get_dihedral_peptoid.cc File Reference

#include <protocols/moves/Mover.hh>
#include <protocols/jd2/JobDistributor.hh>
#include <protocols/moves/MoverContainer.hh>
#include <protocols/moves/PyMOLMover.hh>
#include <protocols/minimization_packing/MinMover.hh>
#include <protocols/simple_moves/ScoreMover.hh>
#include <protocols/simple_moves/CyclizationMover.hh>
#include <core/scoring/ScoreFunction.hh>
#include <core/scoring/ScoreFunctionFactory.hh>
#include <core/scoring/Energies.hh>
#include <core/scoring/EnergyMap.hh>
#include <core/scoring/EnergyGraph.hh>
#include <core/kinematics/MoveMap.hh>
#include <core/pose/Pose.hh>
#include <core/pose/PDBInfo.hh>
#include <core/conformation/Residue.hh>
#include <core/chemical/ResidueType.hh>
#include <core/chemical/VariantType.hh>
#include <utility/graph/Graph.hh>
#include <core/pack/task/operation/TaskOperations.hh>
#include <core/pack/task/TaskFactory.hh>
#include <core/pack/dunbrack/RotamerLibrary.hh>
#include <core/pack/dunbrack/DunbrackRotamer.hh>
#include <core/pack/rotamers/SingleResidueRotamerLibrary.hh>
#include <core/pack/rotamers/SingleResiduePeptoidLibrary.hh>
#include <core/pack/rotamers/RotamericSingleResiduePeptoidLibrary.tmpl.hh>
#include <devel/init.hh>
#include <basic/Tracer.hh>
#include <basic/options/option.hh>
#include <basic/options/keys/run.OptionKeys.gen.hh>
#include <basic/options/keys/cyclization.OptionKeys.gen.hh>
#include <basic/database/open.hh>
#include <numeric/angle.functions.hh>
#include <sstream>
#include <iomanip>
#include <map>

Classes
class	PeptoidDihedralGrabber

Typedefs
typedef utility::pointer::owning_ptr< PeptoidDihedralGrabber >	PeptoidDihedralGrabberOP

Functions
core::Real	get_symm_corrected_angle (core::Size chi_num, std::string tlc, core::Real chi)
core::Real	angle_diff (core::Real a1, core::Real a2)
core::Real	calc_dist (core::conformation::Residue res1, core::conformation::Residue res2)
core::pack::rotamers::SingleResiduePeptoidLibraryCAP	get_rsrpl (core::chemical::ResidueType const &rsd_type)
core::Real	get_omg_from_rsd (core::conformation::Residue const &rsd, core::pose::Pose const &pose)
core::Real	get_phi_from_rsd (core::conformation::Residue const &rsd, core::pose::Pose const &pose)
core::Real	get_psi_from_rsd (core::conformation::Residue const &rsd, core::pose::Pose const &pose)
int	main (int argc, char *argv[])

Variables
static basic::Tracer	TR ("PeptoidDihedralGrabber")
static basic::Tracer	TR_EX ("ExperimentalRotamers")
static basic::Tracer	TR_IR ("InterpolatedRotamers")
basic::options::BooleanOptionKey const	cyclic ("cyclic")
basic::options::BooleanOptionKey const	qms ("qms")
basic::options::BooleanOptionKey const	kmc ("kmc")
std::map< std::string, core::pack::rotamers::SingleResiduePeptoidLibraryCOP >	peptoid_rotlibs_

Typedef Documentation

PeptoidDihedralGrabberOP

typedef utility::pointer::owning_ptr< PeptoidDihedralGrabber > PeptoidDihedralGrabberOP

Function Documentation

angle_diff()

core::Real angle_diff	(	core::Real	a1,
		core::Real	a2
	)

References docking::a1, docking::a2, and numeric::principal_angle_degrees().

Referenced by calc_dist().

calc_dist()

core::Real calc_dist	(	core::conformation::Residue	res1,
		core::conformation::Residue	res2
	)

References angle_diff(), get_symm_corrected_angle(), create_a3b_hbs::i, ObjexxFCL::pow(), erraser_analysis::res1, erraser_analysis::res2, and sd().

get_omg_from_rsd()

core::Real get_omg_from_rsd	(	core::conformation::Residue const &	rsd,
		core::pose::Pose const &	pose
	)

Returns the preceeding omg.

References beta_nonlocal::pose.

get_phi_from_rsd()

core::Real get_phi_from_rsd	(	core::conformation::Residue const &	rsd,
		core::pose::Pose const &	pose
	)

Handle lower-term residues by returning a "neutral" phi value

References beta_nonlocal::pose.

get_psi_from_rsd()

core::Real get_psi_from_rsd	(	core::conformation::Residue const &	rsd,
		core::pose::Pose const &	pose
	)

References beta_nonlocal::pose.

get_rsrpl()

core::pack::rotamers::SingleResiduePeptoidLibraryCAP get_rsrpl

(

core::chemical::ResidueType const &

rsd_type

)

References utility::io::oc::cout, enumerate_junctions::default, basic::database::full_name(), option, vancomycin::pack, peptoid_rotlibs_, qms, basic::options::OptionKeys::motifs::r1, basic::options::OptionKeys::motifs::r2, utility_exit_with_message, and value.

get_symm_corrected_angle()

core::Real get_symm_corrected_angle	(	core::Size	chi_num,
		std::string	tlc,
		core::Real	chi
	)

References numeric::nonnegative_principal_angle_degrees(), and tlc.

Referenced by calc_dist().

main()

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

References argv, basic::options::OptionKeys::cyclization::chains_to_cyclize, cyclic, create_a3b_hbs::i, basic::init(), kmc, option, PeptoidDihedralGrabber::PeptoidDihedralGrabber(), qms, subloop_histogram::size, sm, TR, basic::options::OptionKeys::inout::dbms::user, and value.

Variable Documentation

cyclic

basic::options::BooleanOptionKey const cyclic("cyclic")

(

"cyclic"

)

Referenced by main().

kmc

basic::options::BooleanOptionKey const kmc("kmc")

(

"kmc"

)

Referenced by main().

peptoid_rotlibs_

std::map< std::string, core::pack::rotamers::SingleResiduePeptoidLibraryCOP > peptoid_rotlibs_

Referenced by get_rsrpl().

qms

basic::options::BooleanOptionKey const qms("qms")

(

"qms"

)

Referenced by get_rsrpl(), and main().

TR

basic::Tracer TR("PeptoidDihedralGrabber") ( "PeptoidDihedralGrabber"  )

static

Referenced by main().

TR_EX

basic::Tracer TR_EX("ExperimentalRotamers") ( "ExperimentalRotamers"  )

static

TR_IR

basic::Tracer TR_IR("InterpolatedRotamers") ( "InterpolatedRotamers"  )

static