Version 3.0.0.6¶

OEChem TK 3.0.0.6¶

When reading and writing large OERecord, sometimes memory usage would spike briefly due to temporary copies of data. The memory usage has been optimized to reduce these spikes.

Added the ability to perceive chirality without including nitrogen atoms that could undergo nitrogen inversion. See OEPerceiveChiral for details.
Added a method to clear chiral perception before calling the perception function with a different flag. See OEClearChiralPerception for details.
The performance of converting large proteins to the JSON format has been improved.

Fixed an issue which allowed OERange objects to be created with a low value greater than the high value.
The readonly flag on molecule fields was not being enforced properly in the Python API. Attempting to use a read-only field to set a molecule on an OERecord now raises an exception.
Uninitialized OERange values stored on records were turning into None values on retrieval via the Python API. This has been fixed.
In the Python API, the OERecord.get_fields method would return None values for fields whose types had not been imported. This has been fixed.
Values of NaN and Infinity were causing errors when they appeared in JSON objects being read by any toolkit. This has been fixed.

An issue causing some MTZ files to be read with the wrong space group has been fixed.

A new set of Preliminary API classes has been added as part of the extended set of OEParameter and OEOptions classes:
A new functor, OEIsTermHeavyAtom, has been added that identifies terminal heavy atoms.
A new function, OEOverlayConfsByRMSD, has been added that overlays all conformers of an OEMCMolBase molecule on the first conformer to minimize RMSD.
The molecule database implementation of OESubSearchDatabase now loads scenes into memory using multiple threads.

The full molecule-based multi-conformer OERMSD calculation now returns false when the automorphism flag is set to true and no match can be identified between the reference target molecule (i.e., when no RMSD value can be calculated).
An issue with using deleted atom pointers as templates for creating or recreating new atoms based on the deleted atom template has been fixed. Previously, the newly created atom instance would be marked as a deleted atom.
An issue that caused molecule SMILES string generation to erroneously output reaction information if OERxnRole information was present on atoms has been fixed. Reaction information should only be added to the SMILES output if OEMolBase.IsRxn is true.
OERxnRole_Agent and OERxnRole_Catalyst enums have long had the same value, making them indistinguishable if applied to reaction atoms. The enum values have been changed to make them unique. Formats (e.g., OEB) that support importing and exporting this information can now distinguish and retain this information.
Some of the extraneous warnings about planar stereocenter geometry have been reduced via more rigorous checking of the stereocenter environment during structure file reading.

A set of preliminary APIs for OERecord and its associated classes has been added to OEChem TK. OERecord is a data container for storing and transmitting strongly typed data and its associated metadata. The API set includes the following classes and functions:
A new set of preliminary APIs has been added to combine the concepts of OEParameter with OEOptions. These new APIs provide an interface for configuring OEOptions directly from the command line, making it easier to write command line applications. The new API set includes the following:
A new overload for OEDots.Update has been added that takes a character as an argument to display in lieu of ..