fit_helixparams.cc File Reference

Constructs a piece of secondary structure with repeating mainchain torsion values, and fits the Crick parameters for a helix to the structure. More...

#include <basic/options/option.hh>
#include <core/types.hh>
#include <core/pose/Pose.hh>
#include <core/import_pose/import_pose.hh>
#include <core/conformation/Conformation.hh>
#include <core/conformation/Residue.hh>
#include <core/id/TorsionID.hh>
#include <core/id/AtomID.hh>
#include <devel/init.hh>
#include <utility/exit.hh>
#include <utility/excn/Exceptions.hh>
#include <basic/Tracer.hh>
#include <numeric/xyz.functions.hh>
#include <numeric/conversions.hh>
#include <numeric/crick_equations/HelixParams.hh>
#include <protocols/helical_bundle/FitSimpleHelix.hh>
#include <protocols/helical_bundle/util.hh>
#include <protocols/cyclic_peptide/PeptideStubMover.hh>
#include <basic/options/option_macros.hh>
#include <utility/vector1.hh>

Functions
void	register_options ()
	Set up the options for this pilot app. More...
void	build_polymer (core::pose::Pose &pose, utility::vector1< std::string > const &restypes, core::Size const residues_per_repeat, core::Size const repeats)
	Actually build the geometry that we'll be working with. More...
void	set_pose_conformation (core::pose::Pose &pose, core::Size const total_repeats, core::Size const residues_per_repeat, utility::vector1< core::Real > const &mainchain_torsions, utility::vector1< std::pair< utility::vector1< core::id::AtomID >, core::Real > > const &nonstandard_bondangle_list, utility::vector1< std::pair< utility::vector1< core::id::AtomID >, core::Real > > const &nonstandard_bondlength_list)
	Sets the polymer conformation to the repeating conformation (helix) specified with the option[mainchain_torsions]() vector. More...
void	add_Cu_chains (core::pose::Pose &pose, utility::vector1< core::Real > const &r1_vals, core::Real const &omega1_val, core::Real const &z1_val, utility::vector1< core::Real > const &delta_omega1_vals, utility::vector1< core::Real > const &delta_z1_vals, core::Size const rescount, core::Size const res_per_repeat)
	Add chains of Cu (a convenient single-atom residue) to the pose in the ideal positions of each mainchain atom, based on the fitted Crick parameters. More...
void	parse_nonstandard_angles (utility::vector1< std::pair< utility::vector1< core::id::AtomID >, core::Real > > &nonstandard_angle_list, core::pose::Pose const &pose, core::Size const residues_per_repeat)
	Parse the user flags for nonstandard bond angles, and convert this into a data object that can be passed to the pose conformation setup function. More...
void	parse_nonstandard_bondlengths (utility::vector1< std::pair< utility::vector1< core::id::AtomID >, core::Real > > &nonstandard_bondlength_list, core::pose::Pose const &pose, core::Size const residues_per_repeat)
	Parse the user flags for nonstandard bond lengths, and convert this into a data object that can be passed to the pose conformation setup function. More...
void	initialize_from_pdb (std::string const &filename, utility::vector1< std::string > &restypes_from_input_pdb, utility::vector1< core::Real > &mainchain_torsions_from_input_pdb, utility::vector1< std::pair< utility::vector1< core::id::AtomID >, core::Real > > &nonstandard_angle_list, utility::vector1< std::pair< utility::vector1< core::id::AtomID >, core::Real > > &nonstandard_bondlength_list)
	Initialize the repeating unit from a pose instead of from commandline options. More...
int	main (int argc, char *argv[])

Variables
static basic::Tracer	TR ("apps.pilot.vmullig.fit_helixparams")

Detailed Description

Constructs a piece of secondary structure with repeating mainchain torsion values, and fits the Crick parameters for a helix to the structure.

Updated 29 May 2015 to permit the repeating unit to be more than one residue. Updated 29 March 2018 to permit the repeating unit to be a PDB file.

Author

Vikram K. Mulligan (vmull.nosp@m.ig@u.nosp@m.w.edu)

Function Documentation

add_Cu_chains()

void add_Cu_chains	(	core::pose::Pose &	pose,
		utility::vector1< core::Real > const &	r1_vals,
		core::Real const &	omega1_val,
		core::Real const &	z1_val,
		utility::vector1< core::Real > const &	delta_omega1_vals,
		utility::vector1< core::Real > const &	delta_z1_vals,
		core::Size const	rescount,
		core::Size const	res_per_repeat
	)

Add chains of Cu (a convenient single-atom residue) to the pose in the ideal positions of each mainchain atom, based on the fitted Crick parameters.

References basic::options::OptionKeys::abinitio::cyclic_peptide, create_a3b_hbs::nres, beta_nonlocal::pose, predPRE::t, and numeric::crick_equations::xyz().

Referenced by main().

build_polymer()

void build_polymer	(	core::pose::Pose &	pose,
		utility::vector1< std::string > const &	restypes,
		core::Size const	residues_per_repeat,
		core::Size const	repeats
	)

Actually build the geometry that we'll be working with.

References basic::options::OptionKeys::abinitio::cyclic_peptide, create_a3b_hbs::i, create_a3b_hbs::j, beta_nonlocal::pose, hbscan::restypes, and basic::options::TR.

Referenced by main().

initialize_from_pdb()

void initialize_from_pdb	(	std::string const &	filename,
		utility::vector1< std::string > &	restypes_from_input_pdb,
		utility::vector1< core::Real > &	mainchain_torsions_from_input_pdb,
		utility::vector1< std::pair< utility::vector1< core::id::AtomID >, core::Real > > &	nonstandard_angle_list,
		utility::vector1< std::pair< utility::vector1< core::id::AtomID >, core::Real > > &	nonstandard_bondlength_list
	)

Initialize the repeating unit from a pose instead of from commandline options.

References basic::options::OptionKeys::hotspot::angle, numeric::angle_of(), lactamize::filename, oop_conformations::length, pair, beta_nonlocal::pose, pyrosetta.distributed.io::pose_from_file, and runtime_assert_string_msg.

Referenced by main().

main()

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

References add_Cu_chains(), argv, build_polymer(), demo.D060_Folding::counter, utility::excn::Exception::display(), basic::Tracer::flush(), basic::init(), initialize_from_pdb(), basic::options::OptionKeys::relax::min_tolerance, basic::options::OptionKeys::dna::specificity::min_type, basic::options::option, parse_nonstandard_angles(), parse_nonstandard_bondlengths(), beta_nonlocal::pose, basic::Tracer::precision(), register_options(), hbscan::restypes, runtime_assert_string_msg, set_pose_conformation(), basic::options::TR, basic::options::OptionKeys::inout::dbms::user, basic::Tracer::visible(), and basic::Tracer::width().

parse_nonstandard_angles()

void parse_nonstandard_angles	(	utility::vector1< std::pair< utility::vector1< core::id::AtomID >, core::Real > > &	nonstandard_angle_list,
		core::pose::Pose const &	pose,
		core::Size const	residues_per_repeat
	)

Parse the user flags for nonstandard bond angles, and convert this into a data object that can be passed to the pose conformation setup function.

References create_a3b_hbs::i, basic::options::option, pair, beta_nonlocal::pose, numeric::conversions::radians(), erraser_analysis::res1, erraser_analysis::res2, runtime_assert_string_msg, subloop_histogram::size, and challenge::ss.

Referenced by main().

parse_nonstandard_bondlengths()

void parse_nonstandard_bondlengths	(	utility::vector1< std::pair< utility::vector1< core::id::AtomID >, core::Real > > &	nonstandard_bondlength_list,
		core::pose::Pose const &	pose,
		core::Size const	residues_per_repeat
	)

Parse the user flags for nonstandard bond lengths, and convert this into a data object that can be passed to the pose conformation setup function.

References create_a3b_hbs::i, basic::options::option, pair, beta_nonlocal::pose, erraser_analysis::res1, erraser_analysis::res2, runtime_assert_string_msg, subloop_histogram::size, and challenge::ss.

Referenced by main().

register_options()

void register_options

(

)

Set up the options for this pilot app.

References basic::options::OptionKeys::relax::min_tolerance, basic::options::OptionKeys::dna::specificity::min_type, and NEW_OPT.

Referenced by main().

set_pose_conformation()

void set_pose_conformation	(	core::pose::Pose &	pose,
		core::Size const	total_repeats,
		core::Size const	residues_per_repeat,
		utility::vector1< core::Real > const &	mainchain_torsions,
		utility::vector1< std::pair< utility::vector1< core::id::AtomID >, core::Real > > const &	nonstandard_bondangle_list,
		utility::vector1< std::pair< utility::vector1< core::id::AtomID >, core::Real > > const &	nonstandard_bondlength_list
	)

Sets the polymer conformation to the repeating conformation (helix) specified with the option[mainchain_torsions]() vector.

References demo.D060_Folding::counter, create_a3b_hbs::first, create_a3b_hbs::i, create_a3b_hbs::j, beta_nonlocal::pose, and runtime_assert_string_msg.

Referenced by main().

Variable Documentation

TR

basic::Tracer TR("apps.pilot.vmullig.fit_helixparams") ( "apps.pilot.vmullig.fit_helixparams"  )

static