rblinker2_overlay_bound.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/scoring/ImplicitFastClashCheck.hh>
#include <protocols/viewer/viewers.hh>
#include <sstream>
#include <set>
#include <utility/io/izstream.hh>
#include <apps/pilot/will/will_util.ihh>
#include <apps/pilot/will/mynamespaces.ihh>

Classes
class	SimpleBBMover

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

Functions
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::pose::Pose	build_algned_linker (core::pose::Pose const &alnpose, Size len, core::chemical::ResidueTypeSetCAP resset, Pose const &oldlnk)
void	get_aln (Pose const &lnk, Pose const &psi, Pose const &hyd, Size &psialnlnk, Size &psialnpsi, Size &hydalnlnk, Size &hydalnhyd)
bool	bound_petf_clash (Pose const &lnk, Pose const &psi, Pose const &hyd, Size psialnlnk, Size psialnpsi, Size hydalnlnk, Size hydalnhyd, protocols::scoring::ImplicitFastClashCheck const &psi_ifc, protocols::scoring::ImplicitFastClashCheck const &hyd_ifc, bool &hydpetflnkclash, bool &psipetflnkclash, bool &hydpetfpsiclash, bool &psipetfhydclash)
void *	doit (void *)
int	main (int argc, char *argv[])

Variables
static basic::Tracer	TR ("rblinker2_overlay_bound")

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.

bound_petf_clash()

bool bound_petf_clash	(	Pose const &	lnk,
		Pose const &	psi,
		Pose const &	hyd,
		Size	psialnlnk,
		Size	psialnpsi,
		Size	hydalnlnk,
		Size	hydalnhyd,
		protocols::scoring::ImplicitFastClashCheck const &	psi_ifc,
		protocols::scoring::ImplicitFastClashCheck const &	hyd_ifc,
		bool &	hydpetflnkclash,
		bool &	psipetflnkclash,
		bool &	hydpetfpsiclash,
		bool &	psipetfhydclash
	)

References getxform(), and oop_conformations::psi.

Referenced by doit().

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().

doit()

void* doit

(

void *

)

References bound_petf_clash(), basic::options::OptionKeys::remodel::cbeta, clash(), basic::options::OptionKeys::msd::debug, kmeans_adaptive_kernel_density_bb_dependent_rotlib::fn, test.T020_Pose_Bindings::ft, get_aln(), getxform(), 3d_histogram::hist, create_a3b_hbs::i, create_a3b_hbs::j, ObjexxFCL::lead_zero_string_of(), numeric::max(), numeric::min(), basic::options::OptionKeys::MonteCarlo::MonteCarlo, basic::options::OptionKeys::backrub::ntrials, out::file::o(), option, erraser_single_res_analysis::out, pair, beta_nonlocal::pose, pose2bin(), pyrosetta.distributed.io::pose_from_file, pyrosetta.io::poses_from_files(), oop_conformations::psi, basic::options::OptionKeys::remodel::rama, 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, ObjexxFCL::string_of(), TR, gaussian-sampling::trial, numeric::random::uniform(), utility_exit_with_message, basic::options::OptionKeys::remodel::vdw, xform_pose(), and xform_pose_rev().

Referenced by main().

get_aln()

void get_aln	(	Pose const &	lnk,
		Pose const &	psi,
		Pose const &	hyd,
		Size &	psialnlnk,
		Size &	psialnpsi,
		Size &	hydalnlnk,
		Size &	hydalnhyd
	)

References docking::a1, docking::a2, docking::a3, kmeans_adaptive_kernel_density_bb_dependent_rotlib::dis, kmeans_adaptive_kernel_density_bb_dependent_rotlib::fn, get_aln_resi(), basic::options::OptionKeys::in::in, basic::options::option, oop_conformations::psi, basic::options::OptionKeys::motifs::r1, basic::options::OptionKeys::motifs::r2, basic::options::OptionKeys::inout::dbms::user, and utility_exit_with_message.

Referenced by doit().

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.

Referenced by get_aln().

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.

Variable Documentation

TR

basic::Tracer TR("rblinker2_overlay_bound") ( "rblinker2_overlay_bound"  )

static

Referenced by doit().