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<SecondaryStructure name="(&string, required)"
residue_selector="(&string, TrueSelector)"
use_abego="(&int, optional)"
blueprint="(&string)"
ss="(&string)"
abego="(&string)"
compute_pose_secstruct_by_dssp="(&bool, false)"
threshold="(&real, 1.0)" />
Filter structures by comparing the secondary structure of the pose to a desired secondary structure. The filter reports a value of N_MATCHING / N_TOTAL, where N_MATCHING is the number of selected protein residues with secondary structure matching the desired secondary structure, and N_TOTAL is the total number of selected protein residues.
If compute_pose_secstruct_by_dssp is false (default), the current secondary structure of the pose must be properly set in the pose. This can be done using DsspMover as shown in the example below. If compute_pose_secstruct_by_dssp is false, DSSP will be automatically used on the input pose to determine the pose secondary structure.
Secondary Structure specification :
Example with a blueprint:
<SecondaryStructure name="ss_filter1" use_abego="1" blueprint="input.blueprint" />
Examples with top7 derived structures
(Input)
<FILTERS>
<SecondaryStructure name="ss" ss="LEEEEEEEELLLLEEEEEEEELLLLHHHHHHHHHHHHHHHLLLEEEEEEELLLHHHHHHHHHHHHHHHHHLLLLhhEEEEELLEEEEEEEL"/>
</FILTERS>
<MOVERS>
<Dssp name="dssp"/>
</MOVERS>
<PROTOCOLS>
<Add mover="dssp"/>
<Add filter="ss"/>
</PROTOCOLS>
(Output)
(when passed)
protocols.fldsgn.filters.SecondaryStructureFilter: LEEEEEEEELLLLEEEEEEEELLLLHHHHHHHHHHHHHHHLLLEEEEEEELLLHHHHHHHHHHHHHHHHHLLLLhhEEEEELLEEEEEEEL was filtered with 91 residues matching LEEEEEEEELLLLEEEEEEEELLLLHHHHHHHHHHHHHHHLLLEEEEEEELLLHHHHHHHHHHHHHHHHHLLLLLLEEEEELLEEEEEEEL
(when failed)
protocols.fldsgn.filters.SecondaryStructureFilter: SS filter fail: current/filtered = H/L at position 25
protocols.fldsgn.filters.SecondaryStructureFilter: LEEEEEEEELLLLEEEEEEEELLLLHHHHHHHHHHHHHHHLLLEEEEEEELLLHHHHHHHHHHHHHHHHHLLLLhhEEEEELLEEEEEEEL was filtered with 90 residues matching LEEEEEEEELLLLEEEEEEEELLLHHHHHHHHHHHHHHHHLLLEEEEEEELLLHHHHHHHHHHHHHHHHHLLLLEEEEEEELLEEEEEEEL