T70-2023 Notification regarding BIOVIA Pipeline Pilot Chemistry Collection and SDK 2024

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 ChemDraw 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

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 Web Port, with the following functionality:

·         Visualized the three configuration files in the Web Port,

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

·         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 also 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

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 Web Port and PP Pro Client.

PCHE: Hub Monomer Libraries

Low

PCHE-9044

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 are archived in the "Centralized_Library_Action_Log" library. 

PCHE: Hub Monomer Libraries

Low

PCHE-8958

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

Description

Areas Affected

Risk Level

Jira Issue ID

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

Description

Areas Affected

Risk Level

Jira Issue ID

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

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

PCHE: Pipette

Low

PCHE-8882

Grouped templates such as Cycloheptane, 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

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

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 don't 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 '[A,a]~[A,a]'.

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 Process 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

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

Minor

Fixed the depiction of implicit hydrogen 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 Web Port.

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

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

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

A function is added to StructureChecker class in PPChem API and PPChem SDK to specify whether to check marked stereo on nonstereo 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

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

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

Severity

Description

Areas Affected

Risk

Defect

Minor

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

PCHE: Chemical Perception

1 (Low)

PCHE-8712

Minor

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

PCHE: Pipette

1 (Low)

PCHE-9144