Spruce Output Naming Conventions¶
Output files generated from Spruce follows a general naming scheme.
{StructureID}_{ChainIDs}[alt{AltCode}]__DU__{LigandCode}_{ChainID}-{ResidueNumber}.oedu
The scheme can be prefixed by the user using the -prefix
input parameter. The user can also control
the output to a single file using the -out
, and additionally, set -warts
to append “_#”
to the user specified output name.
Example of a structure without an alternate location, 2 files generate due to two ligand sites detected:
4ICL_AB__DU__T27_A-601.oedu
4ICL_AB__DU__14N_A-607.oedu
Example with an alternate location code:
1XDN_AaltA__DU__ATP_A-501.oedu
For apo structures, the residue named is the one closest to the center of the marked binding site. That is unless the user has provided a binding site residue to indicate the binding site, in which case that is used in the title and filename. Apo pocket example:
1HHP_AB__DU__apo_ASP_A-25.oedu
Peptidic ligand example, where the ligand section is named slightly differently following the scheme chainID-StartingResidueNumber-1LetterCodes-EndingResidueNumber. Only standard residue get 1 letter codes, whereas nonstandard residue will have 3 letter codes separated by dashes.
4OBD_AB__DU__E-2-PGNFFQNRP-10.oedu