Program
BIOVIA Pipeline Pilot Chemistry Collection and 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 Collection and SDK 2023 which includes the following enhancements and fixed defects:
Enhancements
This release of BIOVIA Pipeline Pilot Chemistry Collection and SDK includes the following enhancements.
Description | Areas Affected | Risk Level | Jira Issue ID |
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 | 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 |
Fixed Defects
This release of BIOVIA Pipeline Pilot Chemistry Collection and SDK includes the following fixed defects.
Severity | Description | Areas Affected | Risk | Defect |
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 |
Resolution
BIOVIA Pipeline Pilot Chemistry Collection and SDK 2023 was released in December 2022 and is available for download at https://software.3ds.com under BIOVIA products and can be found under:
Product line: Lab, Scientific and Content Solutions
Release: BIOVIA 2023
Level: BIOVIA 2023 Golden
How to contact BIOVIA Support
If you have any questions, please contact BIOVIA Support.