erraser2.cc File Reference

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

#include <protocols/viewer/viewers.hh>
#include <protocols/stepwise/monte_carlo/options/StepWiseMonteCarloOptions.hh>
#include <protocols/stepwise/monte_carlo/mover/StepWiseMasterMover.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/chemical/ChemicalManager.hh>
#include <core/import_pose/pose_stream/PDBPoseInputStream.hh>
#include <core/conformation/Conformation.hh>
#include <core/pose/Pose.hh>
#include <core/pose/PDBInfo.hh>
#include <core/pose/full_model_info/FullModelInfo.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/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 <core/id/AtomID.hh>
#include <iostream>
#include <string>
#include <core/kinematics/FoldTree.hh>
#include <core/pose/full_model_info/FullModelParameters.hh>
#include <utility/stream_util.hh>

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, int const rank, int const nproc, bool const work_partition=true)
	Perform the erraser2 protocol in a working directory. More...
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

all_pose_residues()

utility::vector1< Size > all_pose_residues

(

core::pose::Pose const &

pose

)

References foo(), create_a3b_hbs::ii, and beta_nonlocal::pose.

analyze_poses_for_convergence()

utility::vector1< Size > analyze_poses_for_convergence

(

utility::vector1< pose::Pose > const &

poses

)

References utility::arg_greatest_several(), create_a3b_hbs::ii, beta_nonlocal::jj, kk, natoms(), beta_nonlocal::pose, basic::options::OptionKeys::mp::assembly::poses, res, subloop_histogram::size, TR, and basic::Tracer::Trace.

Referenced by obtain_start_pose().

atoms_have_bond_to_bonded_atoms()

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

References aj, create_a3b_hbs::ii, beta_nonlocal::jj, natoms(), and beta_nonlocal::pose.

Referenced by bump_check().

atoms_have_mutual_bond_to_atom()

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

References aj, create_a3b_hbs::ii, beta_nonlocal::jj, natoms(), and beta_nonlocal::pose.

Referenced by bump_check().

bump_check()

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

References aj, atoms_have_bond_to_bonded_atoms(), atoms_have_mutual_bond_to_atom(), create_a3b_hbs::ii, beta_nonlocal::jj, natoms(), beta_nonlocal::pose, TR, and basic::Tracer::Trace.

Referenced by determine_residues_to_rebuild().

configure_master_mover()

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

References options, and oop_conformations::scorefxn.

Referenced by resample_full_model().

determine_residues_to_rebuild()

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

References bump_check(), ss_finder::cart, basic::Tracer::Debug, basic::options::OptionKeys::rna::erraser::fixed_res, create_a3b_hbs::ii, option, numeric::random::random_permutation(), numeric::random::rg(), and TR.

Referenced by resample_full_model().

do_erraser2()

void do_erraser2	(	Size const	nstruct,
		ScoreFunctionOP const &	scorefxn,
		int const	rank,
		int const	nproc,
		bool const	work_partition = true
	)

Perform the erraser2 protocol in a working directory.

This function also does pose readin (because it could be resuming from checkpoints). In MPI contexts, this function is run on every core. (We use a work-partition job distribution framework by default, where each core is just assigned a fixed set of nstruct.) As a result, it needs to take two ints, which represent its rank and the total number of processors. Since MPI libraries use signed ints, we follow their convention rather than contorting ourselves to make them Sizes.

References basic::options::OptionKeys::constraints::constraints, debug_assert, first_preminimized_namer(), in::file::fold_tree(), foo(), create_a3b_hbs::ii, cal_vdw_radius_pool::nproc, local::nstruct, obtain_start_pose(), basic::options::option, option, basic::options::OptionKeys::legacy_sewing::rank, resample_full_model(), round_minimized_namer(), round_resampled_namer(), basic::options::OptionKeys::lh::rounds, runtime_assert, in::file::s(), oop_conformations::scorefxn, second_preminimized_namer(), show_accuracy_report(), TR, basic::options::OptionKeys::inout::dbms::user, and value.

Referenced by erraser2_test().

erraser2_test()

void erraser2_test

(

)

References do_erraser2(), basic::options::OptionKeys::score::empty, create_a3b_hbs::ii, bin_torsions::job, cal_vdw_radius_pool::nproc, local::nstruct, out::nstruct(), option, basic::options::OptionKeys::legacy_sewing::rank, in::file::s(), oop_conformations::scorefxn, basic::options::OptionKeys::inout::dbms::user, utility_exit_with_message, and score::weights().

Referenced by my_main().

fill_input_poses()

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

References gaussian-sampling::input, docking::s, and TR.

Referenced by fill_input_poses_based_on_possible_checkpoints().

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 file_exists(), fill_input_poses(), first_preminimized_namer(), local::nstruct, 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().

first_preminimized_namer()

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

References ObjexxFCL::lead_zero_string_of(), local::nstruct, and docking::s.

Referenced by do_erraser2(), and fill_input_poses_based_on_possible_checkpoints().

main()

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

References argv, utility::io::oc::cout, test.T009_Exceptions::e, utility::options::OptionKeys::options::exit, basic::init(), my_main(), NEW_OPT, basic::options::OptionKeys::lh::rounds, and viewer_main().

my_main()

void* my_main

(

void *

)

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

Referenced by main().

obtain_start_pose()

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(), create_a3b_hbs::ii, gaussian-sampling::input, local::nstruct, option, in::file::s(), and subloop_histogram::size.

Referenced by do_erraser2().

resample_full_model()

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(), build_restypes::elem, local::nstruct, oop_conformations::scorefxn, and TR.

Referenced by do_erraser2().

round_minimized_namer()

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

References create_a3b_hbs::ii, ObjexxFCL::lead_zero_string_of(), local::nstruct, and docking::s.

Referenced by do_erraser2(), and fill_input_poses_based_on_possible_checkpoints().

round_resampled_namer()

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

References create_a3b_hbs::ii, ObjexxFCL::lead_zero_string_of(), local::nstruct, and docking::s.

Referenced by do_erraser2(), and fill_input_poses_based_on_possible_checkpoints().

second_preminimized_namer()

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

References ObjexxFCL::lead_zero_string_of(), local::nstruct, and docking::s.

Referenced by do_erraser2(), and fill_input_poses_based_on_possible_checkpoints().

show_accuracy_report()

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

References create_a3b_hbs::ii, round(), tag, and TR.

Referenced by do_erraser2().

third_preminimized_namer()

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

References ObjexxFCL::lead_zero_string_of(), local::nstruct, and docking::s.

Referenced by fill_input_poses_based_on_possible_checkpoints().

Variable Documentation

TR

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