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Rosetta
2020.50
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scores a fragment by its crmsd to the given reference structure More...
#include <FragmentCrmsd.hh>
Public Member Functions | |
FragmentCrmsd (core::Size, core::Real, bool, core::pose::PoseOP) | |
creates a crmsd-based scoring function. More... | |
FragmentCrmsd (core::Size, core::Real, bool, utility::vector1< utility::vector1< core::Real > >) | |
creates a crmsd-based scoring function. More... | |
~FragmentCrmsd () override | |
void | set_pose (core::pose::PoseOP const &pose) |
Update pose/coordinates for rescoring (useful for RosettaScripts implementation of the FragmentPicker). More... | |
void | do_caching (VallChunkOP) override |
void | clean_up () override |
bool | score (FragmentCandidateOP, FragmentScoreMapOP) override |
bool | cached_score (FragmentCandidateOP, FragmentScoreMapOP) override |
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CachingScoringMethod (core::Size priority, core::Real lowest_acceptable_value, bool use_lowest, std::string name) | |
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FragmentScoringMethod (core::Size priority, core::Real lowest_acceptable_value, bool use_lowest, std::string name) | |
std::string & | get_score_name () |
Returns a name of this scoring method. More... | |
core::Size | get_id () |
Returns an integer index assigned to this scoring method by a scoring manager. More... | |
void | set_id (core::Size id) |
Sets a new integer index for this scoring method. More... | |
core::Size | get_priority () |
Returns a priority of this scoring method. More... | |
core::Real | get_min_allowed_score () |
Returns the lowest acceptable score value for this scoring method. More... | |
bool | get_use_lowest () |
Returns the boolean choice on using the above lowest acceptable score value. More... | |
void | set_min_allowed_score (core::Real lowest_acceptable_value) |
Sets a new value of the lowest acceptable score. More... | |
Private Member Functions | |
void | fill_CA_coords (core::pose::Pose const &, ObjexxFCL::FArray2_double &, core::Size) |
Private Attributes | |
std::string | cached_scores_id_ |
core::Size | n_atoms_ |
core::pose::PoseOP | reference_pose_ |
ObjexxFCL::FArray2D_double | reference_coordinates_ |
ObjexxFCL::FArray2D_double | chunk_coordinates_ |
ObjexxFCL::FArray2D_double | fragment_coordinates_ |
ObjexxFCL::FArray2D_double | frag_pos_coordinates_ |
ObjexxFCL::FArray1D_double | weights_ |
Additional Inherited Members | |
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core::Size | id_ |
core::Size | priority_ |
std::string | name_ |
core::Real | lowest_acceptable_value_ |
bool | use_lowest_ |
scores a fragment by its crmsd to the given reference structure
protocols::frag_picker::scores::FragmentCrmsd::FragmentCrmsd | ( | core::Size | priority, |
core::Real | lowest_acceptable_value, | ||
bool | use_lowest, | ||
core::pose::PoseOP | reference_pose | ||
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creates a crmsd-based scoring function.
fragments will be compared to a given pose, which should have the same number of residues a the query sequence
References fill_CA_coords(), n_atoms_, reference_coordinates_, reference_pose_, and weights_.
protocols::frag_picker::scores::FragmentCrmsd::FragmentCrmsd | ( | core::Size | priority, |
core::Real | lowest_acceptable_value, | ||
bool | use_lowest, | ||
utility::vector1< utility::vector1< core::Real > > | xyz | ||
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creates a crmsd-based scoring function.
fragments will be compared to given coordinates, which should have the same number of residues a the query sequence
References n_atoms_, reference_coordinates_, protocols::frag_picker::scores::trRmsScore(), weights_, and protocols::kinmatch::xyz().
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overridedefault |
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overridevirtual |
Reimplemented from protocols::frag_picker::scores::CachingScoringMethod.
References cached_scores_id_, chunk_coordinates_, do_caching(), frag_pos_coordinates_, fragment_coordinates_, protocols::frag_picker::scores::FragmentScoringMethod::id_, protocols::frag_picker::scores::FragmentScoringMethod::lowest_acceptable_value_, reference_coordinates_, core::scoring::rms, and protocols::frag_picker::scores::FragmentScoringMethod::use_lowest_.
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overridevirtual |
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overridevirtual |
Implements protocols::frag_picker::scores::CachingScoringMethod.
References chunk_coordinates_.
Referenced by cached_score().
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private |
References protocols::simple_filters::coords(), core::chemical::ResidueType::has(), core::conformation::Residue::name3(), core::pose::Pose::residue(), protocols::frag_picker::scores::trRmsScore(), core::conformation::Residue::type(), protocols::kinmatch::xyz(), and core::pose::Pose::xyz().
Referenced by FragmentCrmsd(), and set_pose().
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overridevirtual |
Reimplemented from protocols::frag_picker::scores::CachingScoringMethod.
References frag_pos_coordinates_, fragment_coordinates_, protocols::frag_picker::scores::FragmentScoringMethod::id_, protocols::frag_picker::scores::FragmentScoringMethod::lowest_acceptable_value_, reference_coordinates_, core::scoring::rms, and protocols::frag_picker::scores::FragmentScoringMethod::use_lowest_.
Referenced by protocols::frag_picker::FragmentScoreFilter::rescore_fragment_crmsd().
void protocols::frag_picker::scores::FragmentCrmsd::set_pose | ( | core::pose::PoseOP const & | pose | ) |
Update pose/coordinates for rescoring (useful for RosettaScripts implementation of the FragmentPicker).
References fill_CA_coords(), n_atoms_, reference_coordinates_, reference_pose_, and weights_.
Referenced by protocols::frag_picker::FragmentScoreFilter::rescore_fragment_crmsd().
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Referenced by cached_score().
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Referenced by cached_score(), and do_caching().
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Referenced by cached_score(), and score().
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Referenced by cached_score(), and score().
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Referenced by FragmentCrmsd(), and set_pose().
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Referenced by cached_score(), FragmentCrmsd(), score(), and set_pose().
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Referenced by FragmentCrmsd(), and set_pose().
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Referenced by FragmentCrmsd(), and set_pose().