Allene-like stereo and atropisomeric stereo are now supported in ppchemapi's and PPChem SDK's SMILES reader and writer. The stereo is marked with @ or @@ on the central carbon of allene-like molecules and on the first atom in canonical order of the single bond of hindered rotation of atropisomers. The chirality center is marked with @ for P helicity and @@ for M helicity. "Parse Axial Stereo" parameter has been added to "SMILES Reader" and "Molecule from SMILES" components to specify whether to parse axial stereo in SMILES or not. "Include Axial Stereo" parameter has been added to "SMILES Writer" and "Molecule to SMILES" components to specify whether to output axial stereo or not.

PCHE: Chemical Perception

Low

PCHE-3515

Added PAINS Filter component to the Chemistry Collection. The new filter checks the input molecules for the presence of substructures included in the list of undesirable fragments in the publication "New Substructure Filters for Removal of Pan Assay Interference Compounds (PAINS) from Screening Libraries and for Their Exclusion in Bioassays". Jonathan B. Baell and Georgina A. Holloway. J. Med. Chem. 2010, 53, 7, 2719-2740.Added "Num_PAINS" as a calculable property in Pipeline Pilot. Added two methods in Chemistry SDK (Java, .NET and Python) MolPropCalc class to set the location of the PAINS query .sd file and calculate the number of PAINS query mapped in a molecule.

PCHE: Query Mapping

Low

PCHE-5696

Expanded the tautomeric atom donor perception criteria: 1. O S Se and Te atom can be a donor when their next attach atom is a SP2 tautomeric atom. 2. C atom can be a donor when it is attached to an aromatic C atom. These perception is included in the "Apply Perception Enhancements 2022" parameter of the Tautomer generation and identification components.

PCHE: Chemical Perception, PCHE: Enumeration

Low

PCHE-6587

New methods have been added to PPChem SDK to get atoms and bonds that satisfy a predicate. Java SDK APIs are public int[] getAtoms(Function predicate) and public int[] getBonds(Function predicate). Dotnet SDK APIs are public abstract int[] GetAtoms(Func predicate) and public abstract int[] GetBonds(Func predicate). Python SDK APIs are getAtomsPredicate (self, predicate) and getBondsPredicate (self, predicate).

PCHE: PPChemAPI

Low

PCHE-6857

Improved the 2D layout of molecules with Markush bonds and Haptic bonds.

PCHE: Chemistry Depiction, PCHE: Pipette

Low

PCHE-6862

Added table with AlogP atom classification types to the help text of the "AtomAbstraction" parameter in the "Molecular Fingerprints" component. 

PCHE: Property Calculators

Low

PCHE-7743

Added P and S atoms as a SP2 type tautomer atom when they have double bonds. Added tautomer score to PO and PS double bonds.

PCHE: Chemical Perception

Low

PCHE-7842

A new component, HELM to PNG, is provided as a prototype to allow server-side generation of Pipette Biosketcher monomer view images. 

PCHE: Biologics, PCHE: Chemistry Depiction

Low

PCHE-7896

Fixed PPChem 2D-Coords clean crash with Markush bond in a structure repeat unit. 

PCHE: Chemical Perception

Low

PCHE-8043

PPChem Python SDK wheel packages are available for both Windows and Linux systems and can be used to install the PPChem Python SDK fast and effortlessly.

PCHE: Usability

Low

PCHE-8165

Added support for reagents in SMIRKS strings to the Pipeline Pilot "SMIRKS Reader" and "Reaction for SMIRKS" components and to the PPChem SDK

PCHE: File Formats

Low

PCHE-8274

Improved the positioning of subscripts in atom labels to reduce the spacing between the subscript number and the atom type

PCHE: Chemistry Depiction

Low

PCHE-8386

Improved perception and depiction of RNA sense/antisense chains read from HELM strings. When possible, the complimentary bases in the two chains are properly aligned.

PCHE: Biologics

Low

PCHE-8410

*Tautomer Perception and Score enhancements added in 2023* # Expand the atom tautomer donor classification: * O, S, Se, Te atom As Donor: extending the attach atom has double bond condition * C atom as Donor: allow attached C atom being aromatic. # Add P atom as tautomeric in structures like O=P-SH and HO-P=S. Making P an SP2 atom. # Add S atom tautomeric valence change between II and IV. For example: in O=S-H, S is a donor, while in -S-O-H: S is an acceptor. # Tautomer Score Changes for Canonical Tautomer * Modify Keto O atom score from 1.0 to 1.1 * Add Thio-Keto type S, Se atom score 1.0 * Add Tautomer Score for P=O bond (score = 2.0) and P=S bond (score = 1.0) * Add Score for S=O double bond = 1 Added a new parameter "Apply Perception Enhancement 2023" to the PPChem components (Generate Tautomer, Calculate tautomer Score).  Added a setter method to the Generate Tautomer class in the Java, Python and .NET SDK.  * SetApplyPerceptionEnhancements2023(boolean applyEnhancements2023) method in .Net SDK  * setApplyPerceptionEnhancements2023(boolean applyEnhancements2023) method in Java and Python SDK. Setting "applyEnhancements2023" to true to use the 2023 tautomer enhancements. Setting "applyEnhancements2023" to false to keep the SDK behave the same as in 2022 release and before.

PCHE: Chemical Perception, PCHE: Enumeration, PCHE: PPChemAPI

Low

PCHE-8428

Both the PPChem SDK and the Java FixMol example protocol will be installed in a Pipeline Pilot server if a user has a PPChem SDK license, whereas neither will be installed if a user does not have a PPChem SDK license.

PCHE: Molecular API

Low

PCHE-8445

Added error values for the atomic weight and the exact mass (weight of the most common isotope) to the internal elements table in PP Chemistry. Added Molecular_Weight_Error and Molecular_Mass_Error as calculable properties in the Molecular Weight component. Added apis to the Java, .NET and Python PPChem SDK to calculate molecular weight and molecular mass errors.

PCHE: Molecular API

Low

PCHE-8453

A new API SetChemicalNameInputLanguage (DotNet), setChemicalNameInputLanguage (Java), setChemicalInputLanguage (python) has been added to MolIO class of PPChem SDK to set input language of chemical names.

PCHE: Molecular API

Low

PCHE-8464

Two new Output options, MDLQueryKeys960 and MDLQueryKeys166, are added to the MDL Key Fingerprints component. They are also available as calculable properties.

PCHE: Property Calculators

Low

PCHE-8475

Added a set of common ring systems consisting of two rings connected by a single bond to the data file used by the "Replace Ring Assemblies" component. Added an option to allow this type of ring systems as ring replacements to the "Ring Types" parameter in the component. This new option is unchecked by default.

PCHE: Enumeration

Low

PCHE-8476

Implemented a new component, "Enumerate Tautomers(InChI2 Transforms)" to generate tautomers using a set of transformations described in "Toward a Comprehensive Treatment of Tautomerism in Chemoinformatics Including in InChI V2", Devendra K. Dhaked, Wolf-Dietrich Ihlenfeldt, Hitesh Patel, Victorien Delannée, and Marc C. Nicklaus, J. Chem. Inf. Model. 2020, 60, 1253−1275. The new functionality is also available in the PPChem SDK 

PCHE: Chemical Perception, PCHE: Enumeration

Low

PCHE-8496

Added support for SMARTS CACTVS extensions to the SMARTS and SMIRKS readers, including * "e": ring pi electron count of all ESSSR rings the atom is part of * "z": number of heteroatoms connected to the atom * "a" number of aromatic rings the atom is a member of * "\{n1-n2}, \{n1-}, \{-n2}: ranges of numeric values instead of a single value for some of the counters Fixed SMARTS reader to assign correct bond query features to single and double bonds that connect atoms that could be aromatic or aliphatic  

PCHE: Query Mapping

Low

PCHE-8497

Improved sketching and positioning of salt fragments in molecules and reactions in Pipette Sketcher. 

PCHE: Pipette

Low

PCHE-8501

The zlib library in PPChem is updated to the latest version (1.2.12) in which security vulnerabilities associated with previous versions are fixed.

PCHE: OpenEye

Low

PCHE-8502

Improved the Generate Scaffold Tree component to preserve stereochemistry at attachment points when R alpha atoms are added to track where substituents were removed from the parent molecule. 

PCHE: Chemical Perception, PCHE: Enumeration

Low

PCHE-8556

Fixed the conversion of HELM strings containing terminal CHEM monomers to SCSR to avoid perceiving the terminal CHEM monomers as starting a new peptide chain. Now they are included in the same peptide chain where they appear as a N-terminal or C-terminal residue. 

PCHE: Biologics

Low

PCHE-8565

Added a new parameter "Set SCSR Leaving Atom Coordinates With R Atom" to the "HELM Monomer to SCSR Template" component. When "Set SCSR Leaving Atom Coordinates With R Atom" is "True",  the component uses the HELM monomer R atom coordinates as the explicit leaving group atom coordinates. The default for "Set SCSR Leaving Atom Coordinates With R Atom" is "False", where the leaving atom coordinates are generated automatically,  the same as in earlier versions.

PCHE: Chemistry Depiction, PCHE: Hub Monomer Libraries

Low

PCHE-8576

The OpenEye MetaChem library is updated to version 1.6.0.

PCHE: OpenEye

Low

PCHE-8594

Update the "Search Library By Property" protocols with new "Search Entries by Names (PLP)" and "Search Entries by Names (HUB)" components to enable optional parameters searching for HUB and PLP libraries. Added "Search Results Output" parameter to the "Search Library By Property" and "Search Library By substructure" protocols to write out the search results to a sd file.

PCHE: Hub Monomer Libraries

Low

PCHE-8598

Updated criteria for enclosing text fields within double quotes when writing in V3000 molfiles when any of these characters appear anywhere in the text:  space, quote, double-quote, equal sign, left parenthesis and right parenthesis. Harmonized behavior with BIOVIA Draw and Pipette Sketcher.

PCHE: File Formats

Low

PCHE-8647

Added three new parameters to Replace Ring Assemblies component. Keep Exocyclic Double Bonds: When set to True, exocyclic double bonds present in the original ring assembly are always reattached to the new ring assembly. When set to False, exocyclic double bonds are not reattached, allowing the replacement of ring assemblies with exocyclic double bonds by ring assemblies that do not have them. Allow Multiple Attachments to Same Ring Atom: When set to False, open positions in the new ring assembly can only be connected to one of the original attachments. When set to True, one or two attachments can be connected to the same ring atom, if it has enough open valences. Keep Attachments to Same Ring Atom Together: When set to True, attachments that are connected to the same ring atom in the original molecule are kept together when they are reattached to a new ring assembly. When set to False, these fragments can be attached to different ring atoms in a new ring assembly.

PCHE: Enumeration

Low

PCHE-8674

Optimized the 2D coordinates of molecules with Markush bonds and Haptic bonds.

PCHE: Chemistry Depiction

Low

PCHE-7728

Made changes in the PP Chemistry V3000 SD Reader and SD Writer to make sure that the Chiral flag in the M V30 COUNTS line is consistent with the stereo collections present in the molecule. The Chiral flag is set to one if the molecule has absolute chirality as indicated by the presence of only one stereo collection of type STEABS. In all other cases (AND Enantiomer, OR Enantiomer or Mixed stereo) the chiral flag is set to zero in V3000 mol files. Before these changes, V3000 molfiles for molecules with Absolute stereo (as indicated by the STEABS collection)  had the chiral flag in the M V30 COUNTS line set to zero. Note: the counters and chiral flag in the fourth line in the header of V3000 mol files (0 0 0 0 0 999 V3000) are always set to zero and ignored when reading the file.

PCHE: Chemical Perception, PCHE: File Formats

Medium

PCHE-8593

Take into account relative stereo groups (enhanced stereo) in the perception of meso symmetry. Molecules that would have been classified as meso are no longer perceived as meso if they have  enhanced stereo. This change affects the Meso Chirality component and PPChem SDK meso APIs, as well as the chiral labels display in molecular depictions.  

PCHE: Chemical Perception

Medium

PCHE-8597

Take into account relative stereo groups (enhanced stereo) in the perception of meso symmetry. Molecules that would have been classified as meso are no longer perceived as meso if they have  enhanced stereo. This change has implications for Exact and Flexmatch searches that take into account stereo, as molecules with enhanced stereo that were perceived as meso before are now considered chiral and might not match similar molecules with different stereo.

PCHE: Chemical Perception

Medium

PCHE-8619

Critical

Fixed Perceive Sequence From Structure to avoid running into infinite loops for unusual use cases, such as trying to perceive the sequence for small molecules with no known residues.

PCHE: Biologics, PCHE: Chemical Perception

Low

PCHE-8658

Critical

Fixed Perceive Sequence From Structure to avoid running into infinite loops for unusual use cases, such as trying to perceive the sequence for small molecules with no known residues.

PCHE: Biologics, PCHE: Chemical Perception

Low

PCHE-8659

Major

Removed eMolecules from the list of public websites used to convert names to structures in the "Molecule from Name" component. The site can't be access for this purpose without a valid account. The component now contains only DiscoveryGate, NCI/CADD, ChemSpider and PubChem as available sites to select.

PCHE: Chemistry Content

Low

PCHE-8375

Major

Fixed a problem calculating coordinates for expanded granular RNA residues in Clean SCSR Sequence. Added options to Expand SCSR Sequence to clean the sequence after the expansion.

PCHE: Biologics, PCHE: Chemistry Depiction

Low

PCHE-8443

Major

Perceive Sequence from Structure. Fixed the logic to identify LGRP SUP groups to make it more general and cover more use cases. The code was missing cases of Oxygen atoms attached to AA sidechains other than the natural residues D and E.

PCHE: Biologics, PCHE: Chemical Perception

Low

PCHE-8472

Major

Fixed the inconsistency by correcting initialization in the code. (The observed inconsistency is because the first molecule has an atropisomer which caused the 2nd molecule to crash)

PCHE: Chemical Perception

Low

PCHE-8485

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

Added a new parameter to the Generate Scaffold Tree component to control whether fused aromatic rings should be split into smaller rings.

PCHE: Enumeration

Low

PCHE-8555

Major

PPChem SDK Python API references in Pipeline Pilot server are working now.

PCHE: Documentation

Low

PCHE-8570

Major

A problem perceiving aromaticity of six-member rings containing atoms such as sulfur or phosphorus with alternating single and double bonds has been corrected. In previous releases, the perceived aromaticity could depend on the positioning of the double bonds. Now, the aromaticity is perceived identically, regardless of their positions. A previous fix in the 2019 release has a partial fix for the same issue.

PCHE: Chemical Perception

Low

PCHE-8589

Major

Made changes in the PP Chemistry V3000 SD Reader and SD Writer to make sure that the Chiral flag in the M V30 COUNTS line is consistent with the stereo collections present in the molecule. The Chiral flag is set to one if the molecule has absolute chirality as indicated by the presence of only one stereo collection of type STEABS. In all other cases (AND Enantiomer, OR Enantiomer or Mixed stereo) the chiral flag is set to zero in V3000 mol files. This change addresses inconsistencies in the treatment of stereo information by some PP Chemistry manipulator components.

PCHE: Chemical Perception, PCHE: File Formats

Low

PCHE-8617

Major

Modified the positioning and font size for depicting the reactant and product labels in reactions: * Set minimum and maximum values for the font size used to display the labels (5 and 20) * Moved reactant and product labels closer to the bottom of the image

PCHE: Chemistry Depiction

Low

PCHE-8625

Major

Perceive Sequence from Structure. Fixed a bug in the creation of SUP LGRP groups where the label for C-terminal Oxygen atoms was set to "H" instead of "OH"

PCHE: Biologics, PCHE: Chemical Perception

Low

PCHE-8629

Major

Added identification of molecules with Markush system crossing a repeat unit, so the molecule of this type will pass unchanged from PP Chem "2D Coords" component.

PCHE: Chemical Perception

Low

PCHE-8631

Major

Fixed URL used in "Molecule from Name (NCI_CADD)" to get a molfile for a structure based on a name or other identifier. The URL search string needed to be updated after a recent change in the website.

PCHE: Chemistry Content

Low

PCHE-8648

Major

Fixed a bug where the M/P stereo centers were misplaced for axial stereo when generating structures from Smiles.

PCHE: Chemistry Content

Low

PCHE-8687

Minor

Fixed the depiction of Markush bond in bracket, the depiction of variable repeat units. The round bracket is converted to a square bracket in PPChem depiction.

PCHE: Chemistry Depiction

Low

PCHE-6148

Minor

Modified the code that identifies molecular formats in input strings (used by "Molecule from Text" and "Identify Molecular Formats" component) to check specifically for Accord Hex format instead of decoding generic Hex strings, which can lead to false-positive identification of some strings as SMILES or SMARTS.

PCHE: Molecular API

Low

PCHE-7504

Minor

Added a test to verify that the number of characters in the string is a multiple of 4 to the PPChem SDK MolIO method that checks if a string could be Base64-encoded. The method can't be made totally fool-proof without trying to decode the potential base64 string, which will be too expensive. Applications can always call the available method to decode the Base64 string to verify. This function throws an exception that the application can catch.

PCHE: Molecular API

Low

PCHE-7514

Minor

Improved rendering and layout of molecules and reactions with haptic systems in Pipette Sketcher

PCHE: Chemical Perception, PCHE: Chemistry Depiction, PCHE: PPChemAPI

Low

PCHE-7778

Minor

The Generate Maximal Common Substructure component now rejects all partial rings correctly.

PCHE: Chemical Perception

Low

PCHE-8012

Minor

Made general improvements to the "Clean SCSR Sequence" component to try to preserve the average bond length in the original input structure by setting the parameter "Distance Between Residues" to zero. Also, improved the calculation of the X coordinates of the residues in the sequence to handle long residue names.

PCHE: Biologics

Low

PCHE-8059

Minor

Added support for Chemdraw  binary format in ReadReaction() method, available from  PPChemAPI, Java, .NET and Python SDK.

PCHE: PPChemAPI

Low

PCHE-8260

Minor

A new parameter NumberOfPasses is added to the Generate Maximal Common Substructure (MCSS) component to specify the maximum number of iterations during MCSS construction. The default value is 10 and if the limit is reached, the best result obtained so far is returned, which will not be correct for MCSS with 11 or more bonds from its center. In such cases, increasing NumberOfPasses will result in the correct result but a longer computation time.

PCHE: Chemistry Content

Low

PCHE-8335

Minor

Made improvements to the "StandardizeStereo" and "SetStereoFromCoordinates" actions in the "Standardize Molecules" component to set the stereo of double bonds with symmetric attachments to NoStereo instead of Cis or Trans stereo.

PCHE: Chemical Perception

Low

PCHE-8459

Minor

Made improvements to the "StandardizeStereo" and "SetStereoFromCoordinates" actions in the "Standardize Molecules" component to set the stereo of double bonds with symmetric attachments to NoStereo instead of Cis or Trans stereo.

PCHE: Chemical Perception

Low

PCHE-8461

Minor

Fixed the code in Replace Ring Assemblies to enable replacements of ring systems with only a single attachment. In previous releases rings with a single attachment were never replaced.

PCHE: Enumeration

Low

PCHE-8477

Minor

The Discovery Studio Visualizer component, based on ActiveX, is no longer supported. It has been moved to the Deprecated folder and will be removed from the Chemistry collection in the next release.

PCHE: Chemistry Depiction

Low

PCHE-8482

Minor

Fixed an inconsistency where the Meso Chirality component can report an "invalid index value" depending on the order in which records are submitted. The component state is correctly initilizated for each record. (The observed inconsistency is because the first molecule has an atropisomer which caused the 2nd molecule to crash)

PCHE: Chemical Perception, PCHE: Query Mapping

Low

PCHE-8483

Minor

A double either bond stereo (Unknown stereo) is created for molecule from standard InChI which does not define the double bond stereo. A double either bond stereo (Unknown stereo) is created for molecule from none-standard InChI with SUU option when the double bond has undefined stereo.

PCHE: Chemical Perception, PCHE: Chemistry Depiction, PCHE: File Formats

Low

PCHE-8507

Minor

Fixed 5Ring Opening and 6Ring Opening reactions in Enumerate Bioisosteres (Classic). The product should have A atoms as in the reactants instead of N and O.

PCHE: Enumeration

Low

PCHE-8508

Minor

Generate Molecular Mutations An error in the code was preventing some ring closures for being performed. Pairs of atoms that should have been considered as candidates for ring closures were being skipped. This is now fixed.

PCHE: Enumeration

Low

PCHE-8517

Minor

Indexing is enabled for reagent only reactions. An exception was previously thrown when attempting to index such reactions.

PCHE: Chemistry Cartridge

Low

PCHE-8530

Minor

Molecular Composition in Pipeline Pilot now outputs parentheses and comma in correct orders for molecules with SGroup.

PCHE: Property Calculators

Low

PCHE-8645

Minor

Modified the logic used in Perceive Sequence from Structure to classify unknown fragments with two attachment points as aminoacid residues to check that the left attachment point is a Nitrogen and the right attachment point is a carbonyl. If these new requirements are not satisfied the unknown fragment is classified as a linker.

PCHE: Biologics, PCHE: Chemical Perception

Low

PCHE-8679

Minor

Fixed a bug where enhanced stereo information got lost for molecules with axial stereo centers during a Molecule To/From Smiles round trip.

PCHE: Chemistry Content

Low

PCHE-8686

Minor

Fixed code in Clean SCSR Sequence to make orientation of expanded Gly residues consistent with other expanded residues in the sequence.

PCHE: Biologics, PCHE: Chemistry Depiction

Low

PCHE-8691

Trivial

Fixed translation of molecules in Pilotscript MolTranslate or PPChem SDK Molecule.Translate() methods to handle correctly the position of DAT Sgroups

PCHE: Molecular API

Low

PCHE-8362