T50-2021 Notification regarding BIOVIA Pipeline Pilot 2021 Service Pack 1

PPC-10049

The OpenSSL library used in Pipeline Pilot has been updated to the latest available 1.1.1 version

PPC-10007

Foundation Hub now sends Pipeline Pilot notifications when users directly log out of Foundation Hub so that matching Pipeline Pilot sessions can also be terminated. This eliminates an issue where logging out of Foundation Hub would result in a delay before the Pipeline Pilot session would become invalid.

PPC-46717

Some additional settings have been exposed in the server settings to control the maximum allowed file name length for uploaded files, and an option to customize error stack reports.

PPP-45952

The version of PDFBox used by this component has been updated to 2.0.23 to better handle some specific PDF formats.

PPP-46672

Updated the icon displayed in Pipeline Pilot web server pages.

PCHE-7166

Added a new method "attachToSuperatom" to attach an existing Custom Data (DAT SGroup) to an existing Super atom (SUP SGroup). This method is accessed from the CustomData class and is available from the Java, .NET, and Python PP Chemistry SDK.

PCHE-7928

Added an example protocol, "Convert Sequences with Modified Residues to SCSR Templates", to illustrate how to use the "Convert SUP Sequences to SCSR" component. The protocol processes sequences containing expanded residues represented by SUP groups, creates any templates missing in the default global templates, and converts all SUP residues in the sequence to SCSR templates.

PCHE-8098

Added a new method "LoadCustomElementTable" to enable the use of a custom PTable in both the Java and Python Chemistry SDKs. (Also present in version 2021 HF1)

PCHE-8100

Improved the conversions between HELM and SCSR sequence representations:

Ÿ Support for N-terminal and C-terminal SCSR templates in peptide sequences, similar to the terminal PEPTIDE monomers in HELM. This eliminates the need to include inline SMILES to represent the terminal residues in the HELM strings when converting back from SCSR, resulting in a cleaner conversion.

Ÿ Improved handling of LINKER SCSR templates and conversion to CHEM monomers in HELM.

Ÿ Depiction changes to handle terminal residues in peptide sequences.

Ÿ Added support for capping groups in HELM monomers having more than a single atom.

Ÿ Improved orientation of some of the HELM monomers and SCSR templates in the global configuration files to obtain better depictions in expanded state.

Ÿ Added more examples of C-terminal monomers and templates to the default global configuration files.

Ÿ Added example protocols to illustrate how to process and optimize the orientation of HELM monomers and SCSR templates and added them to global configuration files. The two example protocols are "Processing Custom Residues to Create Configuration Files" and "Align HELM Monomers From a SD File".

PCHE-8133

The Chemistry Sketcher now works with ChemDraw 20.

PCHE-8135

Starting in the PP Chemistry 2021 release, Num_Rings and Num_Fragments include all rings and fragments found taken into account both covalent (Single, Double and Triple bonds) and zero-order bonds (Coordination and Hydrogen bonds). The following new counters only take into account covalent bonds. They reproduce the behavior of Num_Rings and Num_Fragments prior to the 2021 release:

1) Counters as calculable properties in Molecular Property Counts and as Molecular Toolkit and PPChem SDK methods

Ÿ Num_RingsOnlyCovalentBonds

Ÿ Num_RingAssembliesOnlyCovalentBonds

Ÿ Num_FragmentsOnlyCovalentBonds

2) Molecular Toolkit and PPChem SDK methods to check if a ring or fragment has only covalent bonds

Ÿ RingHasOnlyCovalentBonds

Ÿ RingAssemblyHasOnlyCovalentBonds

Ÿ FragmentHasOnlyCovalentBonds

PCHE-8168

We now check the names of HELM monomers for special reserved characters before adding them to centralized libraries. Parentheses and commas are allowed, but "$ { } | - : [ ]" are not.

PCHE-8184

Changed the coordinate of atoms in 45 SCSR Templates and their mapping HELM Monomers. These include:

Ÿ 31 HELM RNA Monomers, (1 Base, 5 Phosphate, 25 Sugar SCSR Templates)

Ÿ 8 HELM Peptide Monomers, (8 SCSR Terminal AA Templates)

Ÿ 6 HELM CHEM Monomers, (1 CHEM, 5 LINKER AA Templates)

Aligned Monomers/Templates:

PCHE-8204

Removed an old file with Draw 4.1 SCSR templates (Draw41Templates.mol) from data/HELM folder. This file is not used by any component and contains obsolete templates.

ANC-229

The Experiment Query component now supports searching by countersigned date.

ANC-261

Editing a project section has been extended with functionality to append a project to the ones already in the section as well as clearing all the projects from a section.

ANC-263

It is now possible to retrieve simple section data when querying experiments using the Experiment Query, Experiment Query (Advanced), or Experiment Query by Structure components.

PPP-46254

Fixed an issue where a change to the SameSite Restriction on Session Cookies was not being reflected in the session cookie attributes.

PPP-46724

Fixed an issue with the 2021 Professional Client where scheduling a job from the UI would always schedule the protocol with the default protocol parameter values regardless of any changes made to the parameter values within the dialog. It was similarly not possible to edit the protocol parameter values for any existing scheduled jobs shown within the Jobs tab. If the protocol did not have any required parameters, the scheduled job would execute successfully but with the default values instead of the requested values.

PPD-2827

Fixed an issue where the installer for Pipeline Pilot 2021 did not install the BIOVIA SQL Server 8.0 driver correctly.

PPC-10013

Fixed an issue with Reporting form components, where the Work Protocol (or Protocol Function) are set to "Run as Anonymous User" would result in a "400 Bad Request" failure with the error message "No Protocol Specified" during form submission from a client that was not already logged in as an existing Pipeline Pilot user.

PPP-46469

Upgraded the request signing version used for accessing AWS resources, to support all geographic regions.

PPP-46362

Fixed a problem in the AWS List Files component when encountering some special characters in S3 folder names.

PPP-46361

Fixed an issue where the SQL components did not handle trailing "--"-style comments correctly, if those were not followed by a newline character, which led to crashing protocols.

PPC-9945

Fixed ability of non-administrative users to access Pipeline Pilot data sources via Query Service.

DSB-2315

Fixed an issue where users were unable to logon to DSBuilder when the SSL/TLS Security Level is set to Intermediate in the Pipeline Pilot Server configuration page.

PCHE-8124

Added documentation to the Java SDK in the use of the SGMap class. The setTarget method should be called after the addQuery method. Absent this order, a memory leak can result.

PCHE-8154

The certificate for the legacy plugin SSL communication is renewed to March 26, 2022. This is only relevant if the Desktop Connector is set to Legacy Mode.

PCHE-8220

Fixed an issue of deserializing molecules serialized by previous versions of PPChem. The issue caused incorrect reading of zero-order bonds, Markush bonds, and haptic (pi) bonds from binary representations of molecules stored in cache or Pipeline Pilot Chemistry format and created by previous releases of PPChem.

PCHE-7751

We now create an empty molecule MDL SKC formatted output when the molecular data passed into Sketcher Integration is not an MDL SKC.

PCHE-8128

When the user clicks Connect this browser in a Chromium-based version of Edge, Sketcher now correctly connects to Edge. Previously, it sent its cookie to Chrome.

PCHE-8205

Removed the requirement for a terminal slash "/" in the Pipette Biosketcher and Pipette Monomer Report URLs. Now they can be called with or without the slash, same as for the Pipette Sketcher URL.

PCHE-8172

Fixed the Pipette Help button at the lower-right corner in the Pipette Sketcher to point to the correct ScienceCloud location.

ANC-265

Authentication using Pipeline Pilot session tokens is now successful even if the api2 endpoint has not been defined on the Notebook server.