability to "Search Library By Property (PLP)". The search result is available from the report and can be downloaded as "Search Results.sd" file.

PCHE: Hub Monomer Libraries

Low

PCHE-8955

Validate a SD file which has macromolecule structure and HELM string.

PCHE: Hub Monomer Libraries

Low

PCHE-8956

An entry (HELM Monomer and SCSR Template) in a library is uniquely identified by its "Class and Name", all other properties of the entry can be modified. Entry before and after modification will be saved in "Centralized_Library_Action_Log".

PCHE: Hub Monomer Libraries

Low

PCHE-8957

Added new tabs in the output reports generated from centralized library web port protocols. 

PCHE: Hub Monomer Libraries

Low

PCHE-8959

The enhanced stereo groups are now assigned to the atropisomer bond and to the central atom in allenes.

PCHE: Pipette

Low

PCHE-8975

Pipette now supports enhanced stereochemistry for E/Z double bonds.

PCHE: Pipette

Low

PCHE-8996

Added an example protocol, "Check Structure-Sequence Conversions Roundtrips", to the Examples\Chemistry\Cheminformatics\Self-Contained Sequence Representation (SCSR) folder. The new example protocol illustrates a way to check roundtrip conversions of sequences and the corresponding expanded structures to verify that the initial and final sequences or structures are the same.

PCHE: Examples

Low

PCHE-8999

Added a "View and Copy Configuration Files" protocol which can read and copy the global configuration files.  The publishing of global configuration files to a common area can be done with this protocol from both the Webport and PP Pro client.

PCHE: Hub Monomer Libraries

Low

PCHE-9044

Added check for wedge bond placement which will result in ambiguous tetrahedral stereo. This check is available in PPChem SDK StructureChecker method PPStructureChecker::CheckForBadStereoAtoms(). It is also in Pipeline Pilot "Bad Stereo Filter" component.

PCHE: Chemical Perception

Low

PCHE-9107

Made sure that labels for enhanced stereo groups ('&1', 'or1', ...) for cis/trans double bonds and atropisomer axial bonds are placed close to the bond to avoid confusion with other labels 

PCHE: Chemistry Depiction

Low

PCHE-9130

Monomers deleted from a library is archived in the "Centralized_Library_Action_Log" library. 

PCHE: Hub Monomer Libraries

Low

PCHE-8958

Description

Areas Affected

Risk Level

Jira Issue ID

Bookmarks in Microsoft Word documents may now be targeted for editing by the "Add Content to Word Document" component. You may insert or replace content, either before, within, or after any named Bookmark in a Word document.

TXT: Other

Low

TXT-1070

Description

Areas Affected

Risk Level

Jira Issue ID

Updated imaging collections to work with Pipeline Pilot infrastructure changes.

IMG: Infrastructure

Medium

IMG-2972

Updated imaging collections to work with Pipeline Pilot infrastructure changes.

IMG: Readers/Writers, IMG: Example Protocols, IMG: Infrastructure, IMG: Components

Medium

IMG-3111

The MSC Solidification and Grain Growth PhaseField protocols now support restart using the final field setup from a previous simulation. 

MSC: Application

Low

MSC-5948

The new Material from Chemical Name or SMILES protocol allows you to generate Materials Studio XSD files from SMILES strings or the chemical names of molecules. 

MSC: Application

Low

MSC-6058

You can now use the Solidification and Grain Growth PhaseField protocols to re-mesh the Abaqus input files produced. This allows you to produce a coarser mesh for the microstructure imported into Abaqus, better suited for finite element analysis. Improvements to the Abaqus input files allow you to now work seamlessly with the Micro Mechanics plugin in Abaqus. You can now use GRAIN sets for section definition. The input files now also contain six sets defining the surface voxels at the different cell faces. These sets can be used to impose periodic boundary conditions.

MSC: Phase Diagrams

Low

MSC-6124

New protocols now allow you to prepare, run, and analyze efficient reactive Monte Carlo Molecular Dynamics simulations with specific provisions for electrochemistry. 

MSC: Application

Low

MSC-6305

The Calculate Semiconductor Band Offsets and Calculate Equation of State for Solids protocols now expose a wider set of exchange-correlation functionals.

MSC: Examples

Low

MSC-6433

The PhaseField protocols now include an option to run the phase field simulations using adaptive time stepping. The phase field code now estimates the time step needed for an accurate calculation and continuously updates the step size as the system evolves.

MSC: Phase Diagrams

Low

MSC-6460

You can now use the Calculate Thermal Conductivity protocol to calculate the thermal conductivity in an amorphous system or a given structure in a periodic cell using the Reverse Non-Equilibrium Molecular Dynamics method. 

MSC: Application

Low

MSC-6691

Memory resource management is improved, particularly for coarse-grained pipelines using the Materials Studio Collection (MSC).  If you observe a negative impact on performance of your protocols, you can modify the Perl MaterialsScript (on Server) component's OnFinalize() handler to match that in the protocols provided in the MSC.

MSC: Infrastructure

Low

MSC-6387

Major

An issue is fixed where an sqlite3.dll file located anywhere within the Windows path would cause the Pipeline Pilot session service to fail.

PPC: Server Infrastructure

Low

PPC-11156

Minor

Patched zlib with the fix from the zlib issue https://github.com/madler/zlib/issues/776.

PPC: Server Infrastructure

Low

PPC-11128

Minor

In usage reports, an incorrect dependency was indicated on the deprecated scmobile collection. This is now fixed.

PPP: Core Collection

Low

PPP-49288

Minor

When the Protocol Parameter Injection Handling setting is set to "Restrict", XMLDB paths passed to the Component Reader component should be fully scoped with the xmldb: URI. For example a fully qualified path example is: xmldb:/Protocols/Web Services/Examples/Generic/Beer Filter

PPP: Web Application

Low

PPP-49708

Minor

The Security section pages in the Table of Contents view of the Administration Portal have been reordered to provide a more logical sequence.

PPP: Web Application

Low

PPP-50847

Minor

Attempting to read metadata from the Protocol Database simultaneously while other processes updated data within the database no longer results in invalid information returned from the service.

PPC: Server Infrastructure

Medium

PPC-11097

Minor

Attempting to reconnect to a Pipeline Pilot server based on Foundation authentication after the session had timed out no longer results in a 401 Unauthorized error message within the web page. The server now correctly reestablishes the Pipeline Pilot session via confirmation of a valid session from the Foundation Hub server.

PPC: Security

Low

PPC-11115

Minor

The client tag information is removed from the displayed error message when authorization failures occur during protocol launching.

PPP: Security

Low

PPP-49173

Minor

In a protocol with top-level parameter "Remote Execution" set to True and running on multiple cores, if there is a parallel subprotocol and one of the parallel subprotocols crashes, the parent protocol no longer hangs.

PPP: Integration

Low

PPP-49308

Trivial

The default format of response content from a file upload operation is now consistent between success and failure results. In general, the format (text, HTML, JSON, XML) is determined by the browser Accept header or by an explicit parameter setting, and there is no change in those cases.

PPP: Web Services

Low

PPP-47272

Minor

Remote servers that required calls to set the https hostname via the OpenSSL SSL_set_tlsext_host_name() API no longer fail within Http Connector components when using an Http Proxy server.

PPC: Integration

Low

PPC-10885

Minor

File names containing a '+' character are now usable with a resource connection to S3.

Based on the characters listed under Amazon's '[Object Key Naming Guidelines|https://docs.aws.amazon.com/AmazonS3/latest/userguide/object-keys.html]', the following characters in the 'Characters might require special handling' section:

·         Ampersand ("&"): ok

·         Dollar ("$"): ok

·         ASCII character ranges 00–1F hex (0–31 decimal) and 7F (127 decimal) : not tested

·         'At' symbol ("@"): ok

·         Equals ("="): ok

·         Semicolon (";"): ok

·         Forward Slash ("/"): not ok

·         Colon (":"): *not* ok

·         * Plus ("+"): ok

·         (multiple) Spaces: appear to be ok

·         Comma (","): not ok

·         Question mark ("?"): not ok

Question marks, Forward Slashes, and Colons are part of either Unix or Windows paths, and won't work because we use temporary files to support S3. The Comma character is used as an array delimiter in our reader components.

The characters listed in the 'Characters to avoid' section have not been tested, bugs related to any one of those will not be fixed.

PPP: Integration

Low

PPP-47894

Minor

Molecule images now respect the "Image Size" parameter on the Data Record Tree Viewer.

PPP: Core Collection

Low

PPP-49336

Minor

Long integers (greater than 2147483647 or less than -2147483648) that are input into the "Clean Data" component as either Double or String types now have their values correctly preserved in the output of the component.

PPP: Core Collection

Medium

PPP-49695

Minor

A memory error that could be caused by excess empty lines in the PropertyList parameter of the Keep or Reorder Properties component is fixed.

PPP: Core Collection

Low

PPP-49872

Minor

Added support of the resource URI to the Excel Reader component to enable access to Sharepoint Online files via a defined Sharepoint Online tagged resource.

PPP: Integration

Low

PPP-50188

Minor

The Summarize Data properties component now correctly handles the "Treat Empty Strings as Missing Values" parameter. The summary output for each property now also includes metrics for the number of records with missing values for the property, and also for the number of records where the property was not present. The component has been moved to the folder Components/Analysis and Statistics/Basic Math and Statistics.

PPP: Core Collection

Low

PPP-50684

Minor

Filenames containing Unicode characters are now supported in file operations involving 3D Drive.

PPP: Web Services, PPP: Integration

Low

PPP-50778

Minor

The Http Connector's Asynchronous mode no longer hangs when connecting to remote servers in Pipeline Pilot 2023 and 2023 SP1.

PPP: Integration

Low

PPP-50780

Minor

The Image from File component no longer improperly sends Pipeline Pilot session information to remote servers when the Source for the component is a remote URL. The result of this was failures to access anonymous protocol resources on older Pipeline Pilot servers (< version 2022.1) when the Image from File component was run on new Pipeline Pilot servers (>= version 2022.1)

PPC: Core Collection

Low

PPC-11182

Minor

The reporting numeric histogram component no longer has an issue with items missing from the rightmost bin.

PPP: Core Collection

Low

PPP-47086

Minor

Reduction in warnings when using reporting related to an "illegal reflective access operation".

PPP: Core Collection

Medium

PPP-47088

Minor

Invalid xml was fixed for crosstab reports that used the Word Report Writer.

PPP: Core Collection

Low

PPP-48045

Minor

Fixed a bug in Highcharts-based charts where user-defined Y axis minimum and maximum were overridden by Highcharts defaults. The new behavior will use Highcharts defaults if no Y axis minimum or maximum is defined, and if a minimum and/or maximum is specified, that value will be used instead.

PPP: Core Collection

Low

PPP-48944

Minor

Axis label formatting in Highcharts radar charts is now supported.

PPP: Core Collection

Low

PPP-48957

Minor

Updated the "Interactive Visualization" example protocol to improve interactivity when using Highcharts charts.

PPP: Core Collection

Low

PPP-49189

Minor

A bug was fixed which caused stacked bar charts to render as adjacent when multiple bar charts were included in the same report.

PPP: Core Collection

Low

PPP-49501

Minor

Fixed bug which caused Highcharts symbols to show in an XY chart when symbol type was set to "none."

PPP: Core Collection

Low

PPP-49542

Minor

Highcharts area chart area selection was fixed and now allows selection by clicking on the colored area.

PPP: Core Collection

Low

PPP-49552

Minor

 Added data series axis label support in Highcharts line and area charts.

PPP: Core Collection

Low

PPP-49685

Minor

Empty Highcharts charts now show the same "no data to display" message that is shown in previous JFreeChart-based charts when the chart contains no data.

PPP: Core Collection

Low

PPP-49686

Minor

Improved tooltip rendering for Highcharts heat maps in boost mode.

PPP: Core Collection

Low

PPP-49715

Minor

Fixed an issue where gridlines would be shown for multiple Y axes. Now gridlines are shown only for a single Y axis.

PPP: Core Collection

Low

PPP-49749

Minor

Highcharts Maps were not included in a recent update, but have been added in the current release.

PPP: Core Collection

Low

PPP-49777

Minor

Highcharts chart series which have had their color parameter changed to ExpressionType would incorrectly show a default color in the chart legend. The legend item will now have the same color as the first data point, consistent with the behavior of the image-based charts.

PPP: Core Collection

Low

PPP-49788

Minor

Fixed an issue where Highcharts chart backgrounds would appear black when the server's regional settings used a comma as a decimal separator.

PPP: Core Collection

Low

PPP-49809

Minor

Fixed an issue which would cause Highcharts charts to fail to render in a dynamic content container.

PPP: Core Collection

Low

PPP-49989

Minor

Fixed an issue where background images in reports would fail to appear when the report was generated in an https context, then loaded in http or vice versa

PPP: Integration

Low

PPP-49997

Minor

Fixed an issue where loading a report containing a file chooser button via http: rather than https: would result in a "blocked a frame with origin" (CORS) error when the file chooser was closed by pressing okay.

PPP: Web Application

Low

PPP-50177

Minor

An issue was fixed which caused background images to fail to render when used in reporting component format options.

PPP: Core Collection

Low

PPP-50353

Minor

When using the Single Source File file type option of the File chooser component, there was a bug observed when uploading successive files from the client, without any intervening folder navigation activity. The file path written to the HTML file selection widget would not be replaced with the new value. There are other possible variations of this bug caused by the same underlying behavior. This is now fixed and the text for the Single Source File mode is also corrected.

PPP: Web Application

Low

PPP-50638

Minor

Fixed an issue with the Searchable List Box where pre-selected items in the list box caused the filtering text input to be disabled.

PPP: Web Application

Low

PPP-50738

Trivial

A problem was fixed that would cause the left border of the leftmost bar in a Highcharts bar chart to be hidden.

PPP: Core Collection

Low

PPP-49701

Trivial

The Line Chart, XY Chart, and XY Chart (Categorical) components now use solid colors instead of gradient colors as symbol color defaults.

PPP: Core Collection

Low

PPP-49823

Minor

Fixed an issue where attempting to shut down the Pro Client when the remote Pipeline Pilot server is offline or not accessible results in the Pro Client appearing to shut down, but the "Pipeline Pilot.exe" process does not exit.

PPP: Native Client

Low

PPP-25350

Minor

Fixed an issue where pressing Shift-F4 or F9 while editing the parameter validation scripts in the parameter editor dialog would result in an error message appearing.

PPP: Native Client

Low

PPP-49605

Minor

Fixed an issue where the dialog displayed from the Display Globals component would frequently appear blank. This issue did not affect the Global Data Tree Viewer or Data Record Tree Viewer.

PPP: Native Client

Low

PPP-49610

Minor

Fixed scaling issues in the various Protocol Link dialogs (Protocol Function, Input Form, and Protocol Link parameters) where the dialog controls were not correctly positioned in multiple monitor situations where the primary monitor's resolution is greater than 100%.

PPP: Native Client

Low

PPP-49697

Minor

Fixed the behavior of the horizontal scroll bar for the Keep Properties dialog's property list control when there are a large number of properties present.

PPP: Native Client

Low

PPP-50017

Minor

The buttons within the Keep Properties dialog now become enabled or disabled based on the current selection state of the properties within the lists.

PPP: Native Client

Low

PPP-50021

Minor

Fixed a problem where the Pipeline Pilot.exe process would take 10 seconds or more to shut down if any secondary Pipeline Pilot servers are in a "failed to login" when the client attempted to exit.

PPP: Native Client

Low

PPP-50123

Minor

Fixed an issue in the Pro Client within the Server File Browser where copying a file from a local folder and pasting to a remote folder when connected to Linux server could result in the remote server creating a subfolder within the target directory, then copying the file to that location instead. As an example, copying Desktop/subfolder/file.txt, then pasting to the user directory would end up writing file.txt to userdata:/subfolder/file.txt. Now, the file would correctly write to userdata:/file.txt.

PPP: Native Client

Low

PPP-50297

Minor

Fixed a long-standing issue where the Web Service tab or pane would become visible anytime a component Edit Dialog appears.

PPP: Native Client

Low

PPP-50378

Minor

Dialogs in the Pro Client now correctly resize and rescale when the Windows OS Display Settings change for the monitor with the dialog.

PPP: Native Client

Low

PPP-50425

Minor

Fixed an issue where using the "up one level" button or "look in" drop down list to navigate in subfolders of the "Root Folder" of a server when the server configuration is set to Unrestricted File Browsing results in an error of the form "Directory not found".

PPP: Native Client

Low

PPP-50677

Minor

Using an external Python environment with a Python Script or Python Jupyter Notebook component where the Batch Size parameter is greater than 1 and the Script parameter is empty no longer throws an error.

PPP: Integration

Low

PPP-49578

Minor

The documentation for the Asc() and Chr() functions has been updated to reflect the maximum supported value for Unicode characters.

PPP: Documentation

Low

PPP-49935

Minor

Updated the Python Script and Python Jupyter Notebook components to work with external Python environments with newer versions of pandas (version 1.5.0 and later)

PPP: Integration

Low

PPP-50268

Minor

The current path is now added to Python's sys.path when running the Python Script or Python Jupyter Notebook components, providing more consistency with the behavior when running inside the interactive Python Jupyter Notebook editor.

PPP: Integration

Low

PPP-50450

Minor

Update and fix the Python External Modules examples.

PPP: Integration

Low

PPP-50225

Minor

Update and fix the Stock Statistics example; performs calculations on historical stock data from Yahoo!

PPP: Integration

Low

PPP-50228

Minor

The Google API key has been removed from the location components as well as the location example protocols.

PPP: Integration

Low

PPP-50271

Minor

Examples using the prototype MATLAB and JMP components have been removed.

PPP: Integration

Low

PPP-50470

Severity

Description

Areas Affected

Risk

Defect

Minor

Details on saving components and protocols to a package has been added to the Application Packaging Guide.

PPC: Documentation

Low

PPC-7075

Minor

The package configuration <access> directive can now include an "auth" flag to ensure that access is restricted to authenticated users.

PPP: Server Infrastructure

Low

PPP-50764

Severity

Description

Areas Affected

Risk

Defect

Trivial

Improve the behavior of the Help Center header text when scaled up to a high level.

PPP: Web Application

Low

PPP-49094

Severity

Description

Areas Affected

Risk

Defect

Minor

Example "Read a sas7bdat File with R Custom Script" protocol runs without error when "curl" is not installed. 

PSM: R Statistics

Low

PSM-2460

Minor

Updated the CRAN repository used by component R scripts when calling the loadOrInstall() function to avoid errors when trying to install from the Berkeley repository. 

PSM: R Statistics

Low

PSM-2481

Minor

The "R Help Search Web Site" link in the help text of R components is now all deleted and no longer broken.

PSM: R Statistics

Low

PSM-2486

Major

Updated biology collections to work with Pipeline Pilot infrastructure changes.

PBIO: Analysis

Medium

PBIO-6756

Major

A message explaining the retrieval limit of 9,999 PubMed records was added to Entrez ESearch.

PBIO: Online Components

Low

PBIO-6723

Major

EBI online components are updated.

PBIO: Online Components

Low

PBIO-6750

Minor

"Clean BLAST XML File" can be used to remove file paths from BLAST output.

PBIO: Annotators

Low

PBIO-6710

Minor

"Humanize Antibody Sequences" no longer terminates when it encounters a sequence with an unknown residue. Instead, the data record is sent out the fail port with a message in the ErrorText property.

PBIO: Analysis

Low

PBIO-6734

Minor

"FASTA Sequence Reader" can read zipped files over https.

PBIO: Online Components

Low

PBIO-6737

Minor

NCBI online components are updated.

PBIO: Online Components

Low

PBIO-6741

Minor

"PDB Sequence Fetcher" now uses https.

PBIO: Online Components

Low

PBIO-6749

Minor

Improved parsing of the NCBI BLAST database list.

PBIO: Online Components

Low

PBIO-6769

Minor

"Humanize Antibody Sequences" has been added to Prototypes for predicting sequence mutations to humanize antibodies.

PBIO: Infrastructure

Low

PBIO-6770

Minor

"01 Create Bacteria Repository" is updated to be compatible with NCBI changes.

PBIO: Example Protocols

Low

PBIO-6773

Critical

Enabled depiction of none sequence fragments. Fixed the depiction of MUL brackets.

PCHE: Chemistry Depiction

Low

PCHE-8851

Critical

Enabled depiction of none sequence fragments. Fixed the depiction of MUL brackets.

PCHE: Chemistry Depiction

Low

PCHE-8852

Major

Fixed an issue where exact structure matching in Pipeline Pilot or Direct, in certain cases, matched a structure that specifies a mixture of stereoisomers with a query that specifies a single stereoisomer. These cases involve meso or pseudochiral structures such as 1,4-cyclohexanes.

PCHE: Chemical Perception, PCHE: Query Mapping

Low

PCHE-8552

Major

·         Replaced the SMIRKS definition of the InChI2 transforms by individual rxn files for each rule.

·         Set default value for Maximum Number of Tautomers in Enumerate Tautomers (InChI2 Transforms) component to 1000

·         Added new parameter to Enumerate Tautomers (InChI2 Transforms), MaxNum Successive Transforms Per Molecule, Maximum number of successive tautomer transformations that can be applied to each input molecule. Leave empty to allow an unlimited number of transformations. The default value is set to 3. Added the new parameter to the PPChem SDK API to generate tautomers GenerateInchi2Tautomers(Molecule mol, int maxNumTautomers, int maxSuccessiveTransforms, bool doPT, bool doRC, bool doVT) Note that the new argument requires 2023 PPChem SDK code that uses this API to be updated.

·         Fixed handling of Maximum Number of Tautomers to make sure the enumeration stops when the maximum is reached.

·         Modified Get InChI2 Tautomers from SMILES to work with both All Tautomers and Canonical Tautomer options

PCHE: Chemical Perception, PCHE: Enumeration

Low

PCHE-8630

Major

Adjusted the length of double bond lines connecting two non-Carbon atoms to make sure the atom labels do not make the lines too short and hard to see, especially in rings.

PCHE: Chemistry Depiction

Low

PCHE-8706

Major

Fixed a bug which prevented launch of Pipette from Pipeline Pilot components.

PCHE: Enumeration

Low

PCHE-8730

Major

Added an optional parameter "Remove Duplicates" in the "Generate Tautomer" component.  The "Remove Duplicates" default value in the component is true. If the "Remove Duplicates" parameter is not present (as in an older version), the value of "Remove Duplicates" is false.

PCHE: Chemical Perception

Low

PCHE-8751

Major

Fixed bug in the code that perceives sense/antisense chains in RNA that can result in crashes or wrong assignment of base complementarity. This code is used in sequence depiction and perception of sequence from structure.

PCHE: Biologics, PCHE: Chemistry Depiction

Low

PCHE-8824

Major

Fixed parsing of SMARTS queries that contain two atoms that can be aromatic or aliphatic and are connected by a '~' (any) bond, for example {noformat} '[A,a]~[A,a]'{noformat}.

PCHE: Chemical Perception, PCHE: File Formats

Low

PCHE-8825

Major

Made sure the Check and Normalize Structure component always reports StraightenTripleBonds actions even in cases where the triple bonds were fixed by applying a Transformation Reaction instead of the regular Normalization action.

PCHE: Chemical Perception

Low

PCHE-8839

Major

Pipeline Pilot SKC reader no longer creates invalid data Sgroups for BIOVIA Draw sketch files containing structures and free floating text.

PCHE: Chemistry Content

Low

PCHE-8891

Major

Pipeline Pilot SD and RXN readers no longer multiply invalid Sgroup data. For example, if SD files contain Data SGroups with index of -1, the SD reader used to duplicate the Data Sgroups resulting in totaling n * (n+1) Data Sgroups where n is the original number of Data Sgroups.

PCHE: PPChemAPI

Low

PCHE-8935

Major

The chapter on NEMA Key Search in the BIOVIA Chemical Representation Guide was revised.

PCHE: Documentation

Low

PCHE-8992

Major

Updated the URL parameter default to: "shortcut:/Chemistry Data/data/Queries/FunctionalGroups/*.mol" in the Pocess chemistry for Sketcher protocol.

PCHE: Sketchers

Low

PCHE-9003

Major

Cleaned up and fixed the PAINS Filter component to read the PAINS queries from a text file with SMARTS and removed the SD Reader component that was used in previous releases. The behavior for some PAINS queries might change because the SD Reader that was used before was not reading properly the query features.

PCHE: Chemical Perception, PCHE: File Formats

Low

PCHE-9009

Major

Fixed SD Reader to avoid possible crashes reading query feature properties coming from SMARTS strings

PCHE: File Formats

Low

PCHE-9010

Major

Enhanced stereo in atoms attached to Hydrogen atoms is now preserved after removing the Hydrogen atoms using the Remove Hydrogen component or the corresponding PPChem SDK APIs. 

PCHE: Chemical Perception

Low

PCHE-9017

Major

Fixed conversion of HELM monomers to SCSR templates when the monomer has multiple side chain attachment points

PCHE: Biologics, PCHE: File Formats

Low

PCHE-9020

Major

A function is added to StructureChecker class in PPChem API and PPChem SDK to specify whether to check marked stereo on non-stereo atoms for bad stereo. The Java function setCheckMarkedStereoOnNonStereoAtoms, C# function SetCheckMarkedStereoOnNonStereoAtoms, and Python function setCheckMarkedStereoOnNonStereoAtoms take a boolean argument and return no values.

PCHE: PPChemAPI

Low

PCHE-9041

Major

Allenes that have Up or Down bond stereo wedges but are not stereo because of symmetrical attachments are flagged as having bad stereo by the Bad Stereo Filter component and the corresponding PPChem SDK APIs 

PCHE: Chemical Perception

Low

PCHE-9108

Major

Updated Query Check Filter component to avoid flagging an error when allene central atoms are included in enhanced stereo collections.

PCHE: Chemical Perception

Low

PCHE-9146

Minor

Fixed the depiction of implicit Hydogen inside the MUL group.

PCHE: Chemistry Depiction

Low

PCHE-6435

Minor

Enhanced depiction of biological sequences to handle better cases with two sequence chains connected by two linkers. Now the linkers are always positioned in between the sequence chains.

PCHE: Biologics, PCHE: Chemistry Depiction

Low

PCHE-7767

Minor

Improved the alignment of molecules in reactions by aligning the molecules using the molecule extents (which take into account the text labels on atoms and bonds) instead of just the atom coordinates. Reduced the amount of white space between reactions and captions.

PCHE: Chemistry Depiction

Low

PCHE-8315

Minor

Updated the SD Reader used in the Identity Search Component to the latest to make it work behind a proxy server when trying to search PubChem. Modified the Identity Search component to expose the PubChem downloading file format selection (Download eFormat), so the other file format can be use.

PCHE: Chemistry Content

Low

PCHE-8452

Minor

Improved display of atom and bond labels containing both stereo type (abs, and, or) and chirality (R, S, M, P) or double bond geometry (E, Z). These labels are now displayed in two separate lines and with different colors.

PCHE: Chemistry Depiction

Low

PCHE-8634

Minor

Modified the spacing between Reagent molecules and labels to avoid overlap with atom label.

PCHE: Chemistry Depiction

Low

PCHE-8638

Minor

Fixed an issue where the SMILES Reader component failed with non-ASCII characters.

PCHE: PPChemAPI

Low

PCHE-8699

Minor

Modified molecule from InChI_AuxInfo to use the coordinates in the AuxInfo and always set the stereo centers in the output molecule as absolute. The chiral flag is turned on in the output molecule and the mol file. 

PCHE: File Formats

Low

PCHE-8701

Minor

Fixed an issue where Pipeline Pilot's Standardize Molecule component converted ABS stereo to AND Enantiomer.

PCHE: Chemical Perception

Low

PCHE-8708

Minor

Fixed issue in Enumerate Stereoisomers to make sure enumerated allenes and atropisomers have the chiral flag set to 1

PCHE: Chemical Perception

Low

PCHE-8712

Minor

·         MUL group no longer expanded by 2D-Coords like in the ExampleMul3.mol

·         For MUL SGroups without cross bond, fixed the depiction of the bracket so there is no overlap between the bracket and implicit hydrgen. (The issue in Mil75.mol)

·         For SGroups with more than two cross bonds, skip the recalculation of bracket coordinates in the PP Chemistry and Acoord 2D-Coords algorithm.

PCHE: Chemistry Depiction

Low

PCHE-8715

Minor

Fixed an issue where AND enantiomer query of one atropisomer stereo center matched a structure with undefined stereo in Pipeline Pilot substructure search.

PCHE: Query Mapping

Low

PCHE-8732

Minor

Added a new parameter to the Bad Stereo Filter component to check stereo wedges on atropisomers and allenes. Added a new action to the Standardize Molecule component, RepositionAxialStereoWedges, to fix the wedges if they are inconsistent.

PCHE: Chemical Perception, PCHE: Chemistry Depiction

Low

PCHE-8769

Minor

Updated SMILES Writer to prevent conversion of Hydrogen bonds (bonds of type 10 in molfile format) to single bonds when calculating SMILES strings. Hydrogen bonds are not supported in SMILES, they are now excluded from the SMILES strings. Updated SMILES Writer for molecules with Markush bonds. The bond between the star atom and the rest of the Markush fragment is now represented in the SMILES string as a single bond. This bond was not present in SMILES strings calculated in previous releases.  

PCHE: Chemical Perception, PCHE: File Formats

Low

PCHE-8782

Minor

A function is added to StructuerChecker class in PPChem API and PPChem SDK to check Markush bonds in valence checking. The Java function setCheckMarkushBondsInValenceCheck, C# function SetCheckMarkushBondsInValenceCheck, and Python function setCheckMarkushBondsInValenceCheck take a boolean argument as input and return no values. 

PCHE: PPChemAPI

Low

PCHE-8821

Minor

Modified the code in the PP SD Writer to add the Exact H Count query info read from the SMARTS string in the CTAB Atom block field, even in cases where all the SMARTS query features couldn't be translated into CTAB query features

PCHE: Chemical Perception, PCHE: Query Mapping

Low

PCHE-8848

Minor

Added a new parameter, "Don't Output Molecule If Valence Exceeded", to Enumerate Markush Bonds to control the behavior when valences are exceeded in the enumerated molecules.

PCHE: Enumeration

Low

PCHE-8853

Minor

Fixed an issue where calculation of Chemical Names using the OpenEye Lexichem libraries sometimes miss stereo marks (E/Z) for some double bonds.

PCHE: OpenEye

Low

PCHE-8906

Minor

Added a new check to the final stage of exact/flex mapping in the PLP components to compare the enhanced stereo definitions of query and target molecules. The two molecules need to either have enhanced stereo or don't have it, and if they both have enhanced stereo the relative groups should be the same.

PCHE: Query Mapping

Low

PCHE-8908

Minor

Fixed NEMA key calculation for sequences with expanded residues to avoid ignoring stereo in expanded parts of the sequence

PCHE: Biologics, PCHE: Chemical Perception

Low

PCHE-8994

Minor

Fixed an issue where molecules containing Markush bonds with RGroups failed to pass Register Check Filter.

PCHE: Chemistry Cartridge

Low

PCHE-9007

Minor

Cleaned up and fixed the PAINS Filter component to read the PAINS queries from a text file with SMARTS and removed the SD Reader component that was used in previous releases. The behavior for some PAINS queries might change because the SD Reader that was used before was not reading properly the query features. Fixed SD Reader to avoid possible crashes reading query feature properties coming from SMARTS strings

PCHE: Query Mapping

Low

PCHE-9016

Minor

Fixed an issue where FindMolecularFormat of MolIO class for PPChem Java SDK throws invalid memory access exceptions for strings that are generated by base64 decoding Smiles strings with length of a multiple of 4.

PCHE: PPChemAPI

Low

PCHE-9037

Minor

Fixed a problem in the depiction of sequences with expanded residues when the class of the expanded residue (AA, dAA, ...) was different than for previous contracted residues in the sequence chain.

PCHE: Biologics

Low

PCHE-9039

Minor

Fixed a problem in the Bond Properties component that could result in missing bonds when copying a bond property to an array. The problem was seeing in molecules with number of bonds greater than number of atoms and the property set on a bond with an index greater than Num_Atoms

PCHE: Chemical Perception

Low

PCHE-9045

Minor

Enabled the display of Library description of PLP libraries when list library from PP Pro Client and Webport.

PCHE: Hub Monomer Libraries

Low

PCHE-9054

Minor

The Qt library is updated to version 5.15.14 on Windows.

PCHE: Chemistry Depiction

Low

PCHE-9057
PCHE-9058

Minor

The SQLite library is updated to version 3.42.0.

PCHE: Other

Low

PCHE-9081

Minor

Modified SMILES Writer to preserve the bond type (Single, Double, Triple) of Markush bonds connecting fragments to variable attachment points when writing SMILES.

PCHE: Chemical Perception, PCHE: File Formats

Low

PCHE-9097

Minor

Modified logic inside the 2D Coords (Advanced) component to remove test for the presence of MUL Sgroups to send molecules to Cheshire 2D Coords and just use PP 2D Coords

PCHE: Chemistry Depiction

Low

PCHE-9098

Minor

BIOVIA Desktop Connector.msi is removed from Sketcher Integration release folder on PP server since it is no longer needed.

PCHE: Sketchers

Low

PCHE-9112

Minor

Fixed depiction of LINKER residues at the beginning or end of peptide sequences, where one of the attachments is not connected to a residue. In these cases the LINKER should be treated as a CHEM residue.

PCHE: Chemistry Depiction

Low

PCHE-9121

Minor

Removed ring with unusual N=S=N bonding pattern in the ring from the dataset used by Replace Ring Assemblies.

PCHE: Enumeration

Low

PCHE-9122

Minor

Fixed an issue that monomer chemistry cannot be edited in sequence view.

PCHE: Pipette

Low

PCHE-9144

Trivial

Modified the V3000 SD file parser, to allow 3 characters for the FIELDDISP line.

PCHE: File Formats

Low

PCHE-8412

Trivial

Modified the parsing of mutation information in SCSR DAT Sgroups and in HELM strings to handle cases where the original residue in the mutation is not defined.

PCHE: Biologics, PCHE: File Formats

Low

PCHE-8774

Trivial

Modified the PilotScript example code for the AtomNumExplicitHydrogens method to avoid double-counting explicit hydrogens

PCHE: Examples

Low

PCHE-9127

Major

When using TIFF (OCR) Reader with Tesseract, non-ASCII characters can now be read as long as the correct language option is provided to Tesseract.

TXT: Readers

Low

TXT-1078

Minor

If a Cross Tab component is written to a DOCX file, and then that file is inserted in to a second DOCX file using Add Content to Word Document, then the merged cells in the Cross Tab are not preserved. Only the first merged cell in the column is preserved.

TXT: Other

Low

TXT-1063

Minor

The Search Twitter components work again. However, any previous user of the component must re-generate their authorization key. Keys that were generated prior to April 29, 2023 no longer work after that date. To generate a new key, in the component parameters, click the "..." for the "Authorization Key" parameter and follow the instructions.

TXT: Search Online

Low

TXT-1080

Trivial

"Search US Patents" can perform searches. Due to a change by the USPTO of their authorization requirements, "Search US Patents" had stopped working as of May 2023.

TXT: Search Online

Low

TXT-1083

Trivial

Components have been updated to use new Microsoft Azure endpoints if a new key is provided, but still use Microsoft Cognitive Services if only an old MCS key is provided. Most users should update their keys to use the new Azure as soon as possible.

TXT: Search Online

Low

TXT-1084

Trivial

Standalone Sharepoint APIs are no longer supported by Microsoft. Instead, use: Search Sharepoint Online

TXT: Search Enterprise

Low

TXT-1088

Trivial

Search Wikipedia now works even if http is restricted on the server.

TXT: Search Online

Low

TXT-1092

Severity

Description

Areas Affected

Risk

Defect

Minor

A failure to write mdl files in the example protocol "NMR Predictions and Assignments" has been fixed.

AIC: AIC

Low

AIC-1467

Major

Protocols in the Polymer, Battery and Classical Simulation folders now correctly run in parallel on servers with a queuing system.

MSC: Examples

Medium

MSC-6640

Major

Forcite and Mesocite components now check that the summation method selected is supported on GPUs.

MSC: Application

Low

MSC-6667

Minor

MaterialsScript object ownership by Perl MaterialsScript (on Server) components has been modified so that memory cleanup is done correctly at the end of protocol execution.

MSC: Infrastructure

Low

MSC-5237

Minor

Rare failures of Find Symmetry when using large tolerances.

MSC: Infrastructure

Low

MSC-5305

Minor

Materials Studio Forcite and Mesocite now use higher resolution random seed generator for assignment of random velocities in dynamics simulations.

MSC: Other

Low

MSC-6641

Minor

Calculate Semiconductor Band Offsets protocol help for Pseudopotentials parameter is extended to cover all available options.

MSC: Documentation

Low

MSC-6661

Minor

Calculate Equation of State for Solids protocol now uses more strict calculation settings leading to a more robust behaviour and more accurate results.

MSC: Application

Low

MSC-6666

Minor

Writing archived study table (*.std.zip) now works with any permitted path.

MSC: Infrastructure

Low

MSC-6761

Trivial

In the Calculate Stress-Strain Curves protocol the application of a supercell operation is now made optional.

MSC: Other

Low

MSC-6446

Trivial

Orientation of the 2D cell in the PhaseField protocols have be changed from XY plane to XZ plane in order to accommodate continuous nucleation at the bottom of the cell. The random grain nucleation have been shifted to XY plane at z=0 to conform with the continuous nucleation option. 

MSC: Phase Diagrams

Low

MSC-6541

Trivial

Error messages coming from the Materials scripting layer of the materials studio collection are now more concise and relevant to the actual problem.

MSC: Infrastructure

Low

MSC-6700

Severity

Description

Areas Affected

Risk

Defect

Minor

Now, the Extract Section Content component handles situations where multiple files are uploaded to one section.

ANC: API

Low

ANC-285

Severity

Description

Areas Affected

Risk

Defect

Minor

In the example protocol Morphology Screening B the result files of the morphology screening job was not copied completely into the results zip file, which was fixed for this release. The caused the workflow to fail if the protcol was modified and run several time with in a row. The functionality of the components was not affected. A workaround was available (use of the morphology screening components and not the example protocol).

SOLCHEMC: COSMOtherm

Low

SOLCHEMC-224