PCA_visualizer.cc File Reference

#include <protocols/simple_moves/ScoreMover.hh>
#include <core/scoring/ScoreFunction.hh>
#include <core/pose/util.hh>
#include <core/scoring/symmetry/SymmetricScoreFunction.hh>
#include <core/scoring/ScoreFunctionFactory.hh>
#include <core/chemical/ChemicalManager.hh>
#include <core/import_pose/import_pose.hh>
#include <protocols/cluster/cluster.hh>
#include <protocols/loops/Loops.hh>
#include <core/import_pose/pose_stream/MetaPoseInputStream.hh>
#include <core/import_pose/pose_stream/util.hh>
#include <basic/options/option.hh>
#include <basic/options/option_macros.hh>
#include <devel/init.hh>
#include <iostream>
#include <string>
#include <deque>
#include <basic/options/keys/in.OptionKeys.gen.hh>
#include <basic/options/keys/out.OptionKeys.gen.hh>
#include <basic/options/keys/cluster.OptionKeys.gen.hh>
#include <utility/vector1.hh>
#include <core/scoring/rms_util.hh>
#include <core/scoring/rms_util.tmpl.hh>
#include <ObjexxFCL/format.hh>
#include <core/pose/annotated_sequence.hh>
#include <stdio.h>
#include <stdlib.h>
#include <math.h>
#include <protocols/minimization_packing/MinMover.hh>
#include <core/kinematics/MoveMap.hh>
#include <core/kinematics/Jump.hh>
#include <numeric/EulerAngles.hh>
#include <protocols/minimization_packing/RepackSidechainsMover.hh>
#include <core/chemical/ResidueTypeSet.hh>
#include <core/conformation/ResidueFactory.hh>

Macros
#define	PI   3.1415926535897932384626433832795028841971693993751058

Functions
	OPT_KEY (FileVector, PCAfiles) OPT_KEY(Integer
outcount	OPT_KEY (RealVector, amplitudes) OPT_KEY(RealVector
outcount frequencies	OPT_KEY (RealVector, offsets) OPT_KEY(Boolean
outcount frequencies use_variances	OPT_KEY (Boolean, do_repack) OPT_KEY(Boolean
outcount frequencies use_variances do_minimize	OPT_KEY (Boolean, cyclic) void register_options()
void	betapeptide_setphi (core::pose::Pose &pose, core::Size resnumber, core::Real angle)
void	betapeptide_settheta (core::pose::Pose &pose, core::Size resnumber, core::Real angle)
void	betapeptide_setpsi (core::pose::Pose &pose, core::Size resnumber, core::Real angle)
void	betapeptide_setomega (core::pose::Pose &pose, core::Size resnumber, core::Real angle)
void	read_PCAfile (const char *filename, utility::vector1< core::Real > &variances, utility::vector1< utility::vector1< core::Real > > &PCA_vectors, bool normalize_variances)
void	fix_cyclic_termini (core::pose::Pose &mypose)
bool	checkresiduecount (const core::pose::Pose &mypose, const utility::vector1< core::Real > &pcavect)
int	main (int argc, char *argv[])

Macro Definition Documentation

PI

#define PI   3.1415926535897932384626433832795028841971693993751058

Function Documentation

betapeptide_setomega()

void betapeptide_setomega	(	core::pose::Pose &	pose,
		core::Size	resnumber,
		core::Real	angle
	)

References basic::options::OptionKeys::hotspot::angle, and beta_nonlocal::pose.

Referenced by main().

betapeptide_setphi()

void betapeptide_setphi	(	core::pose::Pose &	pose,
		core::Size	resnumber,
		core::Real	angle
	)

References basic::options::OptionKeys::hotspot::angle, and beta_nonlocal::pose.

Referenced by main().

betapeptide_setpsi()

void betapeptide_setpsi	(	core::pose::Pose &	pose,
		core::Size	resnumber,
		core::Real	angle
	)

References basic::options::OptionKeys::hotspot::angle, and beta_nonlocal::pose.

Referenced by main().

betapeptide_settheta()

void betapeptide_settheta	(	core::pose::Pose &	pose,
		core::Size	resnumber,
		core::Real	angle
	)

References basic::options::OptionKeys::hotspot::angle, and beta_nonlocal::pose.

Referenced by main().

checkresiduecount()

bool checkresiduecount	(	const core::pose::Pose &	mypose,
		const utility::vector1< core::Real > &	pcavect
	)

References count, cyclic, create_a3b_hbs::nres, and basic::options::option.

Referenced by main().

fix_cyclic_termini()

void fix_cyclic_termini

(

core::pose::Pose &

mypose

)

References numeric::dihedral_degrees(), residue_types_from_sequence(), and superimpose_pose().

Referenced by main().

main()

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

References argv, betapeptide_setomega(), betapeptide_setphi(), betapeptide_setpsi(), betapeptide_settheta(), checkresiduecount(), basic::options::OptionKeys::cluster::cluster, cyclic, numeric::dihedral_degrees(), basic::options::OptionKeys::peptide_deriver::do_minimize, utility::options::OptionKeys::options::exit, fix_cyclic_termini(), pyrosetta.distributed.io::get_score_function(), create_a3b_hbs::i, basic::init(), create_a3b_hbs::j, min(), beta_nonlocal::mm, basic::options::option, lactamize::outfile, numeric::EulerAngles< T >::phi_degrees(), PI, pyrosetta.distributed.io::pose_from_file(), printf(), numeric::EulerAngles< T >::psi_degrees(), read_PCAfile(), register_options(), in::file::s(), basic::options::OptionKeys::frags::scoring::scoring, test.T120_core::sfxn, subloop_histogram::size, build::stdout, predPRE::t, numeric::EulerAngles< T >::theta_degrees(), and numeric::EulerAngles< T >::to_rotation_matrix().

OPT_KEY() [1/5]

outcount frequencies use_variances do_minimize OPT_KEY	(	Boolean	,
		cyclic
	)

References cyclic, basic::options::OptionKeys::peptide_deriver::do_minimize, and NEW_OPT.

OPT_KEY() [2/5]

outcount frequencies use_variances OPT_KEY	(	Boolean	,
		do_repack
	)

OPT_KEY() [3/5]

OPT_KEY	(	FileVector	,
		PCAfiles
	)

OPT_KEY() [4/5]

outcount OPT_KEY	(	RealVector	,
		amplitudes
	)

OPT_KEY() [5/5]

outcount frequencies OPT_KEY	(	RealVector	,
		offsets
	)

read_PCAfile()

void read_PCAfile	(	const char *	filename,
		utility::vector1< core::Real > &	variances,
		utility::vector1< utility::vector1< core::Real > > &	PCA_vectors,
		bool	normalize_variances
	)

References fclose(), PREcst::FILE, lactamize::filename, create_a3b_hbs::i, and create_a3b_hbs::j.

Referenced by main().