rblinker2.cc File Reference

#include <basic/basic.hh>
#include <basic/database/open.hh>
#include <basic/options/keys/in.OptionKeys.gen.hh>
#include <basic/options/keys/out.OptionKeys.gen.hh>
#include <basic/options/keys/parser.OptionKeys.gen.hh>
#include <basic/options/keys/rblinker.OptionKeys.gen.hh>
#include <basic/options/keys/score.OptionKeys.gen.hh>
#include <basic/options/option.hh>
#include <basic/Tracer.hh>
#include <core/chemical/AtomType.hh>
#include <core/chemical/ChemicalManager.hh>
#include <core/chemical/ResidueTypeSet.hh>
#include <core/chemical/util.hh>
#include <core/chemical/VariantType.hh>
#include <core/conformation/Residue.hh>
#include <core/conformation/ResidueFactory.hh>
#include <core/fragment/BBTorsionSRFD.hh>
#include <core/fragment/ConstantLengthFragSet.hh>
#include <core/fragment/FragData.hh>
#include <core/fragment/FragmentIO.hh>
#include <core/fragment/FragSet.hh>
#include <core/import_pose/import_pose.hh>
#include <devel/init.hh>
#include <core/kinematics/FoldTree.hh>
#include <core/kinematics/MoveMap.hh>
#include <core/kinematics/Stub.hh>
#include <core/pose/annotated_sequence.hh>
#include <core/pose/Pose.hh>
#include <core/pose/util.hh>
#include <core/scoring/Energies.hh>
#include <core/scoring/ScoreFunction.hh>
#include <core/scoring/ScoreFunctionFactory.hh>
#include <core/scoring/ScoringManager.hh>
#include <numeric/random/random.hh>
#include <numeric/xyz.functions.hh>
#include <numeric/xyz.io.hh>
#include <ObjexxFCL/FArray3D.hh>
#include <ObjexxFCL/format.hh>
#include <ObjexxFCL/string.functions.hh>
#include <protocols/simple_moves/FragmentMover.hh>
#include <protocols/simple_moves/BBGaussianMover.hh>
#include <protocols/moves/MonteCarlo.hh>
#include <protocols/moves/Mover.hh>
#include <protocols/moves/MoverContainer.hh>
#include <protocols/moves/RepeatMover.hh>
#include <protocols/rigid/RigidBodyMover.hh>
#include <protocols/moves/TrialMover.hh>
#include <protocols/scoring/methods/ImplicitClashEnergy.hh>
#include <protocols/viewer/viewers.hh>
#include <sstream>
#include <set>
#include <apps/pilot/will/mynamespaces.ihh>

Classes
class	SimpleBBMover

Typedefs
typedef utility::pointer::owning_ptr< SimpleBBMover >	SimpleBBMoverOP

Functions
void	xform_pose (core::pose::Pose &pose, core::kinematics::Stub const &s, Size sres=1, Size eres=0)
void	xform_pose_rev (core::pose::Pose &pose, core::kinematics::Stub const &s)
std::string	printbits (unsigned long nn)
std::string	bin2string (unsigned long bin, Size nres)
unsigned long	pose2bin (core::pose::Pose const &pose)
Size	get_aln_resi (core::pose::Pose const &pose, core::Size const aln_chain, char const aln_termi)
core::kinematics::Stub	getxform (core::conformation::Residue const &move_resi, core::conformation::Residue const &fixd_resi)
core::kinematics::Stub	getxform (core::conformation::ResidueCOP move_resi, core::conformation::Residue const &fixd_resi)
core::kinematics::Stub	getxform (core::conformation::Residue const &move_resi, core::conformation::ResidueCOP fixd_resi)
core::kinematics::Stub	getxform (core::conformation::ResidueCOP move_resi, core::conformation::ResidueCOP fixd_resi)
core::pose::Pose	build_algned_linker (core::pose::Pose const &alnpose, Size len, core::chemical::ResidueTypeSetCAP resset, Pose const &oldlnk)
void *	doit (void *)
int	main (int argc, char *argv[])

Variables
static basic::Tracer	TR ("rblinker2")

Typedef Documentation

SimpleBBMoverOP

typedef utility::pointer::owning_ptr<SimpleBBMover> SimpleBBMoverOP

Function Documentation

bin2string()

std::string bin2string	(	unsigned long	bin,
		Size	nres
	)

References create_a3b_hbs::bin, create_a3b_hbs::i, create_a3b_hbs::j, ObjexxFCL::lead_zero_string_of(), create_a3b_hbs::nres, and docking::s.

build_algned_linker()

core::pose::Pose build_algned_linker	(	core::pose::Pose const &	alnpose,
		Size	len,
		core::chemical::ResidueTypeSetCAP	resset,
		Pose const &	oldlnk
	)

References kmeans_adaptive_kernel_density_bb_dependent_rotlib::c, test.T020_Pose_Bindings::ft, getxform(), create_a3b_hbs::i, ObjexxFCL::len(), utility_exit_with_message, and xform_pose().

Referenced by doit().

doit()

void* doit

(

void *

)

References build_algned_linker(), basic::options::OptionKeys::remodel::cbeta, basic::options::OptionKeys::msd::debug, utility::file_basename(), kmeans_adaptive_kernel_density_bb_dependent_rotlib::fn, test.T020_Pose_Bindings::ft, 3d_histogram::hist, create_a3b_hbs::i, enumerate_junctions::int, create_a3b_hbs::j, ObjexxFCL::lead_zero_string_of(), kmeans_adaptive_kernel_density_bb_dependent_rotlib::m, numeric::max(), max(), numeric::min(), basic::options::OptionKeys::MonteCarlo::MonteCarlo, basic::options::OptionKeys::backrub::ntrials, out::file::o(), option, pair, beta_nonlocal::pose, pose2bin(), pyrosetta.distributed.io::pose_from_file, basic::options::OptionKeys::remodel::rama, docking::s, in::file::s(), basic::options::OptionKeys::recces::seq1, basic::options::OptionKeys::recces::seq2, basic::options::OptionKeys::out::sf, basic::options::OptionKeys::mh::match::ss1, basic::options::OptionKeys::mh::match::ss2, basic::options::OptionKeys::cutoutdomain::start, ObjexxFCL::string_of(), TR, gaussian-sampling::trial, numeric::random::uniform(), basic::options::OptionKeys::inout::dbms::user, utility_exit_with_message, and basic::options::OptionKeys::remodel::vdw.

Referenced by main().

get_aln_resi()

Size get_aln_resi	(	core::pose::Pose const &	pose,
		core::Size const	aln_chain,
		char const	aln_termi
	)

References create_a3b_hbs::i, beta_nonlocal::pose, pna::resi, ObjexxFCL::string_of(), and utility_exit_with_message.

getxform() [1/4]

core::kinematics::Stub getxform	(	core::conformation::Residue const &	move_resi,
		core::conformation::Residue const &	fixd_resi
	)

References numeric::alignVectorSets(), and docking::s.

Referenced by build_algned_linker(), and getxform().

getxform() [2/4]

core::kinematics::Stub getxform	(	core::conformation::Residue const &	move_resi,
		core::conformation::ResidueCOP	fixd_resi
	)

References getxform().

getxform() [3/4]

core::kinematics::Stub getxform	(	core::conformation::ResidueCOP	move_resi,
		core::conformation::Residue const &	fixd_resi
	)

References getxform().

getxform() [4/4]

core::kinematics::Stub getxform	(	core::conformation::ResidueCOP	move_resi,
		core::conformation::ResidueCOP	fixd_resi
	)

References getxform().

main()

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

References argv, doit(), test.T009_Exceptions::e, func, basic::init(), option, basic::options::OptionKeys::parser::view, and viewer_main().

pose2bin()

unsigned long pose2bin

(

core::pose::Pose const &

pose

)

References create_a3b_hbs::bin, create_a3b_hbs::i, ObjexxFCL::min(), oop_conformations::phi, beta_nonlocal::pose, oop_conformations::psi, and basic::unsigned_periodic_range().

Referenced by doit().

printbits()

std::string printbits

(

unsigned long

nn

)

References create_a3b_hbs::i, basic::options::OptionKeys::cm::nn, and docking::s.

xform_pose()

void xform_pose ( core::pose::Pose &  pose, core::kinematics::Stub const &  s, Size  sres = 1, Size  eres = 0  )

inline

References natoms(), beta_nonlocal::pose, and docking::s.

Referenced by build_algned_linker().

xform_pose_rev()

void xform_pose_rev ( core::pose::Pose &  pose, core::kinematics::Stub const &  s  )

inline

References natoms(), beta_nonlocal::pose, and docking::s.

Referenced by dock(), doit(), dump_unique_atoms(), main(), TEST(), and test_chi_xform().

Variable Documentation

TR

basic::Tracer TR("rblinker2") ( "rblinker2"  )

static

Referenced by doit().