T55-2025 Pipeline Pilot Chemistry SDK 2026

Release of BIOVIA Pipeline Pilot Chemistry SDK 2026

NOV | 27^th, 2025

Program

BIOVIA Pipeline Pilot Chemistry SDK

Operating System

All supported operating systems

Description

We are providing this Technical Note to inform you about the release of BIOVIA Pipeline Pilot Chemistry SDK 2026 which includes the following enhancements and fixed defects:

Enhancements

This release of BIOVIA Pipeline Pilot Chemistry SDK includes the following enhancements.

Description	Areas Affected	Risk	Issue ID
If axial enhanced stereo is present on allene group, switch to PP stereo perception option instead of NEMA option. Modified a backend function in vcMolecule to detect both edge and central allene atoms, this function was not used before in the code, so the change is safe.	PCHE: Molecular API	Low	PCHE-10008
Support of the enhanced stereochemistry is enabled by default when writing SMILES in Pipeline Pilot Chemistry Collection and Pipeline Pilot Chemistry SDK.	PCHE: PPChemAPI	Low	PCHE-10080
Implemented the vcMolecule::atomAlterExplicitValency() method to allow altering the explicit valence set by the user. To support this, added the vcAtom::SetUserDefinedValence() helper function for setting user-defined valency values on atoms. Updated the Pilot Script Molecular Toolkit to include the MolAtomAlterExplicitValency() function to utilize the new method.	PCHE: Molecular API, PCHE: PPChemAPI	Low	PCHE-9035
Added CNS MPO calculator as a new component in ADME chemistry package.	PCHE: PPChemAPI, PCHE: Property Calculators	Low	PCHE-9669
Implemented a new function in the Molecule class to support allene stereochemistry: findStereoAndNonStereoAlleneCenters(): Identifies both stereogenic and non-stereogenic allene centers in the molecule. Once this function is invoked, all other allene-related methods listed below will reflect information for non-stereogenic allene centers as well: # getNumAlleneCenters() # getAlleneAtoms() # getAlleneBonds() # getAlleneDistance() # getAlleneEndpoint1() # getAlleneEndpoint2() # getAlleneStereoParity()	PCHE: Chemical Perception, PCHE: PPChemAPI	Low	PCHE-9870

Fixed Defects

This release of BIOVIA Pipeline Pilot Chemistry SDK includes the following fixed defects.

Severity	Description	Areas Affected	Risk	Defect
Critical	Fixed an issue where data folder is missing in Pipeline Pilot Chemistry Python SDK wheel packages and setting of IsotopeDataFilePath is not working in Python SDK.	PCHE: Other	Low	PCHE-10203
Major	Fixed the issue of matching AND and OR isomers when setting flexmatch using full settings string instead of 'match=all'. Flexmatch string settings bug will be addressed in PCHE-10082.	PCHE: PPChemAPI, PCHE: Query Mapping	Low	PCHE-10060
Major	Setting flexmatch switches behavior is not changed, and setting them resets the mapper. Instead, the behavior is properly documented in the help for API of ExactMap.setFlexMatchString: "Set the FLEXMATCH switches to use for matching." was changed to "Set the FLEXMATCH switches to use for matching. As a side effect, resets the mapper." The decision to keep the old behavior unchanged was due to the fact that a lot of developer-oriented code, as well as tests, relied heavily on the old behavior of setFlexMatchString	PCHE: Chemical Perception	Low	PCHE-10082
Minor	The following are fixed: The mapping and matching methods of ExactMap SDK (canMap, isMatch, etc) not recognizing match=all ExactMap SDK not working correctly due to bugs in implementation The backend function of ExactMap (the same as in PP Client) producing erroneous results for matching of isomers with Absolute configuration of allene group and enhanced stereo of sp3 center Note: Defining flexmatch after adding query resets the mapper and fails to produce matching was documented as a feature.	PCHE: Chemical Perception	Low	PCHE-10062
Minor	RegisterCheck of Pipeline Pilot Chemistry SDK no longer causes access violation exception for a particular reaction.	PCHE: PPChemAPI	Low	PCHE-10191

Resolution

BIOVIA Pipeline Pilot Chemistry SDK 2026 was released in November 2025 and is available for download at https://software.3ds.com under BIOVIA products:

Product line: Lab, Scientific and Content Solutions

Release: BIOVIA 2026

Level: BIOVIA 2026 Golden

Fixes for this level: N/A

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