protocols::hybridization::DDomainParse Class Reference

#include <DDomainParse.hh>

Public Member Functions
	DDomainParse ()
	DDomainParse (core::Real pcut_in, core::Real hcut_in, core::Size length_in)
utility::vector1< loops::Loops >	split (core::pose::Pose const &templ, core::Size nres)

Private Member Functions
void	pulldomain (int isize0, int ist, int ilast, utility::vector1< core::Real > &resect, int &idip)
void	findpos (int mdom, int ndom, int id, utility::vector1< int > &ipdom, int &ist, int &ilast)
void	findpos2 (int ist, int ilast, int imid, int i, int &ista, int &ilasta)
void	small_big (int const &mdom, int const &ipdd, utility::vector1< int > &ipdom)
void	distance (int ist, int ilast, utility::vector1< numeric::xyzVector< core::Real > > const &xs, utility::vector1< utility::vector1< core::Real > > &dij)
void	ddomain_pot (core::Real pw, int ist, int ilast, utility::vector1< utility::vector1< core::Real > > const &dij, utility::vector1< core::Real > &resect)

Private Attributes
core::Real	pcut_
core::Real	hcut_
core::Size	length_
core::Size	mseq_
core::Size	nseq_

Constructor & Destructor Documentation

protocols::hybridization::DDomainParse::DDomainParse ( )

inline

References hcut_, length_, and pcut_.

protocols::hybridization::DDomainParse::DDomainParse ( core::Real  pcut_in, core::Real  hcut_in, core::Size  length_in  )

inline

References hcut_, length_, and pcut_.

Member Function Documentation

void protocols::hybridization::DDomainParse::ddomain_pot ( core::Real  pw, int  ist, int  ilast, utility::vector1< utility::vector1< core::Real > > const &  dij, utility::vector1< core::Real > &  resect  )

private

References mseq_.

Referenced by split().

void protocols::hybridization::DDomainParse::distance ( int  ist, int  ilast, utility::vector1< numeric::xyzVector< core::Real > > const &  xs, utility::vector1< utility::vector1< core::Real > > &  dij  )

private

References mseq_.

Referenced by split().

void protocols::hybridization::DDomainParse::findpos ( int  mdom, int  ndom, int  id, utility::vector1< int > &  ipdom, int &  ist, int &  ilast  )

private

References nseq_.

Referenced by split().

void protocols::hybridization::DDomainParse::findpos2 ( int  ist, int  ilast, int  imid, int  i, int &  ista, int &  ilasta  )

private

Referenced by split().

void protocols::hybridization::DDomainParse::pulldomain ( int  isize0, int  ist, int  ilast, utility::vector1< core::Real > &  resect, int &  idip  )

private

References hcut_, length_, mseq_, and pcut_.

Referenced by split().

void protocols::hybridization::DDomainParse::small_big ( int const &  mdom, int const &  ipdd, utility::vector1< int > &  ipdom  )

private

Referenced by split().

utility::vector1< loops::Loops > protocols::hybridization::DDomainParse::split	(	core::pose::Pose const &	templ,
		core::Size	nres
	)

References core::conformation::Residue::aa(), core::chemical::aa_gly, core::chemical::aa_pro, protocols::loops::Loops::add_loop(), core::conformation::Residue::atom(), ddomain_pot(), distance(), findpos(), findpos2(), core::conformation::Residue::first_sidechain_atom(), mseq_, core::conformation::Residue::nheavyatoms(), nseq_, pulldomain(), core::pose::Pose::residue(), runtime_assert, small_big(), core::pose::Pose::total_residue(), and core::conformation::Atom::xyz().

Referenced by protocols::hybridization::HybridizeProtocol::apply(), and protocols::hybridization::HybridizeSetup::realign_templates().

Member Data Documentation

core::Real protocols::hybridization::DDomainParse::hcut_

private

Referenced by DDomainParse(), and pulldomain().

core::Size protocols::hybridization::DDomainParse::length_

private

Referenced by DDomainParse(), and pulldomain().

core::Size protocols::hybridization::DDomainParse::mseq_

private

Referenced by ddomain_pot(), distance(), pulldomain(), and split().

core::Size protocols::hybridization::DDomainParse::nseq_

private

Referenced by findpos(), and split().

core::Real protocols::hybridization::DDomainParse::pcut_

private

Referenced by DDomainParse(), and pulldomain().

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

• src/protocols/hybridization/DDomainParse.hh
• src/protocols/hybridization/DDomainParse.cc