protocols::match::NumNeighborsMPM Class Reference

removes positions whose numer of neighbors below a 10A cutoff is not within the desired range. if either min_neighbors_ or max_neighbors_ are unspecified (0), this means that they won't be taken into account, i.e. if min is 5 and max is 0, every position that has more than 4 neighbors will be allowed. also offers the possibility of combining the num neighbors cutoff with the angle between the CA->CB vector of the residue and the CA->protein_center_of_mass vector, for example to only allow positions that point inward More...

#include <MatchPositionModifiers.hh>

Inheritance diagram for protocols::match::NumNeighborsMPM:

Public Member Functions
	NumNeighborsMPM (utility::vector1< std::string > const &input_tokens)
	~NumNeighborsMPM () override
utility::vector1< core::Size >	modified_match_positions (utility::vector1< core::Size > const &original_positions, core::pose::Pose const &match_pose, protocols::match::MatcherTaskCOP mtask) const override
	the positions in the vector1< Size > that is returned by this function will replace the match positions in the MatcherTask. More...
bool	passes_com_vector_criterion (core::Size seqpos, core::pose::Pose const &pose, core::Vector const &com) const
Public Member Functions inherited from protocols::match::MatchPositionModifier
	MatchPositionModifier ()
	~MatchPositionModifier () override

Private Attributes
core::Size	min_neighbors_
core::Size	max_neighbors_
bool	com_vector_criterion_
bool	both_criteria_needed_to_pass_
core::Real	min_com_vector_ang_cos_
core::Real	max_com_vector_ang_cos_

Detailed Description

removes positions whose numer of neighbors below a 10A cutoff is not within the desired range. if either min_neighbors_ or max_neighbors_ are unspecified (0), this means that they won't be taken into account, i.e. if min is 5 and max is 0, every position that has more than 4 neighbors will be allowed. also offers the possibility of combining the num neighbors cutoff with the angle between the CA->CB vector of the residue and the CA->protein_center_of_mass vector, for example to only allow positions that point inward

Constructor & Destructor Documentation

protocols::match::NumNeighborsMPM::NumNeighborsMPM

(

utility::vector1< std::string > const &

input_tokens

)

References both_criteria_needed_to_pass_, com_vector_criterion_, max_com_vector_ang_cos_, max_neighbors_, min_com_vector_ang_cos_, min_neighbors_, and protocols::match::tr().

protocols::match::NumNeighborsMPM::~NumNeighborsMPM ( )

overridedefault

Member Function Documentation

utility::vector1< core::Size > protocols::match::NumNeighborsMPM::modified_match_positions ( utility::vector1< core::Size > const &  original_positions, core::pose::Pose const &  match_pose, protocols::match::MatcherTaskCOP  mtask  ) const

overridevirtual

the positions in the vector1< Size > that is returned by this function will replace the match positions in the MatcherTask.

Implements protocols::match::MatchPositionModifier.

References both_criteria_needed_to_pass_, core::pose::center_of_mass(), com_vector_criterion_, core::pose::Pose::energies(), max_neighbors_, min_neighbors_, core::conformation::Residue::nbr_atom_xyz(), passes_com_vector_criterion(), core::pose::Pose::residue(), core::pose::Pose::size(), core::scoring::Energies::tenA_neighbor_graph(), core::id::to_string(), and protocols::match::tr().

bool protocols::match::NumNeighborsMPM::passes_com_vector_criterion	(	core::Size	seqpos,
		core::pose::Pose const &	pose,
		core::Vector const &	com
	)		const

References core::conformation::Residue::aa(), core::chemical::aa_gly, core::conformation::Residue::atom(), max_com_vector_ang_cos_, min_com_vector_ang_cos_, core::pose::Pose::residue(), protocols::kinmatch::xyz(), and core::conformation::Atom::xyz().

Referenced by modified_match_positions().

Member Data Documentation

bool protocols::match::NumNeighborsMPM::both_criteria_needed_to_pass_

private

Referenced by modified_match_positions(), and NumNeighborsMPM().

bool protocols::match::NumNeighborsMPM::com_vector_criterion_

private

Referenced by modified_match_positions(), and NumNeighborsMPM().

core::Real protocols::match::NumNeighborsMPM::max_com_vector_ang_cos_

private

Referenced by NumNeighborsMPM(), and passes_com_vector_criterion().

core::Size protocols::match::NumNeighborsMPM::max_neighbors_

private

Referenced by modified_match_positions(), and NumNeighborsMPM().

core::Real protocols::match::NumNeighborsMPM::min_com_vector_ang_cos_

private

Referenced by NumNeighborsMPM(), and passes_com_vector_criterion().

core::Size protocols::match::NumNeighborsMPM::min_neighbors_

private

Referenced by modified_match_positions(), and NumNeighborsMPM().

---

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

• src/protocols/match/MatchPositionModifiers.hh
• src/protocols/match/MatchPositionModifiers.cc