FragMonteCarlo Class Reference

#include <FragMonteCarlo.hh>

Public Member Functions
	FragMonteCarlo (core::Real wt_dens_in, core::Real wt_overlap_in, core::Real wt_closab_in, core::Real wt_clash_in, core::Real null_frag_score_in_)
void	load_scorefiles (std::string fragidx_file, std::string scorefile_dens, std::string scorefile_overlap, std::string scorefile_nonoverlap)
void	run (bool verbose=false, core::Real sa_start_temp=1000.0, core::Real sa_end_temp=1.0, core::Size sa_nsteps=25, core::Size mc_nsteps=1500)
void	report_score (core::Real temp=0.0)
std::string	report_results (int model_ctr=0, int runid=0)
void	updated_covered_rsds (utility::vector1< int > &covered_rsds, FragID const fragidx)
bool	isOverlapping (int i_fragidx, int j_fragidx)
void	check_file_exists (std::string file_name)
bool	isNullFrag (int fragidx)
std::string	fragid_to_fragfn (FragID fragid)
utility::vector1< int > const &	get_candidate_frags (core::Size pos)
utility::vector1< int >	get_assigned_frags ()
void	initialize_frag_assignment (core::Size init_type)

Private Member Functions
core::Real	cal_frag_score (int candidate_fragidx)

Private Attributes
core::Size	n_total_frags_
core::Size	n_total_rsds_
core::Real	wt_dens_
core::Real	wt_overlap_
core::Real	wt_closab_
core::Real	wt_clash_
core::Real	null_frag_score_
std::map< int, FragID >	fragidx_to_fragid_
std::map< int, utility::vector1< int > >	pos_to_fragcands_
utility::vector1< int >	assigned_frags_
utility::vector1< utility::vector1< core::Real > >	scores_2b_
utility::vector1< core::Real >	scores_1b_
utility::vector1< core::Real >	rmsd_table_

Constructor & Destructor Documentation

FragMonteCarlo()

FragMonteCarlo::FragMonteCarlo ( core::Real  wt_dens_in, core::Real  wt_overlap_in, core::Real  wt_closab_in, core::Real  wt_clash_in, core::Real  null_frag_score_in_  )

inline

Member Function Documentation

cal_frag_score()

core::Real FragMonteCarlo::cal_frag_score ( int  candidate_fragidx )

private

References make_symmdef_file_denovo::pos.

check_file_exists()

void FragMonteCarlo::check_file_exists ( std::string  file_name )

inline

References utility::file::file_exists(), and utility_exit_with_message.

fragid_to_fragfn()

std::string FragMonteCarlo::fragid_to_fragfn ( FragID  fragid )

inline

References int2str(), FragID::mer, FragID::picker_rank, FragID::pos, and FragID::sph_rank.

get_assigned_frags()

utility::vector1<int> FragMonteCarlo::get_assigned_frags ( )

inline

get_candidate_frags()

utility::vector1<int> const& FragMonteCarlo::get_candidate_frags ( core::Size  pos )

inline

References make_symmdef_file_denovo::pos.

initialize_frag_assignment()

void FragMonteCarlo::initialize_frag_assignment

(

core::Size

init_type

)

References basic::Tracer::Info, create_a3b_hbs::j, make_symmdef_file_denovo::pos, numeric::random::random_range(), average_rmsds::rmsd, ObjexxFCL::size(), tr, and utility_exit_with_message.

isNullFrag()

bool FragMonteCarlo::isNullFrag ( int  fragidx )

inline

isOverlapping()

bool FragMonteCarlo::isOverlapping	(	int	i_fragidx,
		int	j_fragidx
	)

References FragID::mer, and FragID::pos.

load_scorefiles()

void FragMonteCarlo::load_scorefiles	(	std::string	fragidx_file,
		std::string	scorefile_dens,
		std::string	scorefile_overlap,
		std::string	scorefile_nonoverlap
	)

References clash_score(), create_a3b_hbs::i, basic::Tracer::Info, isOverlapping(), create_a3b_hbs::j, max(), FragID::mer, overlap_score(), FragID::picker_rank, FragID::pos, average_rmsds::rmsd, FragID::sph_rank, and tr.

report_results()

std::string FragMonteCarlo::report_results	(	int	model_ctr = 0,
		int	runid = 0
	)

References ObjexxFCL::format::F(), ObjexxFCL::format::I(), basic::Tracer::Info, int2str(), ObjexxFCL::format::LJ(), make_symmdef_file_denovo::pos, average_rmsds::rmsd, tag, and tr.

report_score()

void FragMonteCarlo::report_score

(

core::Real

temp = 0.0

)

References create_a3b_hbs::i, basic::Tracer::Info, erraser_analysis::temp, and tr.

run()

void FragMonteCarlo::run	(	bool	verbose = false,
		core::Real	sa_start_temp = 1000.0,
		core::Real	sa_end_temp = 1.0,
		core::Size	sa_nsteps = 25,
		core::Size	mc_nsteps = 1500
	)

References demo.D060_Folding::counter, create_a3b_hbs::i, min(), ObjexxFCL::pow(), numeric::random::random_range(), test_mm_lj::step, erraser_analysis::temp, numeric::random::uniform(), and basic::options::OptionKeys::sc::verbose.

updated_covered_rsds()

void FragMonteCarlo::updated_covered_rsds	(	utility::vector1< int > &	covered_rsds,
		FragID const	fragidx
	)

References basic::Tracer::Debug, create_a3b_hbs::i, int2str(), FragID::mer, FragID::pos, make_symmdef_file_denovo::pos, range, tr, and ObjexxFCL::unique().

Member Data Documentation

assigned_frags_

utility::vector1<int> FragMonteCarlo::assigned_frags_

private

fragidx_to_fragid_

std::map< int, FragID > FragMonteCarlo::fragidx_to_fragid_

private

n_total_frags_

core::Size FragMonteCarlo::n_total_frags_

private

n_total_rsds_

core::Size FragMonteCarlo::n_total_rsds_

private

null_frag_score_

core::Real FragMonteCarlo::null_frag_score_

private

pos_to_fragcands_

std::map< int, utility::vector1<int> > FragMonteCarlo::pos_to_fragcands_

private

rmsd_table_

utility::vector1<core::Real> FragMonteCarlo::rmsd_table_

private

scores_1b_

utility::vector1<core::Real> FragMonteCarlo::scores_1b_

private

scores_2b_

utility::vector1< utility::vector1<core::Real> > FragMonteCarlo::scores_2b_

private

wt_clash_

core::Real FragMonteCarlo::wt_clash_

private

wt_closab_

core::Real FragMonteCarlo::wt_closab_

private

wt_dens_

core::Real FragMonteCarlo::wt_dens_

private

wt_overlap_

core::Real FragMonteCarlo::wt_overlap_

private

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

• src/apps/pilot/rayyrw/FragMonteCarlo.hh