Release Notes

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 -