T13-2024 Notification regarding BIOVIA Pipeline Pilot Chemistry SDK 2024 SP1

Description

Areas Affected

Risk Level

Jira Issue ID

Moved the "Count Sgroup Features" component from Manipulators folder to Calculators folder

PCHE: Property Calculators

Low

PCHE-7781

Enumerate Tautomers now takes into account atoms included in an optional property named DontMapAtoms. Atoms in this list are not included in the tautomerization.

PCHE: Chemical Perception, PCHE: Enumeration

Low

PCHE-9197

Pipette now allows custom HELM monomer sets to be used with the HELM to PNG component.

PCHE: Pipette

Low

PCHE-9239

Added a function in the Molecule Class: 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 the Bond Class: SwapAtoms() to swap the atom1 and atom2 for a bond.

PCHE: Molecular API

Low

PCHE-9260

Added a new option to the "Enumerate Tautomers (InChI2 Transforms)" component to output the number of non-overlapping substructures in the input molecule mapped by the tautomer transformation reactions, without doing the full enumeration. This can be helpful to avoid enumerating tautomers for molecules with many mappings, which can potentially generate a very large number of tautomers and take significant computational time. Added also a new API to the PPChem SDK (Java, Python and .NET versions) to calculate this new counter.

PCHE: Chemical Perception, PCHE: Enumeration

Low

PCHE-9270

Description

Areas Affected

Risk Level

Jira Issue ID

Pipette now supports toggling of E/Z, M/P, and R/S stereochemistry labels.

PCHE: Pipette

Low

PCHE-9216

You can now insert extended atom types from the bottom of the periodic table (A, D, M, Mod, Pol, Q, T, and X).

PCHE: Pipette

Low

PCHE-9218

Pipette now allows custom HELM monomer sets to be used with the HELM to PNG component.

PCHE: Pipette

Low

PCHE-9239

Major

Fixed the SMARTS Reader to parse correctly two-character elements in which the second character is 'e', 'r' or 'a'. This list includes Na, Ca, Ba, Ra, Ga, La, Ta, Pa, Be, Ce, Re, Fe, Ge, Se, Te, Xe, Ne, He, Fr, Sr, Zr, Ir, Er, Ar, Kr, Lr, Cr, Pr, Br. The SMARTS reader was parsing the second character as a special case of CACTVS extensions.

PCHE: Chemical Perception, PCHE: Query Mapping

Low

PCHE-9251

Minor

The 2D coordinates generated for stereo carbons with four explicit bonds are fixed to place the wedge on a bond that does not cause ambiguity and is IUPAC compliant.

PCHE: Chemical Perception, PCHE: Chemistry Depiction

Low

PCHE-8688

Minor

The structure of Rmp, Rsp, Smp, Ssp phosphate HELM Monomers, and SCSR templates are updated. The stereo wedge bond is moved from a bond between the leaving atom and the phosphate atom to the bond between a non-leaving atom and the phosphate atom.

PCHE: Hub Monomer Libraries

Low

PCHE-9201

Minor

Added terms to the calculation of the score value used to sort query residues to take into account the number of stereo atoms. This way residues with more stereo atoms are mapped before other residues with the same number of atoms. Also, incremented the score for D-amino acidd in general, so they are mapped before other non-natural amino acids.

PCHE: Biologics, PCHE: Chemical Perception

Low

PCHE-9211

Minor

Modified "Synthetic Accessibility (SAscore)" component to prevent potential numerical overflows when using fragment fingerprints data files with very large frequencies of occurrence (in the hundreds of millions)

PCHE: Property Calculators

Low

PCHE-9287

Severity

Description

Areas Affected

Risk

Defect

Major

Modified the conversion of granular RNA SCSR representation to HELM strings to avoid using SMILES for representing granular nucleotides without a base. This is necessary because the sugar has only two attachment points to phosphates.

PCHE: Biologics, PCHE: File Formats

Low

PCHE-9159

Severity

Description

Areas Affected

Risk

Defect

Minor

SCSR reactions are now displayed with dynamically calculated sequence block widths. Previously, blocks were always ten monomers wide.

PCHE: Pipette

Low

PCHE-9140

Minor

SCSR files with more than four R groups now load correctly when there is nothing attached to the R groups.

PCHE: Pipette

Low

PCHE-9177