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Rosetta
2015.31
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scores a fragment by its crmsd to the given reference structure More...
#include <FragmentAllAtomCrmsd.hh>
Public Member Functions | |
FragmentAllAtomCrmsd (Size, Real, bool, std::string, core::pose::PoseOP) | |
creates a crmsd-based scoring function. More... | |
FragmentAllAtomCrmsd (Size, Real, bool, std::string, utility::vector1< utility::vector1< Real > >) | |
creates a crmsd-based scoring function. More... | |
~FragmentAllAtomCrmsd () | |
bool | score (FragmentCandidateOP, FragmentScoreMapOP) |
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FragmentScoringMethod (Size priority, Real lowest_acceptable_value, bool use_lowest, std::string name) | |
std::string & | get_score_name () |
Returns a name of this scoring method. More... | |
Size | get_id () |
Returns an integer index assigned to this scoring method by a scoring manager. More... | |
void | set_id (Size id) |
Sets a new integer index for this scoring method. More... | |
Size | get_priority () |
Returns a priority of this scoring method. More... | |
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 (Real lowest_acceptable_value) |
Sets a new value of the lowest acceptable score. More... | |
Private Member Functions | |
void | fill_coords (core::pose::Pose const &, FArray2_double &, Size, std::string) |
Private Attributes | |
std::string | cached_scores_id_ |
Size | total_ref_resids_ |
std::string | query_sequence_ |
pose::PoseOP | reference_pose_ |
pose::PoseOP | fragment_pose_ |
FArray2D_double | reference_coordinates_ |
FArray2D_double | chunk_coordinates_ |
FArray2D_double | fragment_coordinates_ |
FArray2D_double | frag_pos_coordinates_ |
FArray1D_double | weights_ |
Additional Inherited Members | |
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Size | id_ |
Size | priority_ |
std::string | name_ |
Real | lowest_acceptable_value_ |
bool | use_lowest_ |
scores a fragment by its crmsd to the given reference structure
protocols::frag_picker::scores::FragmentAllAtomCrmsd::FragmentAllAtomCrmsd | ( | Size | priority, |
Real | lowest_acceptable_value, | ||
bool | use_lowest, | ||
std::string | query_sequence, | ||
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_coords(), fragment_pose_, core::pose::make_pose_from_sequence(), reference_coordinates_, reference_pose_, total_ref_resids_, and weights_.
protocols::frag_picker::scores::FragmentAllAtomCrmsd::FragmentAllAtomCrmsd | ( | Size | priority, |
Real | lowest_acceptable_value, | ||
bool | use_lowest, | ||
std::string | query_sequence, | ||
utility::vector1< utility::vector1< 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 fragment_pose_, core::pose::make_pose_from_sequence(), reference_coordinates_, reference_pose_, total_ref_resids_, protocols::frag_picker::scores::trRmsScore(), weights_, and protocols::kinmatch::xyz().
protocols::frag_picker::scores::FragmentAllAtomCrmsd::~FragmentAllAtomCrmsd | ( | ) |
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Implements protocols::frag_picker::scores::FragmentScoringMethod.
References fill_coords(), frag_pos_coordinates_, fragment_coordinates_, fragment_pose_, 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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Referenced by score().
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Referenced by score().
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Referenced by FragmentAllAtomCrmsd(), and score().
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Referenced by FragmentAllAtomCrmsd(), and score().
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Referenced by FragmentAllAtomCrmsd().
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Referenced by FragmentAllAtomCrmsd().
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Referenced by FragmentAllAtomCrmsd().