a single erraser app. no python! More...

#include <protocols/viewer/viewers.hh>
#include <protocols/stepwise/monte_carlo/util.hh>
#include <protocols/stepwise/monte_carlo/options/StepWiseMonteCarloOptions.hh>
#include <protocols/stepwise/monte_carlo/mover/StepWiseMasterMover.hh>
#include <protocols/stepwise/modeler/rna/util.hh>
#include <protocols/stepwise/modeler/util.hh>
#include <core/types.hh>
#include <devel/init.hh>
#include <core/scoring/ScoreFunction.hh>
#include <core/scoring/Energies.hh>
#include <core/scoring/ScoreFunctionFactory.hh>
#include <core/scoring/rms_util.hh>
#include <core/scoring/rna/RNA_ScoringInfo.hh>
#include <core/chemical/ChemicalManager.hh>
#include <core/io/silent/SilentFileData.hh>
#include <core/io/silent/BinarySilentStruct.hh>
#include <core/import_pose/import_pose.hh>
#include <core/import_pose/pose_stream/PDBPoseInputStream.hh>
#include <core/pose/Pose.hh>
#include <core/pose/PDBInfo.hh>
#include <core/pose/util.hh>
#include <core/pose/rna/util.hh>
#include <core/pose/full_model_info/FullModelInfo.hh>
#include <core/pose/full_model_info/util.hh>
#include <core/import_pose/FullModelPoseBuilder.hh>
#include <protocols/rna/movers/ErraserMinimizerMover.hh>
#include <core/pose/rna/RNA_SuiteName.hh>
#include <utility/file/file_sys_util.hh>
#include <basic/Tracer.hh>
#include <basic/options/option.hh>
#include <basic/options/option_macros.hh>
#include <basic/options/keys/OptionKeys.hh>
#include <basic/options/keys/in.OptionKeys.gen.hh>
#include <basic/options/keys/out.OptionKeys.gen.hh>
#include <basic/options/keys/rna.OptionKeys.gen.hh>
#include <basic/options/keys/chemical.OptionKeys.gen.hh>
#include <basic/options/keys/score.OptionKeys.gen.hh>
#include <utility/vector1.hh>
#include <utility/vector1.functions.hh>
#include <utility/excn/Exceptions.hh>
#include <utility/io/izstream.hh>
#include <numeric/random/random.hh>
#include <numeric/random/random_permutation.hh>
#include <ObjexxFCL/format.hh>
#include <iostream>
#include <string>

Functions
std::string	first_preminimized_namer (std::string const &s, Size const nstruct)

std::string	second_preminimized_namer (std::string const &s, Size const nstruct)

std::string	third_preminimized_namer (std::string const &s, Size const nstruct)

std::string	round_minimized_namer (std::string const &s, Size const ii, Size const nstruct)

std::string	round_resampled_namer (std::string const &s, Size const ii, Size const nstruct)

void	fill_input_poses (utility::vector1< PoseOP > &input_poses, std::string const &s)

void	fill_input_poses_based_on_possible_checkpoints (utility::vector1< PoseOP > &input_poses, Size &checkpoints_to_pass, Size const nstruct)

void	resample_full_model (Size const resample_round, pose::Pose &start_pose, ScoreFunctionOP const &scorefxn, utility::vector1< Size > const &definite_residues, Size const nstruct)

utility::vector1< Size >	all_pose_residues (core::pose::Pose const &pose)

void	show_accuracy_report (pose::Pose const &start_pose, std::string const &tag, Size const round)

utility::vector1< Size >	analyze_poses_for_convergence (utility::vector1< pose::Pose > const &poses)

PoseOP	obtain_start_pose (Size const nstruct, utility::vector1< Size > &unconverged_res, Size &checkpoints_to_pass)

void	do_erraser2 (Size const nstruct, ScoreFunctionOP const &scorefxn)

void	erraser2_test ()

bool	atoms_have_bond_to_bonded_atoms (pose::Pose const &pose, Size const ai, Size const ii, Size const aj, Size const jj)

bool	atoms_have_mutual_bond_to_atom (pose::Pose const &pose, Size const ai, Size const ii, Size const aj, Size const jj)

bool	bump_check (pose::Pose const &pose, Size const ii)

utility::vector1< Size >	determine_residues_to_rebuild (utility::vector1< Size > const &definite_residues, pose::Pose const &start_pose)

mover::StepWiseMasterMover	configure_master_mover (ScoreFunctionOP const &scorefxn, Pose const &start_pose)

void *	my_main (void *)

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

Variables
static basic::Tracer	TR ("apps.public.rna.erraser.erraser2")

Detailed Description

a single erraser app. no python!

Author: Andy Watkins, amw57.nosp@m.9@st.nosp@m.anfor.nosp@m.d.ed.nosp@m.u

Function Documentation

utility::vector1< Size > all_pose_residues ( core::pose::Pose const & pose )

References foo(), and test.T200_Scoring::ii.

utility::vector1< Size > analyze_poses_for_convergence ( utility::vector1< pose::Pose > const & poses )

References utility::arg_greatest_several(), numeric::xyzVector< typename >::distance_squared(), test.T200_Scoring::ii, demo.D010_Pose_structure::pose, res, amino_acids::size, TR, and basic::Tracer::Trace.

Referenced by obtain_start_pose().

bool atoms_have_bond_to_bonded_atoms	(	pose::Pose const &	pose,
		Size const	ai,
		Size const	ii,
		Size const	aj,
		Size const	jj
	)

Referenced by bump_check().

bool atoms_have_mutual_bond_to_atom	(	pose::Pose const &	pose,
		Size const	ai,
		Size const	ii,
		Size const	aj,
		Size const	jj
	)

Referenced by bump_check().

bool bump_check	(	pose::Pose const &	pose,
		Size const	ii
	)

References atoms_have_bond_to_bonded_atoms(), atoms_have_mutual_bond_to_atom(), TR, and basic::Tracer::Trace.

Referenced by determine_residues_to_rebuild().

mover::StepWiseMasterMover configure_master_mover	(	ScoreFunctionOP const &	scorefxn,
		Pose const &	start_pose
	)

References options.

Referenced by resample_full_model().

utility::vector1< Size > determine_residues_to_rebuild	(	utility::vector1< Size > const &	definite_residues,
		pose::Pose const &	start_pose
	)

References bump_check(), basic::Tracer::Debug, basic::options::OptionKeys::rna::erraser::fixed_res, test.T200_Scoring::ii, option, options, numeric::random::random_permutation(), numeric::random::rg(), TR, and value.

Referenced by resample_full_model().

void do_erraser2	(	Size const	nstruct,
		ScoreFunctionOP const &	scorefxn
	)

References utility::io::izstream::close(), first_preminimized_namer(), in::file::fold_tree(), foo(), test.T200_Scoring::ii, obtain_start_pose(), option, resample_full_model(), round_minimized_namer(), round_resampled_namer(), basic::options::OptionKeys::lh::rounds, in::file::s(), second_preminimized_namer(), show_accuracy_report(), TR, basic::options::OptionKeys::inout::dbms::user, and value.

Referenced by erraser2_test().

void erraser2_test ( )

References do_erraser2(), basic::options::OptionKeys::score::empty, test.T200_Scoring::ii, basic::options::OptionKeys::run::nproc, local::nstruct, out::nstruct(), option, basic::options::OptionKeys::legacy_sewing::rank, in::file::s(), basic::options::OptionKeys::DisulfideInsertion::scorefxn, basic::options::OptionKeys::inout::dbms::user, utility_exit_with_message, and score::weights().

Referenced by my_main().

void fill_input_poses	(	utility::vector1< PoseOP > &	input_poses,
		std::string const &	s
	)

References TR.

Referenced by fill_input_poses_based_on_possible_checkpoints().

void fill_input_poses_based_on_possible_checkpoints	(	utility::vector1< PoseOP > &	input_poses,
		Size &	checkpoints_to_pass,
		Size const	nstruct
	)

This function looks in the current working directory to see if there are any checkpoint files. (These are based off the name of option[ in::file::s ](). In fact, we have now abstracted those naming systems into functions. It sets the 'checkpoints_to_pass' counter to the number of checkpointing opportunities that can be crossed now that we have recovered a file with this type of name...

References utility::file::file_exists(), fill_input_poses(), first_preminimized_namer(), option, round(), round_minimized_namer(), round_resampled_namer(), basic::options::OptionKeys::lh::rounds, in::file::s(), second_preminimized_namer(), third_preminimized_namer(), and value.

Referenced by obtain_start_pose().

std::string first_preminimized_namer	(	std::string const &	s,
		Size const	nstruct
	)

References ObjexxFCL::lead_zero_string_of().

Referenced by do_erraser2(), and fill_input_poses_based_on_possible_checkpoints().

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

References utility::io::oc::cout, test.T009_Exceptions::e, utility::options::OptionKeys::options::exit, devel::init(), utility::excn::Exception::msg(), my_main(), NEW_OPT, and basic::options::OptionKeys::lh::rounds.

void* my_main ( void * )

References erraser2_test(), and utility::options::OptionKeys::options::exit.

Referenced by main().

PoseOP obtain_start_pose	(	Size const	nstruct,
		utility::vector1< Size > &	unconverged_res,
		Size &	checkpoints_to_pass
	)

References analyze_poses_for_convergence(), fill_input_poses_based_on_possible_checkpoints(), test.T200_Scoring::ii, option, in::file::s(), and amino_acids::size.

Referenced by do_erraser2().

void resample_full_model	(	Size const	resample_round,
		pose::Pose &	start_pose,
		ScoreFunctionOP const &	scorefxn,
		utility::vector1< Size > const &	definite_residues,
		Size const	nstruct
	)

References configure_master_mover(), basic::Tracer::Debug, determine_residues_to_rebuild(), and TR.

Referenced by do_erraser2().

std::string round_minimized_namer	(	std::string const &	s,
		Size const	ii,
		Size const	nstruct
	)

References ObjexxFCL::lead_zero_string_of().

Referenced by do_erraser2(), and fill_input_poses_based_on_possible_checkpoints().

std::string round_resampled_namer	(	std::string const &	s,
		Size const	ii,
		Size const	nstruct
	)

References ObjexxFCL::lead_zero_string_of().

Referenced by do_erraser2(), and fill_input_poses_based_on_possible_checkpoints().

std::string second_preminimized_namer	(	std::string const &	s,
		Size const	nstruct
	)

References ObjexxFCL::lead_zero_string_of().

Referenced by do_erraser2(), and fill_input_poses_based_on_possible_checkpoints().

void show_accuracy_report	(	pose::Pose const &	start_pose,
		std::string const &	tag,
		Size const	round
	)

References test.T200_Scoring::ii, and TR.

Referenced by do_erraser2().

std::string third_preminimized_namer	(	std::string const &	s,
		Size const	nstruct
	)

References ObjexxFCL::lead_zero_string_of().

Referenced by fill_input_poses_based_on_possible_checkpoints().

Variable Documentation

basic::Tracer TR("apps.public.rna.erraser.erraser2")

static

Referenced by analyze_poses_for_convergence(), bump_check(), determine_residues_to_rebuild(), do_erraser2(), fill_input_poses(), resample_full_model(), and show_accuracy_report().

Functions

Variables

Detailed Description

Function Documentation

Variable Documentation