Release Notes

Release V1.2.1

Bug Fixes

  • Fix for function Pharm::removePositionalDuplicates(Pharmacophore&) which erroneously retained the duplicate features (to be removed) instead of the desired features all having unique position and type

Improvements

  • Additional Python cookbook scripts

  • Documentation updates

  • All disk space consumed by an existing pharmacophore screening database (PSD) that is specified as destination file for a new database to be created by the tool subsearch is now completely freed and not just internally marked as unallocated space

Release V1.2.0

New Functionality and Features

  • New utility functions for the manipulation of pharmacophore data

  • New command line tool subsearch for substructure searching on molecular data files with support for multiple query substructures and customizable logical expressions

  • Added support for the I/O of molecular structure data in CML format

  • Added support for the I/O of macromolecular structure data in mmCIF format

  • New atom classification functions for the detection of bridgehead atoms and spirocenters in complex ring systems

  • The residue database now also provides parent structure and single letter code information for a query residue

  • New class implementing substructure searching with multiple query substructures that can be combined by boolean expressions

  • New class implementing the generation of variably sized hashed 2D and 3D pharmacophore fingerprints

  • New class implementing the generation of 881 bit PubChem fingerprints

  • New class implementing the generation of 166 bit MACCS key fingerprints

  • New class implementing the perception of the extended smallest set of smallest rings of molecular graphs (ESSSR)

  • New class implementing the visualization of multiple molecules as separate 2D structure diagrams arranged in a grid of arbitrary size

  • New 2D graphics primitive for the rendering of multi-line text blocks supporting several options for the styling of individual text fragments

  • New control-parameter allowing to customize the resolution of 2D structure/reaction depictions saved in a pixel-based output format

  • Support for atom and bond highlighting in 2D structure/reaction depictions

  • Support for the rendering of custom atom and bond labels in 2D structure/reaction depictions

Improvements

  • Improved the visual appearance of command line tool progress bars

  • Additional Python cookbook scripts

  • Sphinx documentation updates

  • Improved support for different Python installation flavors on macOS (the help provided by Yakov Pechersky is greatly appreciated)

  • Perception of atom/bond stereochemistry from input 3D coordinates in the conformer generation molecule preprocessing stage now does not require the presence of explicit hydrogens anymore

  • Updated PDB/mmCIF residue dictionary which now features 44906 chemical components

  • CDPL Python bindings now support NumPy V≥2.0

  • Program ChOX now uses the same file open/save dialog instance for all opened main windows

  • Program ChOX now supports basic cut/copy/paste as well as drag and drop operations

  • Program ChOX now allows to perform substructure searching with logical combinations of SMARTS patterns

  • Program ChOX now allows to highlight substructures defined by SMARTS patterns

  • The SDF data reader (class Chem::SDFMoleculeReader) now also accepts input data that do not end with a newline character

  • Made the MOL2 data reader (class Chem::MOL2MoleculeReader) more tolerant regarding missing sections

  • Extended the set of supported chemical elements to atomic number 114

  • Control-parameter Vis::BACKGROUND_COLOR was replaced by Vis::BACKGROUND_BRUSH which now allows to also specify a background fill pattern (see class Vis::Brush) for 2D structure renderings

  • Class Vis::CairoRenderer2D now supports the rendering of overlined, underlined and striked-out text

  • Support for setting the image output scaling factor in the program ChOX

Bug Fixes

  • Fixed an issue concerning the calculation of pharmacophore fit scores that previously also considered mappings of multiple query features to the same target feature. Now, more correctly, the best score that could be calculated for all possible one-to-one feature mappings is reported.

  • Fixed a bug in program ChOX that prevented the successful saving of data in *.psd format

  • Fixed the missing support for certain chemical element symbols in class Chem::SMARTSMoleculeReader

  • Fixed a bug in class Math::RegularSpatialGrid that caused an erroneous transformation of world to grid-local coordinates

  • Fixed a problem in Chem::RECAPFragmentGenerator that lead to the generation of too few fragments for H-depleted molecules

  • Fixed a problem in Chem::BRICSFragmentGenerator that lead to the generation of too few fragments for H-depleted molecules

  • Fixed an issue with the calculation of text bounds in the implementation of classes Vis::CairoFontMetrics and Vis::QtFontMetrics that lead to too small bounding boxes in the presence of leading and/or trailing whitespace

  • Fixed an issue with whitespace-only data elements that were missing in the DOM-trees generated by the internally used RapidXml XML-parser library

  • Fixed an issue in program ChOX where the background color setting of 2D structure/reaction depictions got ignored when saving data in an image output format

  • Fixed several minor bugs in Python cookbook scripts

API Changes

  • New setter/getter method pair groupReferenceFeatures()/referenceFeaturesGrouped() in class Pharm::PharmacophoreFitScore for controlling whether multiple directed features of the same type at the same position shall be considered as independent individual features or as different orientation options of a single feature

  • New utility functions Pharm::clearOrientations(), Pharm::removePositionalDuplicates(), Pharm::removeFeaturesWithType() for the manipulation of pharmacophore data

  • Unified the naming of control-parameters and associated functions in namespaces Chem, Pharm, Grid, and Biomol

  • Renamed function MolProp::isCarbonylLikeAtom() into MolProp::isCarbonylLike()

  • Renamed function MolProp::isAmideCenterAtom() into MolProp::isAmideCenter()

  • New atom classification functions MolProp::isBridgehead() and MolProp::isSpiroCenter()

  • New control-parameters, properties and associated functions in namespace Chem for CML data I/O

  • New constants in namespace Biomol::ResidueType which now fully cover the set of residue types defined by the mmCIF/PDBX specification

  • Renamed some previously PDB format-specific control-parameters and associated functions in namespace Biomol for dual-use by the mmCIF data I/O code

  • New class Biomol::MMCIFMoleculeReader for reading macromolecular data in mmCIF format

  • New class Biomol::MMCIFMolecularGraphWriter for writing macromolecular data in mmCIF format

  • New class Chem::CMLMoleculeReader for reading molecular data in CML format

  • New class Chem::CMLMolecularGraphWriter for writing molecular data in CML format

  • New data format descriptors in namespaces Chem::DataFormat and Biomol::DataFormat

  • New class Biomol::MMCIFData for the in-memory storage and postprocessing of mmCIF formatted input data

  • Added new method getParentCode() to classes Biomol::ResidueDictionary and Biomol::ResidueDictionary::Entry for the lookup of residue parent structure information

  • Added new method getOneLetterCode() to classes Biomol::ResidueDictionary and Biomol::ResidueDictionary::Entry for the lookup of residue single letter codes

  • New control-parameters, atom properties and associated functions in namespace Biomol for mmCIF data I/O

  • Removed function Biomol::convertMOL2ToPDBResidueInfo() (the conversion of MOL2 substructure to PDB residue/sequence information is now carried out automatically)

  • New class Chem::MultiSubstructureSearch for performing substructure searching with multiple query substructures that can be combined by boolean expressions

  • New classes Descr::NPoint2DPharmacophoreFingerprintGenerator and Descr::NPoint3DPharmacophoreFingerprintGenerator for the generation of variably sized hashed 2D and 3D pharmacophore fingerprints

  • Removed methods setNumBits() and getNumBits() of class Descr::PathFingerprintGenerator (fp-length is now implicitly given by the size of the Util::BitSet instance provided as argument to method generate())

  • New class Descr::PubChemFingerprintGenerator for the generation of 881 bit PubChem fingerprints

  • New class Chem::ExtendedSSSR for the perception of the extended smallest set of smallest rings (ESSSR)

  • New class Descr::MACCSFingerprintGenerator for the generation of 166 bit MACCS key fingerprints

  • New class Vis::StructureGridView2D for the visualization of molecules as 2D structure diagrams arranged in a grid of arbitrary size

  • New class Vis::TextBlockPrimitive2D for the rendering of multi-line text blocks supporting several options for the styling of individual text fragments

  • New control-parameter Vis::OUTPUT_SCLAING_FACTOR that allows to achieve higher resolutions of 2D structure/reaction depictions saved in pixel-based output formats

  • New control-parameters, properties and associated functions in namespace Vis for the rendering of custom atom and bond labels in 2D structure/reaction depictions

  • New control-parameters, properties and associated functions in namespace Vis for the customization of the atom and bond highlighting style in 2D structure/reaction depictions

  • Additional constants in namespace Chem::AtomType increasing the coverage of chemical elements up to atomic number 114

Miscellaneous Changes

  • CDPL Python bindings wheel files for Linux are now built for a manylinux_2_28 environment

  • Updated embedded MessagePack library to version 6.1.1

  • Updated embedded SQLite3 database to version 3.46.1

  • Updated embedded MMTF library to version 1.1.0

  • Updated the internally used RapidXml XML-parser library to version 1.13

  • Unit test case updates for functionality in namespace CDPL::Vis

Release V1.1.1

Improvements

  • Significantly improved the generation of 2D coordinates for macrocyclic structures

Bug Fixes

  • Fixed an issue with the generation of conformers under application of a fixed substructure template where the generated conformers sometimes displayed the mirror image of the specified 3D template structure

  • The command line tools structgen and confgen erroneously used the already reserved letter p as shortcut for the option –fixed-substr-min-atoms. The new shortcut is ~

Miscellaneous Changes

  • Rewrote code that uses the boost filesystem library to use C++17 equivalents

  • Compiling CDPKit now requires a compiler with C++17 support

Release V1.1.0

New Functionality and Features

  • The tool tautgen provides two new tautomer generation modes BEST_SCORING and BEST_SCORING_UNIQUE (the new default mode) for generating only the chemically most reasonable tautomers

  • New option in class Chem::TautomerGenerator that allows to suppress the output of generated tautomers which represent just a different resonance structure of a previously reported tautomeric form

  • New structgen feature that allows to enforce a particular 3D structure for defined parts of the input molecules

  • New confgen feature that allows to specify substructures of the input molecules that shall adopt a particular conformation which is then kept ‘fixed’ during conformer generation (more information and examples can be found here)

  • Conformer generator settings now allow to specify rotatable bond count dependent values for RMSD threshold, energy window and max. output ensemble size

  • The pharmacophore screening application psdscreen provides a new option –unique-hits which enforces that a database molecule matched by multiple query pharmacophores is saved only once to the output hit list

  • New Python example script for database preparation

  • New Python example script demonstrating how the torsion driving functionality can be used for conformer sampling

  • The visual molecule and reaction data inspection tool ChOX now allows to display atom and bond configuration labels

  • The 2D molecule structure rendering code (implemented by class Vis::StructureView2D) now allows to display atom and bond configuration labels

  • Full implementation of the CIP sequence rule stack for the correct labeling of atom and bond stereocenters (new class Chem::CIPConfigurationLabeler)

  • Support for reading/writing molecular structures in XYZ format (classes Chem::XYZMoleculeReader and Chem::XYZMolecularGraphWriter)

  • New command line application isogen for the enumeration of R/S and E/Z stereoisomers of molecules

  • New class Chem::StereoisomerGenerator for the exhaustive enumeration of R/S and E/Z stereoisomers

  • New 2D drawing primitives (classes Vis::Path2D and Vis::PathPrimitive2D) and support for clipping operations (class Vis::ClipPathPrimitive2D)

  • New class Chem::BemisMurckoAnalyzer for the extraction of Bemis-Murcko scaffolds

  • New functions for the alignment conformers

  • New utility functions Chem::calcBasicProperties() that ease the recurring task of initializing Chem::MolecularGraph and Chem::Reaction instances for further processing

Improvements

  • Overhaul of the tautomer generation code for increased efficiency and flexibility

  • The output conformer ensemble compilation process now strives for higher energetic diversity among the picked conformers which, on average, leads to higher accuracy in the reproduction of experimental structures (benchmarking results can be found here)

  • Update of the torsion library used for systematic conformer generation (more information can be found here)

  • Systematic conformer sampling speed optimizations

  • Reduction of the memory footprint of the conformer generation procedure which could become unacceptably large under some circumstances

  • Documentation updates and corrections

  • Refactoring of stereochemistry related code

  • Cleanup of the CDPL Python bindings code

  • When deep copying Chem::Reaction or Chem::Molecule instances, values of properties referencing atoms and/or bonds (e.g. stereodescriptors, SSSR) now get automatically translated to values referencing the corresponding atoms/bonds of the copying target

  • Cleanup of CDPL C++ header files

  • Added support for building CDPL Python bindings pip installer wheel files under Windows

  • Added support for building manylinux2014 compliant CDPL Python bindings pip installer wheel files

  • Build system cleanup

Bug Fixes

  • Fixed bugs in classes Chem::MaxCommonAtomSubstructureSearch and Chem::MaxCommonBondSubstructureSearch that led to a loss of expected matches

  • Fix for a bug in the SMARTS parser that lead to the storage of wrong bond directions

  • Bond direction specifications (up/down) in SMILES and SMARTS strings are now correctly interpreted

  • Fixed a bug that may lead to the generation of conformers with wrong geometries at exocyclic double bonds

  • Fixed a bug in the shapescreen tool that lead to the calculation of erroneous similarity scores when option –score-only was set

  • Fix for a minor bug that affected the indentation of SD-file property entries

  • Function overload resolution order fixes in the CDPL.Math Python package

  • Prevented the throwing of exceptions when the env. variable LC_ALL has not been initialized

API Changes

  • New getter/setter method pair in class Chem::TautomerGenerator for suppressing the output of generated tautomers which represent just a different resonance structure of a previously reported tautomer

  • Data structures with names ForceField::MMFF94XXXInteractionData were renamed into ForceField::MMFF94XXXInteractionList (XXX = force field interaction type)

  • New class ForceField::ElasticPotential plus elastic potential energy and gradient calculation functions

  • New class Chem::CIPConfigurationLabeler for the labeling of atom and bond stereocenters

  • New class Chem::StereoisomerGenerator for the exhaustive enumeration of R/S and E/Z stereoisomers

  • New classes Chem::XYZMoleculeReader and Chem::XYZMolecularGraphWriter implementing reading and writing of molecule data in XYZ format

  • New 2D drawing primitives (classes Vis::Path2D and Vis::PathPrimitive2D) and support for clipping operations (class Vis::ClipPathPrimitive2D)

  • New class Chem::BemisMurckoAnalyzer for the extraction of Bemis-Murcko scaffolds

  • New CDPL::Chem functions for the alignment conformers

  • Python exports of Util::Map and Util::MultiMap do not provide the properties keys, values, and entries anymore. They were replaced by the corresponding methods keys(), values() and items()

  • The MolProp::getAtomCount() function has been extended by a strict argument which, if set to false, instructs the accounting procedure to regard the meaning of generic atom types (e.g. any halogen)

  • New utility functions Chem::calcBasicProperties() for a more comfortable initialization of Chem::MolecularGraph and Chem::Reaction instances for further processing

  • Code in class GRAIL::GRAILDescriptorCalculator now calculates a shorter GRAIL descriptor (35 elements) with not further subdivided H-bond donor/acceptor feature types

  • Class GRAIL::GRAILDescriptorCalculator was renamed into GRAIL::GRAILXDescriptorCalculator

Release V1.0.0

- Initial release -