cs_rosetta_rna.cc File Reference

#include <core/types.hh>
#include <core/chemical/AA.hh>
#include <core/chemical/ChemicalManager.hh>
#include <core/chemical/VariantType.hh>
#include <core/scoring/ScoreFunction.hh>
#include <core/scoring/ScoreFunctionFactory.hh>
#include <core/scoring/ScoringManager.hh>
#include <core/scoring/constraints/ConstraintSet.hh>
#include <core/scoring/constraints/ConstraintSet.fwd.hh>
#include <core/scoring/constraints/ConstraintIO.hh>
#include <core/scoring/Energies.hh>
#include <core/scoring/rna/chemical_shift/RNA_ChemicalShiftPotential.hh>
#include <core/sequence/util.hh>
#include <core/import_pose/pose_stream/SilentFilePoseInputStream.hh>
#include <core/import_pose/import_pose.hh>
#include <core/pose/Pose.hh>
#include <core/pose/annotated_sequence.hh>
#include <core/init/init.hh>
#include <core/io/pdb/pose_io.hh>
#include <core/sequence/Sequence.hh>
#include <protocols/toolbox/AllowInsert.hh>
#include <protocols/farna/RNA_Minimizer.fwd.hh>
#include <protocols/farna/RNA_Minimizer.hh>
#include <protocols/farna/RNA_StructureParameters.hh>
#include <protocols/farna/RNA_DeNovoProtocol.hh>
#include <protocols/farna/RNA_LoopCloser.hh>
#include <iostream>
#include <string>
#include <basic/database/open.hh>
#include <basic/options/option.hh>
#include <basic/options/option_macros.hh>
#include <basic/options/keys/out.OptionKeys.gen.hh>
#include <basic/options/keys/in.OptionKeys.gen.hh>
#include <basic/options/keys/rna.OptionKeys.gen.hh>
#include <basic/options/keys/score.OptionKeys.gen.hh>
#include <utility/file/file_sys_util.hh>
#include <utility/excn/Exceptions.hh>
#include <ObjexxFCL/string.functions.hh>
#include <protocols/viewer/viewers.hh>
#include <utility/vector1.hh>

Functions
ScoreFunctionOP	create_cs_rosetta_rna_scorefxn ()
RNA_StructureParametersOP	setup_rna_struct_params (core::pose::Pose &pose)
utility::vector1< RNA_Pairing >	get_obligated_rna_pairings (RNA_StructureParametersOP rna_struct_params)
RNA_MinimizerOP	setup_rna_minimizer (ScoreFunctionOP scorefxn, RNA_StructureParametersOP rna_struct_params, core::pose::Pose &pose)
Real	compute_chem_shift_RMSD (Pose const &pose)
void	close_chain_breaks (Pose &pose)
void	cs_rosetta_rna_pdb (bool perform_minimize)
void *	my_main (void *)
int	main (int argc, char *argv[])

Function Documentation

void close_chain_breaks

(

Pose &

pose

)

Referenced by cs_rosetta_rna_pdb().

Real compute_chem_shift_RMSD

(

Pose const &

pose

)

References option, app.surface_docking.surface_docking::pose, score::rna_chemical_shift_exp_data(), basic::options::OptionKeys::inout::dbms::user, and utility_exit_with_message.

Referenced by cs_rosetta_rna_pdb().

ScoreFunctionOP create_cs_rosetta_rna_scorefxn

(

)

References utility::io::oc::cout, and PyMOL_demo::scorefxn.

Referenced by cs_rosetta_rna_pdb().

void cs_rosetta_rna_pdb

(

bool

perform_minimize

)

References basic::options::OptionKeys::ProQ::basename, close_chain_breaks(), compute_chem_shift_RMSD(), utility::io::oc::cout, create_cs_rosetta_rna_scorefxn(), basic::options::OptionKeys::matdes::dock::dump_pdb, option, basic::options::OptionKeys::in::path::pdb, app.surface_docking.surface_docking::pose, score::rna_chemical_shift_exp_data(), PyMOL_demo::scorefxn, setup_rna_minimizer(), setup_rna_struct_params(), basic::options::OptionKeys::inout::dbms::user, and utility_exit_with_message.

Referenced by my_main().

utility::vector1< RNA_Pairing > get_obligated_rna_pairings

(

RNA_StructureParametersOP

rna_struct_params

)

References utility::io::oc::cout, and basic::options::OptionKeys::frags::j.

Referenced by setup_rna_minimizer().

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

References utility::io::oc::cout, basic::init(), basic::options::OptionKeys::dna::specificity::mode, utility::excn::EXCN_Base::msg(), my_main(), NEW_OPT, basic::options::OptionKeys::flexPepDocking::params_file, and basic::options::OptionKeys::in::path::pdb.

void* my_main

(

void *

)

References cs_rosetta_rna_pdb(), utility::options::OptionKeys::options::exit, basic::options::OptionKeys::dna::specificity::mode, option, and utility_exit_with_message.

Referenced by main().

RNA_MinimizerOP setup_rna_minimizer	(	ScoreFunctionOP	scorefxn,
		RNA_StructureParametersOP	rna_struct_params,
		core::pose::Pose &	pose
	)

References utility::io::oc::cout, and get_obligated_rna_pairings().

Referenced by cs_rosetta_rna_pdb().

RNA_StructureParametersOP setup_rna_struct_params

(

core::pose::Pose &

pose

)

References basic::database::full_name(), option, and basic::options::OptionKeys::flexPepDocking::params_file.

Referenced by cs_rosetta_rna_pdb().