homolog_cst.hh File Reference

#include <core/types.hh>
#include <core/id/SequenceMapping.hh>
#include <core/sequence/RichSequenceMapping.hh>
#include <core/scoring/constraints/ConstraintSet.hh>
#include <core/scoring/constraints/ConstraintSet.fwd.hh>
#include <core/scoring/constraints/AtomPairConstraint.hh>
#include <core/scoring/func/MixtureFunc.hh>
#include <core/scoring/func/HarmonicFunc.hh>
#include <core/id/AtomID.hh>
#include <core/pose/Pose.hh>
#include <basic/options/option.hh>
#include <ObjexxFCL/format.hh>
#include <ObjexxFCL/string.functions.hh>
#include <iosfwd>
#include <string>
#include <sstream>
#include <basic/options/keys/constraints.OptionKeys.gen.hh>

Functions
void	add_constraints (core::pose::Pose *pose, std::string fn)
void	create_starting_template (core::pose::Pose &pose, std::string fn)
	reads a .homolog_stats file with information from templates, creates a starting structure with appropriate constraints added. Assumes as input an extended Pose with the proper sequence. Backbone torsions from the template structure are copied into into aligned residues within the provided pose, and sidechain torsions are copied if the amino acids at this position are identical. More...
utility::vector1< int >	calculate_burial (core::pose::Pose mypose)

Detailed Description

Author

James Thompson

Function Documentation

add_constraints()

void add_constraints	(	core::pose::Pose *	pose,
		std::string	fn
	)

References a, ObjexxFCL::abs(), compute_difference::b, kmeans_adaptive_kernel_density_bb_dependent_rotlib::c, utility::io::oc::cerr, basic::options::OptionKeys::constraints::constraints, data, dist(), utility::options::OptionKeys::options::exit, kmeans_adaptive_kernel_density_bb_dependent_rotlib::fn, getline(), basic::init(), line, constraints::max_cst_dist(), option, beta_nonlocal::pose, SmotifHasher::query_id, pna::resi, and basic::options::OptionKeys::cmiles::jumping::resj.

calculate_burial()

utility::vector1< int > calculate_burial

(

core::pose::Pose

mypose

)

References basic::options::OptionKeys::in::file::burial, create_a3b_hbs::i, create_a3b_hbs::j, pna::resi, and basic::options::OptionKeys::cmiles::jumping::resj.

Referenced by main().

create_starting_template()

void create_starting_template	(	core::pose::Pose &	pose,
		std::string	fn
	)

reads a .homolog_stats file with information from templates, creates a starting structure with appropriate constraints added. Assumes as input an extended Pose with the proper sequence. Backbone torsions from the template structure are copied into into aligned residues within the provided pose, and sidechain torsions are copied if the amino acids at this position are identical.

References a, ObjexxFCL::abs(), compute_difference::b, kmeans_adaptive_kernel_density_bb_dependent_rotlib::c, utility::io::oc::cerr, utility::io::oc::cout, data, dist(), utility::options::OptionKeys::options::exit, kmeans_adaptive_kernel_density_bb_dependent_rotlib::fn, getline(), create_a3b_hbs::i, line, beta_nonlocal::pose, pyrosetta.distributed.io::pose_from_file, SmotifHasher::query_id, pna::resi, basic::options::OptionKeys::cmiles::jumping::resj, and internal_coordinates::torsions.

Referenced by build_template().