anneal_align.cc File Reference

#include <core/types.hh>
#include <devel/init.hh>
#include <basic/Tracer.hh>
#include <core/chemical/AA.hh>
#include <core/sequence/Sequence.hh>
#include <utility/exit.hh>
#include <utility/vector1.hh>
#include <utility/io/izstream.hh>
#include <ObjexxFCL/format.hh>
#include <numeric/random/random.hh>
#include <fstream>
#include <iostream>
#include <string>
#include <utility/excn/Exceptions.hh>

Functions
MultipleSequenceAlignment	random_alignment_move (MultipleSequenceAlignment const &msa)
Real	blosum_score_alignment (MultipleSequenceAlignment &msa)
Real	score_alignment (MultipleSequenceAlignment &msa)
Real	get_temp (Size current_iter, Size)
int	main (int argc, char *argv[])

Detailed Description

Author

James Thompson

Function Documentation

blosum_score_alignment()

Real blosum_score_alignment

(

MultipleSequenceAlignment &

msa

)

References aa, basic::options::OptionKeys::chemical::chemical, utility::io::oc::cout, end, getline(), create_a3b_hbs::i, basic::init(), gaussian-sampling::input, create_a3b_hbs::j, line, pyrosetta.utility.array::message, kmeans_adaptive_kernel_density_bb_dependent_rotlib::p, create_a3b_hbs::score, subloop_histogram::size, and utility_exit_with_message.

Referenced by score_alignment().

get_temp()

Real get_temp	(	Size	current_iter,
		Size
	)

References compute_difference::alpha, create_a3b_hbs::i, and erraser_analysis::temp.

Referenced by main().

main()

int main	(	int	argc,
		char *	argv[]
	)

References argv, utility::io::oc::cout, test.T009_Exceptions::e, end, get_temp(), create_a3b_hbs::i, basic::init(), create_a3b_hbs::j, create_a3b_hbs::k, max(), min(), basic::options::OptionKeys::mp::quickrelax::nmoves, random_alignment_move(), score_alignment(), basic::options::OptionKeys::recces::seq1, basic::options::OptionKeys::recces::seq2, local::temperature, and numeric::random::uniform().

random_alignment_move()

MultipleSequenceAlignment random_alignment_move

(

MultipleSequenceAlignment const &

msa

)

References numeric::random::random_range().

Referenced by main().

score_alignment()

Real score_alignment

(

MultipleSequenceAlignment &

msa

)

References blosum_score_alignment().

Referenced by main().