Spruce TK 1.0.0¶
A new function,
OEMakeDesignUnits, has been added that generates
OEDesignUnitfrom structures read from PDB or mmCIF files. The function takes a number of options to control its behavior; therefore, the following options classes have been defined:
OEMakeDesignUnitOptions: a high-level options class that holds the options classes below.
OEDesignUnitPrepOptions: a high-level options class that holds other options classes, determining how a design unit is prepped.
OEDesignUnitBuildOptions: a low-level class that sets whether to build caps and missing sidechains.
OEProtonateDesignUnitOptions: a low-level class that sets whether and how to protonate the design unit, including whether to generate tautomers.
OEDesignUnitSplitOptions: a low-level class that determines how to handle alternate locations, how a system is split, locating the ligand, etc.
OEMakeDesignUnitsfunction also takes the
OEStructureMetadataclass as input. The
OEStructureMetadataclass holds experimental data if known and can be used to indicate which is the ligand, what the sequence of the protein is, and other relevant pieces of information.
OEMakeDesignUnitsis a high-level function that works on the two intermediate functions,
OEEnumerateSites, which can be run separately if intermediate results are desired. The high-level
OEMakeDesignUnitsfunction has a deduplication step built in; this function is highly recommended.
A new function,
OEProtonateDesignUnit, has been added that ensures that protons in an
OEDesignUnitare optimized. The high-level function
OEMakeDesignUnitscalls this by default unless it is turned off in options.
OEBuildSidechainsfunction has been updated to allow building all possible clusters even if one fails due to clashes. The function still returns
falsein this case.
Major bug fixes¶
An issue in the
OEExtractBioUnitsfunction that caused a segfault due to an improper PDB header format has been fixed.
An issue in the alternate location expansion that left atoms on top of each other due to unconventional location definitions has been fixed.