SPRUCE 1.5.0¶

Spring 2022

New Features¶

Spruce has been enhanced to perform standardization and a filter checks before Spruce preparation.
The following are detected and fixed:
- invalid component names
- invalid residue states
- invalid metal bonds
The following are detected and fail the structure:
- invalid CRYST1 from header file
- low overlap between the electron density map and the structure
- invalid sequence alignment
- blank Chain IDs
- invalid alternate locations
Spruce has been enhanced to perform checks on the generated design unit after running Spruce preparation.
Issues detected and reported include:
- partial side chains
- missing loops
- implicit hydrogens
- incorrect partial charges
- termini that are not capped properly
- heavy atoms overlapping with each other
- broken chains
A new command line option -enum_pockets has been added. When enabled it automatically detects pockets and generates design units from them.

An issue with the value of the parameter -min_align_score not being properly respected has been fixed.

The new OESpruceFilter class has been added to provide checks and corrections on input to Spruce. For input it can take an OEMolBase, OEStructureMetadata, or an options class, OESpruceFilterOptions, that holds the options to turn on each of the fixing options.
The new OEValidateDesignUnit class has been added for validation of Spruce produced design units. For input it can take an OEDesignUnit or OEStructureMetadata.

An issue was fixed in OEBuildLoops to allow better sequence alignment for peptides.
An issue was fixed in OEBuildLoops where free amino acids, as co-factors or ligands, were incorrectly included in sequence alignments and causing mismatched alignments to the SEQRES.
An issue was fixed in OEExtractBioUnits to be able to lower the minimum sequence alignment score threshold.