Rosetta 3.4
Public Types | Public Member Functions
protocols::toolbox::task_operations::RestrictConservedLowDdgOperation Class Reference

a Task operation that will check whether the amino acid at a position is conserved in the sequence profile and has an unfavorable ddG when mutated to ala. all positions that match this criterion will get set to repacking. More...

#include <SeqprofConsensusOperation.hh>

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List of all members.

Public Types

typedef SeqprofConsensusOperation Parent

Public Member Functions

 RestrictConservedLowDdgOperation ()
 ~RestrictConservedLowDdgOperation ()
virtual TaskOperationOP clone () const
 make clone
void parse_tag (TagPtr tag)
 Used to parse an xml-like tag to load parameters and properties.
virtual void apply (Pose const &pose, PackerTask &task) const
 apply
bool position_untouchable (core::Size seqpos, core::chemical::AA seqprof_wt) const
 returns true if seqpos has a sequence profile frequency > conservation_cutoff_ and an X->A ddG of > ddG_cutoff_
core::chemical::AA seqprof_wt_aa (core::Size seqpos) const
core::Real position_ala_ddG (core::Size seqpos) const
 convenience function to query what the ddG is for a to ala mutation at a certain position
bool verbose () const

Detailed Description

a Task operation that will check whether the amino acid at a position is conserved in the sequence profile and has an unfavorable ddG when mutated to ala. all positions that match this criterion will get set to repacking.

wt ala positions are set to repacking based on seqprof criterion only. If the input pose contains a forbidden (i.e. non wildtype ) residue at an untouchable position, the residue currently in the pose is also allowed.


Member Typedef Documentation


Constructor & Destructor Documentation

protocols::toolbox::task_operations::RestrictConservedLowDdgOperation::RestrictConservedLowDdgOperation ( )
protocols::toolbox::task_operations::RestrictConservedLowDdgOperation::~RestrictConservedLowDdgOperation ( )

Member Function Documentation

void protocols::toolbox::task_operations::RestrictConservedLowDdgOperation::apply ( Pose const &  pose,
PackerTask task 
) const [virtual]
core::pack::task::operation::TaskOperationOP protocols::toolbox::task_operations::RestrictConservedLowDdgOperation::clone ( ) const [virtual]
void protocols::toolbox::task_operations::RestrictConservedLowDdgOperation::parse_tag ( TagPtr  tag) [virtual]
core::Real protocols::toolbox::task_operations::RestrictConservedLowDdgOperation::position_ala_ddG ( core::Size  seqpos) const

convenience function to query what the ddG is for a to ala mutation at a certain position

References core::chemical::aa_ala, core::io::PositionDdGInfo::PositionDdGInfo::mutation_ddGs(), and seqprof_wt_aa().

bool protocols::toolbox::task_operations::RestrictConservedLowDdgOperation::position_untouchable ( core::Size  seqpos,
core::chemical::AA  seqprof_wt 
) const
core::chemical::AA protocols::toolbox::task_operations::RestrictConservedLowDdgOperation::seqprof_wt_aa ( core::Size  seqpos) const
bool protocols::toolbox::task_operations::RestrictConservedLowDdgOperation::verbose ( ) const [inline]

The documentation for this class was generated from the following files:
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