Autogenerated Tag Syntax Documentation:
Author: Jared Adolf-Bryfogle (jadolfbr@gmail.com) @brief Add Cluster-based CDR Profiles as the task operation for the set of CDRs by default. See ResidueProbTaskOperation for more.
CDR definitions used are North/Dunbrack as the clusters are defined using it.
@details If Cluster-based profiles cannot be used, will use the fallback strategy. This can happen if the the CDR is of an unknown cluster or there is too little data about the cluster to use profiles.
FALLBACK STRATEGIES: seq_design_conservative adds a conservative mutation set to the possible residue types (blosum62 default), seq_design_basic will do nothing (as the default for design is to allow all residue positions); seq_design_none will disable design for that CDR (essentially your saying that if it doesn't have profiles, don't design it)
This TaskOperation is not currently recommended for H3 as it does not cluster well.
Optionally sample whole CDR sequences via the primary strategy of: seq_design_profile_sets (use sets instead of profile probability) seq_design_profile_sets_combined (use profile sets and profile probability)
<AddCDRProfilesOperation name="(&string;)" cdrs="(&string;)"
fallback_strategy="(seq_design_conservative &string;)"
include_native_restype="(true &bool;)"
picking_rounds="(1 &non_negative_integer;)"
force_north_paper_db="(false &bool;)" use_outliers="(false &bool;)"
stats_cutoff="(10 &non_negative_integer;)"
sample_zero_probs_at="(0.0 ℜ)"
cons_design_data_source="(blosum62 &string;)"
no_probabilities="(false &bool;)" input_ab_scheme="(&string;)"
cdr_definition="(&string;)" />