Rosetta  2021.07
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Namespaces | Functions
SequenceMotifTaskOperation.cc File Reference

A TaskOp that takes a regex-like pattern and turns it into a set of design residues. The string should identify what to do for each position. An X indicates any residue, and is the same as [A_Z]. Anything other than a charactor should be in []. The ^ denotes a not. An example Regex for glycosylation is NX[ST]. This would design an ASN into the first position, skip the second, and allow S and T mutations only at the third position. N[^P][ST] would denote that at the second position, we do not allow proline. Sets of charactors using _ can be denoted, even though this doesnt really help us in design. In the future one can imagine having sets of polars, etc. etc. This TaskOp is like a simple RESFILE in a string. More...

#include <protocols/task_operations/SequenceMotifTaskOperation.hh>
#include <protocols/task_operations/SequenceMotifTaskOperationCreator.hh>
#include <core/pack/task/util.hh>
#include <core/pack/task/operation/TaskOperation.hh>
#include <core/pack/task/ResfileReader.hh>
#include <core/pack/task/operation/task_op_schemas.hh>
#include <core/pack/task/PackerTask.hh>
#include <core/pose/Pose.hh>
#include <core/select/residue_selector/ResidueSelector.hh>
#include <core/select/residue_selector/util.hh>
#include <core/sequence/sequence_motif.hh>
#include <protocols/rosetta_scripts/util.hh>
#include <basic/Tracer.hh>
#include <utility/tag/Tag.hh>
#include <utility/string_util.hh>
#include <utility/tag/XMLSchemaGeneration.hh>
#include <basic/datacache/DataMap.hh>

Namespaces

 protocols
 The instance of Loops contained by AbrelaxApplication should be replaced by a LoopsOP.
 
 protocols::task_operations
 

Functions

static basic::Tracer TR ("protocols.task_operations.SequenceMotifTaskOperation")
 

Detailed Description

A TaskOp that takes a regex-like pattern and turns it into a set of design residues. The string should identify what to do for each position. An X indicates any residue, and is the same as [A_Z]. Anything other than a charactor should be in []. The ^ denotes a not. An example Regex for glycosylation is NX[ST]. This would design an ASN into the first position, skip the second, and allow S and T mutations only at the third position. N[^P][ST] would denote that at the second position, we do not allow proline. Sets of charactors using _ can be denoted, even though this doesnt really help us in design. In the future one can imagine having sets of polars, etc. etc. This TaskOp is like a simple RESFILE in a string.

Creator for A TaskOp that takes a regex-like pattern and turns it into a set of design residues. The string should identify what to do for each position. An X indicates any residue, and is the same as [A_Z]. Anything other than a charactor should be in []. The ^ denotes a not. An example Regex for glycosylation is NX[ST]. This would design an ASN into the first position, skip the second, and allow S and T mutations only at the third position. N[^P][ST] would denote that at the second position, we do not allow proline. Sets of charactors using _ can be denoted, even though this doesnt really help us in design. In the future one can imagine having sets of polars, etc. etc. This TaskOp is like a simple RESFILE in a string.

Author
Jared Adolf-Bryfogle (jadol.nosp@m.fbr@.nosp@m.gmail.nosp@m..com)

Function Documentation

static basic::Tracer TR ( "protocols.task_operations.SequenceMotifTaskOperation"  )
static