FragmentAssemblyMover Class Reference

Public Member Functions
	FragmentAssemblyMover ()
void	run ()
core::Real	score (bool)
virtual std::string	get_name () const

Private Attributes
core::Real	overlap_wt_
core::Real	clash_wt_
core::Real	close_wt_
core::Real	dens_wt_
core::Real	null_frag_
utility::vector1< FragID >	allfrags
std::map< FragID, int >	frag2idx
utility::vector1 < utility::vector1< int > >	pos2frags
utility::vector1< int >	assigned_frags
utility::vector1 < utility::vector1< float > >	scores_2b
utility::vector1< core::Real >	scores_1b
utility::vector1< core::Real >	rmses
utility::vector1 < utility::vector1< float > >	clash2b
utility::vector1 < utility::vector1< float > >	overlap2b
utility::vector1 < utility::vector1< float > >	close2b

Constructor & Destructor Documentation

FragmentAssemblyMover::FragmentAssemblyMover

(

)

References clash_wt_, close_wt_, dens_wt_, null_frag_, option, overlap_wt_, and basic::options::OptionKeys::inout::dbms::user.

Member Function Documentation

virtual std::string FragmentAssemblyMover::get_name ( ) const

inlinevirtual

void FragmentAssemblyMover::run

(

)

References allfrags, assigned_frags, clash_wt_, close_wt_, dens_wt_, distance(), basic::options::OptionKeys::cutoutdomain::end, frag2idx, basic::options::OptionKeys::in::in, ObjexxFCL::index(), basic::options::OptionKeys::mp::mutate_relax::iter, min(), clean_pdb_keep_ligand::nres, local::nstruct, out::nstruct(), null_frag_, option, clean_pdb_keep_ligand::outfile, overlap_wt_, make_symmdef_file_denovo::pos, pos2frags, ObjexxFCL::pow(), numeric::random::random_range(), ObjexxFCL::right_string_of(), rmses, score(), basic::options::OptionKeys::out::file::scorefile, scores_1b, scores_2b, in::file::silent(), out::file::silent(), tag, TR, basic::options::OptionKeys::frags::contacts::type, numeric::random::uniform(), and basic::options::OptionKeys::inout::dbms::user.

Referenced by main().

core::Real FragmentAssemblyMover::score

(

bool

verbose = false

)

References assigned_frags, basic::options::OptionKeys::frags::j, clean_pdb_keep_ligand::nres, null_frag_, rmses, scores_1b, scores_2b, TR, and basic::options::OptionKeys::rescore::verbose.

Referenced by app.pyrosetta_toolkit.window_modules.pymol_integration.PyMOL.AdvancedPyMOL::makeWindow(), run(), and app.pyrosetta_toolkit.window_modules.pymol_integration.PyMOL.AdvancedPyMOL::SendPose().

Member Data Documentation

utility::vector1< FragID > FragmentAssemblyMover::allfrags

private

Referenced by run().

utility::vector1<int> FragmentAssemblyMover::assigned_frags

private

Referenced by run(), and score().

utility::vector1< utility::vector1< float > > FragmentAssemblyMover::clash2b

private

core::Real FragmentAssemblyMover::clash_wt_

private

Referenced by FragmentAssemblyMover(), and run().

utility::vector1< utility::vector1< float > > FragmentAssemblyMover::close2b

private

core::Real FragmentAssemblyMover::close_wt_

private

Referenced by FragmentAssemblyMover(), and run().

core::Real FragmentAssemblyMover::dens_wt_

private

Referenced by FragmentAssemblyMover(), and run().

std::map< FragID, int > FragmentAssemblyMover::frag2idx

private

Referenced by run().

core::Real FragmentAssemblyMover::null_frag_

private

Referenced by FragmentAssemblyMover(), run(), and score().

utility::vector1< utility::vector1< float > > FragmentAssemblyMover::overlap2b

private

core::Real FragmentAssemblyMover::overlap_wt_

private

Referenced by FragmentAssemblyMover(), and run().

utility::vector1< utility::vector1<int> > FragmentAssemblyMover::pos2frags

private

Referenced by run().

utility::vector1<core::Real> FragmentAssemblyMover::rmses

private

Referenced by run(), and score().

utility::vector1<core::Real> FragmentAssemblyMover::scores_1b

private

Referenced by run(), and score().

utility::vector1< utility::vector1< float > > FragmentAssemblyMover::scores_2b

private

Referenced by run(), and score().

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

• src/apps/public/electron_density/denovo_density.cc