msd.cc File Reference

Experimental multi state design implementation. Written to encourage convergence in protein designs occurring simultaneously, rather than enforce that they have identical sequences. More...

#include <core/scoring/ScoreFunction.hh>
#include <core/scoring/ScoreFunctionFactory.hh>
#include <core/pack/task/operation/TaskOperations.hh>
#include <core/pack/task/TaskFactory.hh>
#include <core/import_pose/import_pose.hh>
#include <core/pose/Pose.hh>
#include <protocols/task_operations/RestrictToInterfaceVectorOperation.hh>
#include <core/pose/PDBInfo.hh>
#include <core/kinematics/MoveMap.hh>
#include <core/scoring/constraints/ResidueTypeConstraint.hh>
#include <core/scoring/constraints/ResidueTypeLinkingConstraint.hh>
#include <core/chemical/ResidueType.hh>
#include <protocols/minimization_packing/MinPackMover.hh>
#include <protocols/minimization_packing/PackRotamersMover.hh>
#include <protocols/simple_moves/NegativePackRotamersMover.hh>
#include <protocols/minimization_packing/MinMover.hh>
#include <protocols/minimization_packing/TaskAwareMinMover.hh>
#include <devel/init.hh>
#include <protocols/protein_interface_design/design_utils.hh>
#include <basic/options/keys/run.OptionKeys.gen.hh>
#include <basic/options/keys/out.OptionKeys.gen.hh>
#include <basic/options/keys/in.OptionKeys.gen.hh>
#include <basic/options/keys/packing.OptionKeys.gen.hh>
#include <basic/options/keys/constraints.OptionKeys.gen.hh>
#include <basic/options/option.hh>
#include <utility/io/izstream.hh>
#include <utility/json_spirit/json_spirit_reader.h>
#include <protocols/jobdist/standard_mains.hh>
#include <basic/Tracer.hh>
#include <sstream>
#include <utility/string_util.hh>
#include <core/conformation/Residue.hh>
#include <core/scoring/Energies.hh>
#include <core/scoring/ScoreType.hh>
#include <core/scoring/constraints/util.hh>
#include <core/scoring/constraints/ConstraintIO.hh>
#include <core/scoring/constraints/ConstraintSet.hh>

Namespaces
	basic
	Tags used to tag messeges sent by MPI functions used to decide whether a slave is requesting a new job id or flagging as job as being a bad input.
	basic::options
	basic::options::OptionKeys
	basic::options::OptionKeys::msd

Functions
std::string	get_out_number (core::Size in)
void	add_fnr_constraints (core::pose::PoseOP pose, core::pose::PoseOP reference_pose, utility::vector1< core::Size > corr_pairs, core::Real penalty, bool positive)
void	apply_linked_constraints (utility::vector1< std::pair< core::pose::PoseOP, bool > > poses, utility::vector1< utility::vector1< core::Size > > corr_pairs, core::Real positive_penalty, core::Real negative_penalty, core::Size current_pose)
utility::vector1< core::Size >	parse_resfile (core::pack::task::PackerTaskCOP design_task, core::pose::Pose &pose)
utility::vector1< utility::vector1< core::Size > >	parse_resfiles (utility::vector1< core::pack::task::TaskFactoryOP > task_factories, utility::vector1< std::pair< core::pose::PoseOP, bool > > poses)
void	update_constraints (utility::vector1< std::pair< core::pose::PoseOP, bool > > poses, utility::vector1< std::pair< core::pose::PoseOP, bool > > reference_poses, utility::vector1< utility::vector1< core::Size > > res_links, core::Real positive_linked_penalty, core::Real negative_linked_penalty, core::Real fnr_penalty, core::Size current_pose)
utility::vector1< core::Size >	parse_chains (std::string chains)
int	main (int argc, char *argv[])

Variables
static basic::Tracer	TR ("msd_pilot.main")
basic::options::StringVectorOptionKey	basic::options::OptionKeys::msd::positive_states ("msd:positive_states")
basic::options::StringVectorOptionKey	basic::options::OptionKeys::msd::negative_states ("msd:negative_states")
basic::options::StringOptionKey	basic::options::OptionKeys::msd::upper_chains ("msd:upper_chains")
basic::options::StringOptionKey	basic::options::OptionKeys::msd::lower_chains ("msd:lower_chains")
basic::options::IntegerOptionKey	basic::options::OptionKeys::msd::n_iterations ("msd:n_iterations")
basic::options::BooleanOptionKey	basic::options::OptionKeys::msd::find_consensus ("msd:find_consensus")
basic::options::BooleanOptionKey	basic::options::OptionKeys::msd::debug ("msd:debug")
basic::options::BooleanOptionKey	basic::options::OptionKeys::msd::restrict_design_to_interface ("msd:restrict_design_to_interface")
basic::options::BooleanOptionKey	basic::options::OptionKeys::msd::restrict_min_to_interface ("msd:restrict_min_to_interface")
basic::options::IntegerOptionKey	basic::options::OptionKeys::msd::design_rounds ("msd:design_rounds")
basic::options::StringOptionKey	basic::options::OptionKeys::msd::ramp ("msd:weight_ramp")
basic::options::RealOptionKey	basic::options::OptionKeys::msd::favor_native ("msd:favor_native")
basic::options::BooleanOptionKey	basic::options::OptionKeys::msd::soft_design ("msd:soft_design")
basic::options::BooleanOptionKey	basic::options::OptionKeys::msd::fixed_bb ("msd:fixed_bb")
basic::options::FileVectorOptionKey	basic::options::OptionKeys::msd::multiple_resfiles (" msd:multiple_resfiles")
basic::options::FileVectorOptionKey	basic::options::OptionKeys::msd::multiple_constraints (" msd:multiple_constraints")

Detailed Description

Experimental multi state design implementation. Written to encourage convergence in protein designs occurring simultaneously, rather than enforce that they have identical sequences.

Author

Alex Sevy

Function Documentation

add_fnr_constraints()

void add_fnr_constraints	(	core::pose::PoseOP	pose,
		core::pose::PoseOP	reference_pose,
		utility::vector1< core::Size >	corr_pairs,
		core::Real	penalty,
		bool	positive
	)

References create_a3b_hbs::k, beta_nonlocal::pose, and test.Workshop8test::reference_pose.

Referenced by update_constraints().

apply_linked_constraints()

void apply_linked_constraints	(	utility::vector1< std::pair< core::pose::PoseOP, bool > >	poses,
		utility::vector1< utility::vector1< core::Size > >	corr_pairs,
		core::Real	positive_penalty,
		core::Real	negative_penalty,
		core::Size	current_pose
	)

References basic::options::OptionKeys::msd::debug, create_a3b_hbs::first, create_a3b_hbs::i, create_a3b_hbs::k, basic::options::option, basic::options::OptionKeys::mp::assembly::poses, and basic::options::TR.

Referenced by update_constraints().

get_out_number()

std::string get_out_number

(

core::Size

in

)

References basic::options::OptionKeys::in::in.

Referenced by main().

main()

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

References utility::options::OptionCollection::add(), argv, utility::options::BooleanOptionKey::clone(), comp(), pyrosetta::create_score_function, basic::options::OptionKeys::constraints::cst_fa_file, basic::options::OptionKeys::constraints::cst_file, basic::options::OptionKeys::debug, basic::options::OptionKeys::msd::debug, utility::options::ScalarOption_T_< K, T >::def(), basic::options::OptionKeys::msd::design_rounds, erraser_analysis::diff, test.T009_Exceptions::e, basic::options::OptionKeys::msd::favor_native, basic::options::OptionKeys::msd::find_consensus, create_a3b_hbs::first, basic::options::OptionKeys::msd::fixed_bb, get_out_number(), create_a3b_hbs::i, basic::init(), create_a3b_hbs::j, basic::options::OptionKeys::msd::lower_chains, min(), min_index(), vancomycin::min_mover, SmotifHasher::min_score, basic::options::OptionKeys::dna::specificity::min_type, basic::options::OptionKeys::run::min_type, basic::options::OptionKeys::in::file::movemap, basic::options::OptionKeys::msd::multiple_constraints, basic::options::OptionKeys::msd::multiple_resfiles, kmeans_adaptive_kernel_density_bb_dependent_rotlib::n, basic::options::OptionKeys::msd::n_iterations, basic::options::OptionKeys::msd::negative_states, local::nstruct, basic::options::OptionKeys::out::nstruct, basic::options::option, parse_chains(), parse_resfiles(), beta_nonlocal::pose, pyrosetta.distributed.io::pose_from_file, basic::options::OptionKeys::mp::assembly::poses, basic::options::OptionKeys::msd::positive_states, basic::options::OptionKeys::msd::ramp, basic::options::OptionKeys::packing::resfile, basic::options::OptionKeys::msd::restrict_design_to_interface, basic::options::OptionKeys::msd::restrict_min_to_interface, basic::options::OptionKeys::sc::rp, legacy_score_vs_rmsd::scores, basic::options::OptionKeys::msd::soft_design, basic::options::OptionKeys::packing::soft_rep_design, utility::string_split(), basic::options::OptionKeys::out::suffix, basic::options::TR, update_constraints(), basic::options::OptionKeys::msd::upper_chains, basic::options::OptionKeys::inout::dbms::user, and utility_exit_with_message.

parse_chains()

utility::vector1< core::Size > parse_chains

(

std::string

chains

)

References chains, and create_a3b_hbs::i.

Referenced by main().

parse_resfile()

utility::vector1< core::Size > parse_resfile	(	core::pack::task::PackerTaskCOP	design_task,
		core::pose::Pose &	pose
	)

References create_a3b_hbs::i, create_a3b_hbs::pdb_info, and beta_nonlocal::pose.

Referenced by parse_resfiles().

parse_resfiles()

utility::vector1< utility::vector1< core::Size > > parse_resfiles	(	utility::vector1< core::pack::task::TaskFactoryOP >	task_factories,
		utility::vector1< std::pair< core::pose::PoseOP, bool > >	poses
	)

References create_a3b_hbs::first, create_a3b_hbs::i, parse_resfile(), basic::options::OptionKeys::mp::assembly::poses, subloop_histogram::size, and utility_exit_with_message.

Referenced by main().

update_constraints()

void update_constraints	(	utility::vector1< std::pair< core::pose::PoseOP, bool > >	poses,
		utility::vector1< std::pair< core::pose::PoseOP, bool > >	reference_poses,
		utility::vector1< utility::vector1< core::Size > >	res_links,
		core::Real	positive_linked_penalty,
		core::Real	negative_linked_penalty,
		core::Real	fnr_penalty,
		core::Size	current_pose
	)

References add_fnr_constraints(), apply_linked_constraints(), utility::options::StringVectorOptionKey::clone(), basic::options::OptionKeys::constraints::constraints, create_a3b_hbs::first, create_a3b_hbs::i, basic::options::OptionKeys::mp::assembly::poses, and basic::options::OptionKeys::blivens::score_type.

Referenced by main().

Variable Documentation

TR

basic::Tracer TR("msd_pilot.main") ( "msd_pilot.main"  )

static