rblinker.cc File Reference

#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/option.hh>
#include <basic/database/open.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 <devel/init.hh>
#include <core/import_pose/import_pose.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/ScoreFunction.hh>
#include <core/scoring/ScoreFunctionFactory.hh>
#include <core/scoring/ScoringManager.hh>
#include <basic/Tracer.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/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/viewer/viewers.hh>
#include <sstream>
#include <utility/io/izstream.hh>
#include <utility/io/ozstream.hh>
#include <apps/pilot/will/mynamespaces.ihh>

Classes
struct	ClashCheck
class	BBMover

Functions
void	xform_pose (core::pose::Pose &pose, Stub const &s)
void	read_fragdata (vector1< core::fragment::FragDataOP > &fds, utility::io::izstream &in, bool)
std::map< string, vector1< core::fragment::FragDataOP > >	get_frags_map (bool design=false)
core::fragment::FragSetOP	make_frag_set (Pose const &pose, string ss, std::map< string, vector1< core::fragment::FragDataOP > > fds)
Real	hyd_petf_sf4_dis (Pose const &hyd, Stub const &shyd, Pose const &petf, Stub const &spetf)
Real	psI_petf_sf4_dis (Pose const &psI, Pose const &petf, Stub const &spetf)
Stub	getxform (Residue const &r1, Residue const &r2)
void *	doit (void *)
int	main (int argc, char *argv[])

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

Function Documentation

doit()

void* doit

(

void *

)

References clash(), ClashCheck::clash_check(), pyrosetta::create_score_function, kmeans_adaptive_kernel_density_bb_dependent_rotlib::fn, numeric::random::gaussian(), getxform(), hyd_petf_sf4_dis(), create_a3b_hbs::i, test.T110_numeric::I, numeric::xyzMatrix< Real >::identity(), create_a3b_hbs::j, ObjexxFCL::lead_zero_string_of(), max(), min(), basic::options::OptionKeys::MonteCarlo::MonteCarlo, test_terpenes::naccept, beta_sc_scan::name3, numeric::xyzVector< T >::normalized(), basic::options::OptionKeys::out::nstruct, out::file::o(), basic::options::option, option, output_pdb(), beta_nonlocal::pose, pyrosetta.distributed.io::pose_from_file, psI_petf_sf4_dis(), basic::options::OptionKeys::remodel::rama, numeric::random::rg(), numeric::rotation_matrix_degrees(), create_a3b_hbs::score, 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(), erraser_analysis::temp, TR, numeric::random::uniform(), basic::options::OptionKeys::inout::dbms::user, utility_exit_with_message, basic::options::OptionKeys::parser::view, and xform_pose().

Referenced by main().

get_frags_map()

std::map<string, vector1<core::fragment::FragDataOP> > get_frags_map

(

bool

design = false

)

References revert_app::design, basic::options::OptionKeys::in::in, basic::database::open(), read_fragdata(), and TR.

getxform()

Stub getxform	(	Residue const &	r1,
		Residue const &	r2
	)

References numeric::alignVectorSets(), basic::options::OptionKeys::motifs::r1, basic::options::OptionKeys::motifs::r2, and docking::s.

Referenced by doit().

hyd_petf_sf4_dis()

Real hyd_petf_sf4_dis ( Pose const &  hyd, Stub const &  shyd, Pose const &  petf, Stub const &  spetf  )

inline

References numeric::xyzVector< T >::distance().

Referenced by doit().

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().

make_frag_set()

core::fragment::FragSetOP make_frag_set	(	Pose const &	pose,
		string	ss,
		std::map< string, vector1< core::fragment::FragDataOP > >	fds
	)

References end, fi(), basic::options::OptionKeys::frags::frags, numeric::kinematic_closure::frame(), create_a3b_hbs::i, subloop_histogram::iterator, create_a3b_hbs::j, create_a3b_hbs::k, extract_by_sidechain_sasa_score::l, beta_nonlocal::pose, challenge::ss, basic::options::OptionKeys::mh::match::ss1, basic::options::OptionKeys::mh::match::ss2, and TR.

psI_petf_sf4_dis()

Real psI_petf_sf4_dis ( Pose const &  psI, Pose const &  petf, Stub const &  spetf  )

inline

References numeric::xyzVector< T >::distance().

Referenced by doit().

read_fragdata()

void read_fragdata	(	vector1< core::fragment::FragDataOP > &	fds,
		utility::io::izstream &	in,
		bool
	)

References cal_vdw_radius_pool::buf, count, create_a3b_hbs::i, test.T008_Serialization::iss, kmeans_adaptive_kernel_density_bb_dependent_rotlib::n, and kic_runner::pdb.

Referenced by get_frags_map().

xform_pose()

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

inline

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

Referenced by build_algned_linker(), dock(), doit(), TCDock::dump_pdb(), get_rmsd_debug(), main(), make_dock_olig(), make_olig(), run(), TEST(), and HBondedPairIterator::update_hb().

Variable Documentation

TR

basic::Tracer TR("rblinker") ( "rblinker"  )

static

Referenced by doit(), get_frags_map(), and make_frag_set().