T176-2023 Notification regarding BIOVIA Pipeline Pilot Chemistry Collection 2022

Added support to represent enhanced stereo to Pipeline Pilot SMILES using CXSMILES extensions. CXSMILES represent enhanced stereo information using the labels "a" for Absolute stereo atoms, "&" for atoms in AND stereo groups, and "o" for atoms in OR stereo groups. Stereo molecules without enhanced stereo groups but with the Chiral flag set to zero (racemic mixtures) are represented in CXSMILES by the letter "r".

Low

PCHE-5389

Added a new parameter to the Pipeline Pilot Chemistry depiction components and to the PPChem SDK to choose between one-letter (default) and three-letter symbol depiction for residues in sequences. For example, "Ala" instead of "A".

Low

PCHE-5513

Added a new depiction parameter, "Always Display Reaction in One Line", to force the reaction to be displayed in one line. It forces the display of all reactant and product molecules in the same horizontal line, even in cases where the presence of multiple reactants or products creates long images where the X dimension is much bigger than the Y dimension. When this option is set to False, the reactant and product molecules can be displayed on more than one line to create a reaction image with more even dimensions.

Low

PCHE-7010

Added Pipeline Pilot components and protocols to support centralized libraries on the Pipeline Pilot server, which does not need a connection to the Foundation Hub. Protocols to manage Pipeline Pilot server-based centralized libraries are similar to those used to manage Foundation Hub-based centralized libraries, and can be accessed from both the Web Port and Pipeline Pilot Pro Client

Medium

PCHE-7150

Chemistry Sketcher now supports V3000 format and can display chemical molecules with enhanced stereochemistry using IUPAC standards where &/OR/ABS are displayed at stereocenters and the OR/AND Enantiomer/MIXED text is not displayed.

Low

PCHE-7315

Added support for reading fragments above and below the reaction arrow in Chemdraw .cdx and .cdxml files. These fragments are mapped to the reagents in Pipeline Pilot chemistry reaction object.

Updated the Chemdraw cdx and cdxml files writer to take input reaction records with reagents. The input reagents are written as fragments above and below the reaction arrow.

Low

PCHE-7911

Improved the API documentation for the Python PPChem SDK.

Low

PCHE-8040

Improved the perception and depiction of sequences consisting of two complementary nucleic acid chains (sense and antisense). The "Perceive Sequence from Structure" and "Clean SCSR Sequence" components perceive the presence of complementary chains, align their coordinates to place matching base pairs close to each other, and define hydrogen bond connections between them.

Low

PCHE-8065

When the Name and Comments field of the reagent molecule contains markup for Greek letters (for example, .alpha. .beta), the Greek letter is now displayed in the reagent depiction.

Low

PCHE-8071

The Pipeline Pilot Chemistry SDK documentation zip file now includes the BIOVIA Databases CTFile Formats documentation.

Low

PCHE-8074

Updated the "Check SCSR Template" component to:

Check supported SCSR template classes, only allow predefined template classes (AA, dAA, Sugar, Linker, Chem, Phosphate, RNA, and DNA.)

Allow terminal templates in AA, dAA, Sugar, Phosphate, RNA, and DNA classes.

Updated "Bad Entry Filter" component with a check on HEML_NAME and SCSR_NAME for the following reserved characters $  |  : [  ] {  }.

Low

PCHE-8107

Modified the sequence perception code in Perceive Sequence From Structure to combine a peptide backbone map and a linker map into a single unknown residue map.

Low

PCHE-8117

A Jupyter Notebook user is now able to call the PPChemistry SDK in both Windows and Linux machines.

Low

PCHE-8134

Updated the Desktop Connector installation packages for Sketcher Integration.

Low

PCHE-8151

Pipette Biosketcher now has tools to add Phosphate monomers to the 3' or 5' terminals in RNA sequences with one click.

Low

PCHE-8160

Added two new methods to the SGMap class in the PPChem SDK (Java, .NET, Python) to calculate the number of times a target molecule is mapped by the queries. The two new methods are "NumTotalMappings" to calculate the number of mappings by all the queries, and "NumMappingsForQuery" to calculate the number of mappings for the specified query.

Low

PCHE-8177

When using Perform Reaction or Combinatorial Reaction in the PPChem SDK APIs, properties present in the reactant molecules are preserved in the transformed products. You can access the product properties by creating a new molecule when retrieving each product.

Low

PCHE-8192

Exception handling in PPChemAPI and PPChem SDK  (Java, Python, .NET) has been significantly improved. PPChem SDK API headers and signatures are backwards compatible. Applications that call Java PPChem SDK methods that now throw exceptions need to handle or re-throw exceptions if it was not already in place. A list of Java SDK functions with the improvement can be found at https://r1132100503382-eu1-3dswym.3dexperience.3ds.com/#community:FV3_L4yySoKZ4k2DYvnQ6Q/post:SoWl28kATEm1gFXmeWUOqA.  Please refer to Pipeline Pilot and PPChem SDK documents for more details.

High

PCHE-8198

PCHE-8126

PCHE-8127

Added support to create InChI for large molecules with more than 1024 atoms.

Low

PCHE-8211

This release uses the latest OpenEye's Lexichem release, 1.5.6, for computation of chemical names.

High

PCHE-8218

Updated the Pipeline Pilot Chemistry InChI components and Chemistry SDK to the InChI V1.06 API.

Low

PCHE-8221

The nature of SGroup brackets in structures are no longer ignored by PPChem SDK when calculating molecular formulas, which makes the PPChem SDK calculation of chemical formulas equivalent with Cheshire based calculations. For example, the formula of a Polyethylene/Polyproplylene copolymer returned by the SDK is ((C3H6)n(C2H4)n)co now and polymer specific connectivity information is preserved.

Low

PCHE-8229

PCHE-8196

PCHE-8197

WriteMoleculeString of MolIO now creates Chime strings successfully for molecules containing Unicode text data. This is fixed for PPChem API and PPChem SDK.

Low

PCHE-8225

Modified the test for AmineNitrogen in the Molecular Toolkit PilotScript function AtomIs to also perceive aromatic amines. This function stopped perceiving aromatic amines after the Nitrogen hybridization changes done in the 2021 Pipeline Pilot Chemistry release.

Low

PCHE-8246

Added support for UDM Version 6 in Pipeline Pilot UDM Reader and UDM Writer Component. Pipeline Pilot can read and write both Version 5 and Version 6 UDM files.

Low

PCHE-8250

Added a method, SetCustomPTableFilePath, to StructureChecker in PPChemAPI and PPChem SDK to set pathname of a Pipeline Pilot or Direct 9 or later periodic table file, which defines additional allowed atom types.

Low

PCHE-8251

Added a method, SetAllowedNonStandardElements, to StructureChecker in PPChemAPI and PPChem SDK to allow non-standard element symbols or non-standard element labels when checking for the presence of query features, even though these are normally considered to be query features.

Low

PCHE-8252

DAT Sgroups (custom data) attached to the entire molecule in the reactants or products of a reaction with a name (Field Description) equals to "SMMX:RXNMOLLABEL" are displayed centered on the molecule in the x direction and all at the same y coordinate at the bottom of the reaction. DAT Sgroups that do not satisfy these requirements are displayed as usual, following the positioning defined in the DAT Sgroup.

Low

PCHE-8258

Modified the molecular depictions to highlight Coordination and Hydrogen bonds the same way the standard bonds are highlighted (single, double, triple).

Low

PCHE-8271

Added support to Pipette Biosketcher to use RNA Sugar monomers with four attachment points in RNA sequences.

Low

PCHE-8276

Updated the default global files with HELM monomers and SCSR templates used by Pipeline Pilot Chemistry components and the PPChem SDK to read HELM strings and SCSR sequences, interconvert between HELM and SCSR, and perceive sequences from expanded structures. The new files contain 786 HELM monomers (438 RNA, 348 PEPTIDE, 10 CHEM) and the corresponding SCSR templates (327 AA, 21 dAA, 231 SUGAR, 182 BASE, 15 PHOSPHATE, 7 LINKER, 3 CHEM, 3 DNA, 5 RNA). The new monomers and templates are based on new datasets published by the Pistoia Alliance. 

Low

PCHE-8277

The "-" character in monomer names in is now allowed in HELM strings.

Low

PCHE-8291

The Pipeline Pilot depiction components and the PPChem SDK have been updated to use Qt 5.15 in Windows.

Medium

PCHE-8324

Updated the calculation of stereo or chirality label in molecular depictions to take into account stereo centers in the SCSR templates that represent contracted sequence atoms in addition to stereo centers present in the expanded atoms.

Low

PCHE-8387

The Pipette Sketcher has been updated to version 3.5. Main changes include:

¡  Ensure redo button appears correctly when required for Peptides.

¡  Ensure cutting with ctrl-x clears the sequence view.

¡  Add buttons to add a phosphate to a RNA ribose with a single click.

¡  Ensure only two rows of monomers are shown when the monomer names are long.

¡  Allow RNA bases to have a R2 and R3 connections.

¡  To make it easier to build DNA chains, the default when building changes from R to dR when it is the most common ribose monomer used in the chain.

¡  Partially mask monomer names when they are long to make the monomer names easier to read.

¡  Allow ribose monomers to have R4 groups.

¡  Allow RNA bases to have an R2 and R3 connection when reviewing monomers.

¡  Allow monomer names to contain - and _ when reviewing monomers.

¡  Ensure the chiral counts line flag is applied to each molecule in a reaction file.

¡  Correctly support reaction files where the number of reactants on products does not match those present in the ctabs.

¡  Do not include $$$$ at the end of v2000 molfile downloads.

¡  Match the implicit hydrogen display defaults of Pipeline Pilot.

¡  Add support for plp prefix on Biosketcher for some BIOVIA cloud environments.

Low

PCHE-8411

Major

The PilotScript AtomChirality() function no longer throws an "invalid index value" error when traversing a large molecule.

Low

PCHE-8131

Major

The latest version of the OpenEye OEMetaChem libraries (1.5.6) fixed issues calculating chemical names for molecules with MUL Sgroups.

Low

PCHE-8161

Major

Improved the treatment of pseudo stereo atoms by the Standardized Stereo action in the Standardize Molecule component to prevent valid pseudo stereo atoms from being flagged as invalid stereo

Low

PCHE-8170

Major

Pipette Sketcher now uses the same Periodic Table data as Pipeline Pilot Chemistry. Implicit Hydrogen display now is always consistent with Pipeline Pilot Chemistry depictions.

Low

PCHE-8228

Major

Modified the format of SVG molecular images created by Pipeline Pilot depiction components and the PPChem SDK to use viewBox. This allows the SVG images to scale based on the size of the hosting html element.  The height and width attributes are set to "100%" and the actual image width and height are added as a viewBox attribute with the value = "0  0 width height".

Low

PCHE-8259

Major

Fixed an issue where some molecules with zero-order bonds did not map themselves in substructure searches.

Low

PCHE-8279

Major

Fixed the RXN Reader to handle reactions with multiple reactants or products with SCSR templates. Previous changes made in the Pipeline Pilot Chemistry 2021 release allowed reactions with SCSR containing a single reactant and a single product, but not reactions with multiple reactants or products with SCSR templates.

Low

PCHE-8280

Major

Fixed the calculation of Num_FragmentsCovalentBonds, Num_RingsCovalentBonds, and Num_RingAssembliesCovalentBonds in Molecular Property Counts. They now return the values corresponding to doing the chemical perception while taking into account only covalent bonds (single, double, and triple) and not zero-order bonds (Coordination bonds and Hydrogen bonds). These counters, which were introduced in the 2021 SP1 release, were erroneously doing the perception while taking into account all bonds (covalent and zero-order bonds) and then calculating the number of fragments, rings, and ring assemblies that did not contain zero-order bonds. The results are similar but not exactly the same in some cases.
This fix also applies to the corresponding PPChem SDK and Molecular Toolkit methods. For example, in the Java PPChem SDK, mol.getNumFragmentsOnlyCovalentBonds(), mol.getNumRingsOnlyCovalentBonds(), and mol.getNumRingAssembliesOnlyCovalentBonds().

Medium

PCHE-8290

Major

Changed the treatment of solvation waters in the Mol2 Reader to make sure that the atom order in the resulting macromolecule is always the same as in the original Mol2 file.

Low

PCHE-8305

Major

Fixed an issue that occurred when writing CTABS with multiple SPL lines.

Low

PCHE-8313

Major

Improved the perception and treatment of unknown RNA Sugar residues in Perceive Sequence from Structure. For the perception to work well in these cases, it is better to do a first pass to identify the unknown Sugar templates, and then add them as global templates to do the sequence perception.

Low

PCHE-8328

Major

Added support for the SMILES enhanced stereo options in the MolIO readChemistry method in the PPChem SDK.

Low

PCHE-8344

Major

Fixed an issue where the SD Reader incorrectly parsed V2000 molfiles with atom lines that terminate with one trailing space after a single-letter element type field and then a newline. The SD Reader was assigning unknown atom type in these cases.

Low

PCHE-8363

Major

Fixed the display of expanded residues in SCSR sequences triggered by mouse-over events in molecular depictions created by the "Image from SCSR" and "Sequence Table" components.

Low

PCHE-8380

Minor

Molecule to Chemical Structure now correctly converts simple halogen names, such as Iodine and Chlorine.

Low

PCHE-7342

Minor

Improved the reaction depiction of super/sub script in reagent names and comments.

Low

PCHE-8025

Minor

Improved perception of C-terminal residues in Perceive Sequence from Structure to avoid treating them as modified residues displayed in red in the sequence depictions.

Low

PCHE-8051

Minor

The Pipette Sketcher component now supports the display of reagent information (Structure, Name, Comment) above or below the reaction arrow.

Low

PCHE-8052

Minor

Updated the Chemistry Sketcher Updated from Table example protocol include the latest version of the Sketcher component, which fixed an issue that prevented Draw from opening from the protocol.

Low

PCHE-8053

Minor

Removed the extra "+" sign from reading a reaction. When the parent of the text plus sign is the page, it will not be associated to a fragment as text. 

Low

PCHE-8054

Minor

Fixed the 03 Find Estrogen Antagonist MCSS example protocol to correctly highlight the bonds that are part of the MCSS.

Low

PCHE-8078

Minor

Mol files with explicit oligonucleotide structures that are exported from the Pistoia HELM Editor are now perceived correctly by the Perceive Sequence from Structure component. These structures do not usually have a phosphate group at the 5' terminal, which was a problem before the introduction of granular nucleic acid representation in Pipeline Pilot Chemistry and in BIOVIA Draw. 

Low

PCHE-8099

Minor

Fixed depiction of monoradicals on atoms in EMF format. In previous releases, the dot representing the monoradical was not being displayed at all. Now it is displayed close to the top right corner of the atom label. 

Low

PCHE-8132

Minor

The new version of the OpenEye OEMetaChem libraries (1.5.6) creates the correct structure from the chemical name "ethylmethylamine". The structure was incorrect in previous releases.

Low

PCHE-8189

Minor

Fixed change of atom type for attachment points and alpha atoms in Generate Fragments to make sure to clear charge, radical, isotope, and other non-standard settings when replacing with A, R, or Z atom types.

Low

PCHE-8232

Minor

Improved display of monomers with long names (more than 3 characters) in the Pipette Biosketcher

Low

PCHE-8237

Minor

Fixed a problem in the Mol2 Reader that in some cases prevented the assignment of formal charges read from atom properties in the Mol2 file when the parameter Maximum Number of Waters for Perception was set to a non-zero value and the file consisted of a solvated system.

Low

PCHE-8247

Minor

Fixed a problem in the Mol2 Reader that could produce crashes or invalid perception when the parameter Maximum Number of Waters for Perception was set to a non-zero value and the file consisted of a solvated system with regular atoms listed in between solvent atoms (instead of having all solvent atoms after the regular atoms). 

Low

PCHE-8248

Minor

Improved depiction of reactions by increasing the spacing between molecules and plus signs and the reaction arrow to avoid potential overlaps.

Low

PCHE-8261

Minor

The PPChem SDK Java method atom.getChirality() no longer crashes with a memory error for a particular highly symmetric large molecule with many stereo centers.

Low

PCHE-8273

Minor

Summary of changes to PPChem SDK APIs related to zero-order bonds covering PP Chemistry 2021, 2021 SP1 and 2022 releases:

2021 release
Bond class
Added CoordinationBond and HydrogenBond to BondType enum
Added new CoordinationBondDisplay enum
Added new HydrogenBondDisplay enum
Added new getCoordinationBondDisplayType(), setCoordinationBondDisplayType(), getHydrogenBondDisplayType() and setHydrogenBondDisplayType methods

Molecule class
Renamed getNumDativeBonds() to getNumCoordinationBonds()
Removed getHydrogenBondAtom1(index)
Removed getHydrogenBondAtom2(index)
Removed getDativeBondAtom1(index)
Removed getDativeBondAtom2(index)
Added clearHydrogenBonds()
Added clearCoordinationBonds()
Added getNumRingsWithCoordinationBonds()
Added getNumRingsWithHydrogenBonds()
Added getNumRingAssembliesWithCoordinationBonds()
Added getNumRingAssembliesWithHydrogenBonds()
Added getNumFragmentsWithCoordinationBonds()
Added getNumFragmentsWithHydrogenBonds()
Added ringHasCoordinationBonds(index)
Added ringHasHydrogenBonds(index)
Added ringAssemblyHasCoordinationBonds(index)
Added ringAssemblyHasHydrogenBonds(index)
Added fragmentHasCoordinationBonds(index)
Added fragmentHasHydrogenBonds(index)

2021 SP1 release
Molecule class
Added getNumRingsOnlyCovalentBonds()
Added getNumRingAssembliesOnlyCovalentBonds()
Added getNumFragmentsOnlyCovalentBonds()
Added ringHasOnlyCovalentBonds(index)
Added ringAssemblyHasOnlyCovalentBonds(index)
Added fragmentHasOnlyCovalentBonds(index)

2022 release (fixed methods added in 2021 SP1 release to improve the perception of rings and fragments with only covalent bonds)
Molecule class
Fixed getNumRingsOnlyCovalentBonds()
Fixed getNumRingAssembliesOnlyCovalentBonds()
Fixed getNumFragmentsOnlyCovalentBonds()
Fixed ringHasOnlyCovalentBonds(index)
Fixed ringAssemblyHasOnlyCovalentBonds(index)
Fixed fragmentHasOnlyCovalentBonds(index)

Medium

PCHE-8278

Minor

Improved the depiction of reactions with one reactant and three or more product molecules when the parameter Always Display Reaction in One Line is set to False. The width of the reactant molecule was not being taken into account in the calculation of the positions of the arrow and the product molecules, which resulted in poorly depicted reaction arrows and molecules overlapping each other.

Low

PCHE-8283

Minor

Updated the HELM monomer Alignment filter and Align HELM Monomer components.

¡  Align the vector connecting R1 and R2 attachment atoms horizontally (x axis).

¡  When a HELM monomer can be mapped to a SCSR Sugar template, align the monomer so R3 is below R1/R2. 

Low

PCHE-8303

Minor

MolIO.writeMoleculeString of PPChem Python SDK no longer fails for molecules containing Unicode text data.

Low

PCHE-8304

Minor

Pipette Sketcher no longer adds a "$$$$" line when a molecule is saved in V2000 Molfile format.

Low

PCHE-8320

Minor

Improved molecular depictions to ensure the stereo label (Absolute or AND ENANTIOMER) is correctly displayed for molecules that have only atropisomer or allene stereo centers (no tetrahedral stereo centers) and no relative stereo groups.

Low

PCHE-8321

Minor

Improved the treatment of expanded N and C terminal residues in the Clean SCSR Sequences component to improve alignment with the sequence when depicted in Non-Sequence view.

Low

PCHE-8369

Minor

Fixed an issue where HELM strings that contain SMILES, for example PEPTIDE1{[[H]NCCCC[C@H(NC(CCSSc(ncc1)cc1)=O)C(=O)[*:2]]"Modification:SPDPAttachment,ModifiedResidue:K".Q.W.E.R}$$$$V2.0 were not parsed successfully.

Low

PCHE-8378

Trivial

Updated PPChem SDK SD file methods to make sure that when the molecule name property is removed or set to an empty string, the name is removed from the Molfile header.

Low

PCHE-8174

Trivial

Added 22.1 and removed 4.2 and 16.1 to the supported BIOVIA Draw version list in Global Properties > Sketcher Integration.

Low

PCHE-8333