rna_denovo.cc File Reference

#include <core/types.hh>
#include <basic/options/option.hh>
#include <basic/options/option_macros.hh>
#include <protocols/viewer/viewers.hh>
#include <core/pose/Pose.hh>
#include <core/init/init.hh>
#include <utility/vector1.hh>
#include <protocols/farna/RNA_DeNovoProtocol.hh>
#include <protocols/farna/setup/RNA_DeNovoSetup.hh>
#include <protocols/farna/options/RNA_DeNovoProtocolOptions.hh>
#include <iostream>
#include <string>
#include <basic/options/keys/out.OptionKeys.gen.hh>
#include <basic/options/keys/in.OptionKeys.gen.hh>
#include <basic/options/keys/chemical.OptionKeys.gen.hh>
#include <basic/options/keys/rna.OptionKeys.gen.hh>
#include <basic/options/keys/stepwise.OptionKeys.gen.hh>
#include <basic/options/keys/constraints.OptionKeys.gen.hh>
#include <basic/options/keys/score.OptionKeys.gen.hh>
#include <basic/options/keys/full_model.OptionKeys.gen.hh>
#include <core/pose/annotated_sequence.hh>
#include <core/sequence/Sequence.hh>
#include <utility/file/file_sys_util.hh>
#include <utility/excn/Exceptions.hh>

Functions
vector1< pose::PoseOP >	get_refine_pose_list (std::string const &input_silent_file, std::pair< utility::vector1< int >, utility::vector1< char > > const &output_res_and_chain, core::chemical::ResidueTypeSetCOP rsd_set)
void	rna_denovo_test ()
void *	my_main (void *)
int	main (int argc, char *argv[])

Detailed Description

Author

Rhiju Das

Function Documentation

vector1<pose::PoseOP> get_refine_pose_list	(	std::string const &	input_silent_file,
		std::pair< utility::vector1< int >, utility::vector1< char > > const &	output_res_and_chain,
		core::chemical::ResidueTypeSetCOP	rsd_set
	)

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

References rna::farna::allow_bulge(), rna::farna::allow_consecutive_bulges(), rna::farna::allowed_bulge_res(), rna::farna::autofilter(), rna::farna::binary_output(), rna::farna::bps_moves(), rna::farna::close_loops(), rna::farna::close_loops_after_each_move(), utility::io::oc::cout, constraints::cst_file(), full_model::cutpoint_closed(), full_model::cutpoint_open(), rna::farna::cycles(), basic::options::OptionKeys::rna::data_file, rna::farna::dump(), rna::farna::minimize::extra_minimize_chi_res(), rna::farna::minimize::extra_minimize_res(), in::file::fasta(), rna::farna::filter_chain_closure(), rna::farna::filter_chain_closure_distance(), rna::farna::filter_chain_closure_halfway(), rna::farna::filter_lores_base_pairs(), rna::farna::filter_lores_base_pairs_early(), rna::farna::fixed_stems(), rna::farna::heat(), basic::init(), in::file::input_res(), rna::farna::jump_change_frequency(), rna::farna::lores_scorefxn(), rna::farna::minimize::minimize_bps(), rna::farna::minimize_rna(), rna::farna::minimize::minimizer_use_coordinate_constraints(), rna::farna::move_first_rigid_body(), utility::excn::EXCN_Base::msg(), my_main(), in::file::native(), out::nstruct(), rna::farna::obligate_pair(), rna::farna::obligate_pair_explicit(), rna::farna::offset(), option, options, rna::farna::output_filters(), rna::farna::output_lores_silent_file(), rna::farna::output_res_num(), rna::farna::params_file(), basic::options::OptionKeys::chemical::patch_selectors, rna::farna::refine_native(), rna::farna::refine_silent_file(), rna::farna::rna_lores_chainbreak_weight(), rna::farna::rna_lores_linear_chainbreak_weight(), rna::farna::root_at_first_rigid_body(), rna::farna::secstruct(), rna::farna::secstruct_file(), rna::farna::sequence(), out::file::silent(), rna::farna::staged_constraints(), rna::farna::suppress_bp_constraint(), rna::farna::tag(), rna::farna::temperature(), rna::farna::use_1jj2_torsions(), basic::options::OptionKeys::rna::farna::vall_torsions, rna::vary_geometry(), and score::weights().

void* my_main

(

void *

)

References utility::options::OptionKeys::options::exit, and rna_denovo_test().

Referenced by main().

void rna_denovo_test

(

)

References basic::options::OptionKeys::rna::farna::farna, and app.surface_docking.surface_docking::pose.

Referenced by my_main().