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Rosetta
2016.11
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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>
Public Types | |
typedef SeqprofConsensusOperation | Parent |
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typedef std::string | String |
typedef core::Real | Real |
typedef core::pose::Pose | Pose |
typedef core::pack::task::PackerTask | PackerTask |
typedef core::pack::task::operation::TaskOperation | TaskOperation |
typedef core::pack::task::operation::TaskOperationOP | TaskOperationOP |
typedef TaskOperation | parent |
typedef utility::tag::TagCOP | TagCOP |
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typedef utility::tag::TagCOP | TagCOP |
typedef basic::datacache::DataMap | DataMap |
typedef pose::Pose | Pose |
Private Attributes | |
std::string | ddG_predictions_filename_ |
std::map< core::Size, core::io::PositionDdGInfo::PositionDdGInfoOP > | position_ddGs_ |
core::Real | conservation_cutoff_ |
core::Real | ddG_cutoff_ |
bool | verbose_ |
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.
typedef SeqprofConsensusOperation protocols::toolbox::task_operations::RestrictConservedLowDdgOperation::Parent |
protocols::toolbox::task_operations::RestrictConservedLowDdgOperation::RestrictConservedLowDdgOperation | ( | ) |
References ddG_predictions_filename_, protocols::stepwise::modeler::rna::file_exists(), position_ddGs_, and core::io::PositionDdGInfo::read_ddg_predictions_file().
Referenced by clone().
protocols::toolbox::task_operations::RestrictConservedLowDdgOperation::~RestrictConservedLowDdgOperation | ( | ) |
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apply
all AA that have a higher probability in the seqprofile than the native residue are allowed. probability also needs to be higher than min_aa_probability_
NOTE ON SYMMETRIC POSE BEHAVIOR: pssm files are usually for one chain only, therefore this task operation will only set the residue behavior for the first chain/asymetric unit. it could be possible to handle the symmetry setup here, i.e. set up the residue level task for every symmetric copy, but it's prolly better to let the symmetry machinery deal with that mode of packer task symmetrization should be intersection
Reimplemented from protocols::toolbox::task_operations::SeqprofConsensusOperation.
References core::chemical::ResidueType::aa(), core::chemical::ResidueType::is_protein(), core::pack::task::PackerTask::nonconst_residue_task(), core::chemical::num_canonical_aas, position_ddGs_, position_untouchable(), core::pose::Pose::residue_type(), core::pack::task::ResidueLevelTask::restrict_absent_canonical_aas(), core::pack::task::ResidueLevelTask::restrict_to_repacking(), protocols::toolbox::task_operations::SeqprofConsensusOperation::seqprof(), seqprof_wt_aa(), and core::pose::Pose::total_residue().
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make clone
clone
Reimplemented from protocols::toolbox::task_operations::SeqprofConsensusOperation.
References RestrictConservedLowDdgOperation().
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Used to parse an xml-like tag to load parameters and properties.
Reimplemented from protocols::toolbox::task_operations::SeqprofConsensusOperation.
References conservation_cutoff_, ddG_cutoff_, ddG_predictions_filename_, protocols::toolbox::task_operations::SeqprofConsensusOperation::parse_tag(), position_ddGs_, core::io::PositionDdGInfo::read_ddg_predictions_file(), and verbose_.
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, ddG_predictions_filename_, core::io::PositionDdGInfo::PositionDdGInfo::mutation_ddGs(), position_ddGs_, seqprof_wt_aa(), and core::id::to_string().
bool protocols::toolbox::task_operations::RestrictConservedLowDdgOperation::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_
References core::chemical::aa_ala, conservation_cutoff_, ddG_cutoff_, ddG_predictions_filename_, core::io::PositionDdGInfo::PositionDdGInfo::mutation_ddGs(), position_ddGs_, protocols::toolbox::task_operations::SeqprofConsensusOperation::seqprof(), core::id::to_string(), protocols::toolbox::tr(), verbose_, and core::io::PositionDdGInfo::PositionDdGInfo::wt_aa().
Referenced by apply().
core::chemical::AA protocols::toolbox::task_operations::RestrictConservedLowDdgOperation::seqprof_wt_aa | ( | core::Size | seqpos | ) | const |
References core::chemical::aa_from_oneletter_code(), and protocols::toolbox::task_operations::SeqprofConsensusOperation::seqprof().
Referenced by apply(), and position_ala_ddG().
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Referenced by parse_tag(), and position_untouchable().
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Referenced by parse_tag(), and position_untouchable().
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Referenced by parse_tag(), position_ala_ddG(), position_untouchable(), and RestrictConservedLowDdgOperation().
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Referenced by apply(), parse_tag(), position_ala_ddG(), position_untouchable(), and RestrictConservedLowDdgOperation().
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Referenced by parse_tag(), and position_untouchable().