smhybrid.cc File Reference

#include <basic/database/open.hh>
#include <basic/options/keys/edensity.OptionKeys.gen.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/smhybrid.OptionKeys.gen.hh>
#include <basic/options/option.hh>
#include <basic/options/util.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/conformation/symmetry/SymDof.hh>
#include <core/conformation/symmetry/SymmData.hh>
#include <core/conformation/symmetry/SymmetricConformation.hh>
#include <core/conformation/symmetry/SymmetryInfo.hh>
#include <core/conformation/symmetry/util.hh>
#include <core/conformation/symmetry/VirtualCoordinate.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/io/pdb/pdb_writer.hh>
#include <core/kinematics/FoldTree.hh>
#include <core/kinematics/MoveMap.hh>
#include <core/pack/dunbrack/DunbrackRotamer.fwd.hh>
#include <core/pack/dunbrack/RotamerLibrary.hh>
#include <core/pack/dunbrack/RotamerLibraryScratchSpace.hh>
#include <core/pack/optimizeH.hh>
#include <core/pack/task/PackerTask.hh>
#include <core/pack/task/TaskFactory.hh>
#include <core/pose/Pose.hh>
#include <core/pose/util.hh>
#include <core/scoring/constraints/AmbiguousConstraint.hh>
#include <core/scoring/constraints/AngleConstraint.hh>
#include <core/scoring/constraints/AtomPairConstraint.hh>
#include <core/scoring/constraints/ConstraintSet.hh>
#include <core/scoring/constraints/DihedralConstraint.hh>
#include <core/scoring/func/HarmonicFunc.hh>
#include <core/scoring/constraints/MultiConstraint.hh>
#include <core/scoring/constraints/util.hh>
#include <core/scoring/func/XYZ_Func.hh>
#include <core/scoring/dssp/Dssp.hh>
#include <core/scoring/electron_density/util.hh>
#include <core/scoring/Energies.hh>
#include <core/scoring/packstat/compute_sasa.hh>
#include <core/scoring/rms_util.hh>
#include <core/scoring/sasa.hh>
#include <core/scoring/ScoreFunction.hh>
#include <core/scoring/ScoreFunctionFactory.hh>
#include <core/scoring/ScoringManager.hh>
#include <core/scoring/symmetry/SymmetricScoreFunction.hh>
#include <numeric/model_quality/rms.hh>
#include <numeric/random/random.hh>
#include <numeric/xyz.functions.hh>
#include <numeric/xyz.io.hh>
#include <ObjexxFCL/FArray2D.hh>
#include <ObjexxFCL/format.hh>
#include <ObjexxFCL/string.functions.hh>
#include <protocols/simple_moves/FragmentMover.hh>
#include <protocols/electron_density/util.hh>
#include <protocols/flxbb/FlxbbDesign.hh>
#include <protocols/jobdist/standard_mains.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/symmetry/SetupForSymmetryMover.hh>
#include <protocols/minimization_packing/symmetry/SymMinMover.hh>
#include <protocols/minimization_packing/symmetry/SymPackRotamersMover.hh>
#include <protocols/moves/TrialMover.hh>
#include <protocols/symmetry/SymDockingInitialPerturbation.hh>
#include <protocols/symmetric_docking/SymDockingLowRes.hh>
#include <protocols/viewer/viewers.hh>
#include <sstream>
#include <utility/io/izstream.hh>
#include <utility/io/ozstream.hh>
#include <utility/string_constants.hh>
#include <apps/pilot/will/mynamespaces.ihh>

Classes
class	AbsFunc
class	RepFunc
class	CoupledFunc
struct	PoseWrap
class	ChiMover
class	MySlideMover
class	MyTransMover
class	MyRotMover
class	FloatScRotMover
class	FloatScRandomChi
class	FloatScMonteCarlo
class	ScMinMover
class	BBMover

Typedefs
typedef numeric::xyzVector< Real >	Vec
typedef numeric::xyzMatrix< Real >	Mat
typedef owning_ptr< PoseWrap >	PoseWrapOP
typedef access_ptr< PoseWrap >	PoseWrapAP
typedef owning_ptr< const PoseWrap >	PoseWrapCOP
typedef access_ptr< const PoseWrap >	PoseWrapCAP

Functions
string &	replace_string (string &s, string const &f, string const &r)
core::pose::Pose	append_jumpless_pose (core::pose::Pose const &pose1, core::pose::Pose const &pose2)
string	process_ss_str (string in)
int	up_jump_tree (Pose &pose, int rsd)
void	add_apc (core::pose::Pose &pose, core::id::AtomID aid1, core::id::AtomID aid2, core::Real mean, core::Real sd, core::scoring::ScoreType st=core::scoring::atom_pair_constraint)
void	add_agc (core::pose::Pose &pose, core::id::AtomID aid1, core::id::AtomID aid2, core::id::AtomID aid3, core::Real mean, core::Real sd)
void	change_floating_sc_geometry (Pose &pose, Size rsd_in, Size nres)
void	change_floating_sc_geometry_reverse (Pose &pose, Size rsd, Size nres)
vector1< Size >	read_res_list (string fn)
vector1< xyzVector< Size > >	read_jumpcut_file (string fn)
string	select_string (string in, Size &fp)
Size	to_integer (string s)
PoseWrap	posewrap_from_command_line (string symm_def_template="", string symm_def_template_reduced="")
void	read_fragdata (vector1< core::fragment::FragDataOP > &fds, std::istream &in, bool)
std::map< string, vector1< core::fragment::FragDataOP > >	get_frags_map (bool design=false)
core::fragment::FragSetOP	make_frag_set (PoseWrap const &pw, std::map< string, vector1< core::fragment::FragDataOP > > fds)
core::fragment::FragSetOP	make_frag_set_9mers (Size nres)
void	get_res_downstream_of_jump (FoldTree const &ft, Size j, vector1< Size > &resout)
void	print_movemap (core::kinematics::MoveMap const &movemap)
void	jumps_to_root (Pose &pose, Size rsd, vector1< Size > &jumps)
MoverOP	make_float_sc_min_mover (core::pose::Pose &pose, vector1< Size > rsd_, Real tol)
void	repack (PoseWrap &pw, ScoreFunctionOP sf, bool fsc_only=false)
void	design (PoseWrap &pw, ScoreFunctionOP sf, bool do_trp=false)
void	cen_design (PoseWrap &pw, ScoreFunctionOP sf)
void	minimize (PoseWrap &pw, ScoreFunctionOP sf, int bb=0, bool jmp=true, bool chi1=false)
core::scoring::ScoreFunctionOP	cen_fold (PoseWrap &pw, Size NCYCLES, core::fragment::FragSetOP frags0, core::fragment::FragSetOP frags3)
core::scoring::ScoreFunctionOP	fa_refine_and_design (PoseWrap &pw, Size NCYCLE)
ScoreFunctionOP	flxbb_nobu (PoseWrap &pw)
vector1< Real >	interface_energy_ratio (core::pose::Pose const &pose, ScoreFunctionOP sf)
Real	symm_self_rep (PoseWrap &pw, ScoreFunctionOP sf, Size rsd)
std::map< std::pair< Size, Size >, Real >	find_clashes (PoseWrap &pw)
void	report (PoseWrap &pw, ScoreFunctionOP sf_fa, std::ostringstream &oss, Real censcore)
string	make_rand_ss_hs (core::Size)
string	make_rand_ss_h (core::Size len)
void *	doit (void *)
void *	doit_refine (void *)
int	main (int argc, char *argv[])

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

Typedef Documentation

Mat

typedef numeric::xyzMatrix<Real> Mat

PoseWrapAP

typedef access_ptr<PoseWrap> PoseWrapAP

PoseWrapCAP

typedef access_ptr<const PoseWrap> PoseWrapCAP

PoseWrapCOP

typedef owning_ptr<const PoseWrap> PoseWrapCOP

PoseWrapOP

typedef owning_ptr<PoseWrap> PoseWrapOP

Vec

typedef numeric::xyzVector<Real> Vec

Function Documentation

add_agc()

void add_agc	(	core::pose::Pose &	pose,
		core::id::AtomID	aid1,
		core::id::AtomID	aid2,
		core::id::AtomID	aid3,
		core::Real	mean,
		core::Real	sd
	)

References basic::options::OptionKeys::ddg::mean, beta_nonlocal::pose, and sd().

add_apc()

void add_apc	(	core::pose::Pose &	pose,
		core::id::AtomID	aid1,
		core::id::AtomID	aid2,
		core::Real	mean,
		core::Real	sd,
		core::scoring::ScoreType	st = core::scoring::atom_pair_constraint
	)

References basic::options::OptionKeys::ddg::mean, beta_nonlocal::pose, and sd().

Referenced by PoseWrap::add_apcs_local().

append_jumpless_pose()

core::pose::Pose append_jumpless_pose	(	core::pose::Pose const &	pose1,
		core::pose::Pose const &	pose2
	)

References create_a3b_hbs::i, beta_nonlocal::pose, test.T008_Serialization::pose1, and test.T008_Serialization::pose2.

cen_design()

void cen_design	(	PoseWrap &	pw,
		ScoreFunctionOP	sf
	)

References PoseWrap::check_scattach_res(), PoseWrap::floating_scs_, create_a3b_hbs::i, PoseWrap::nres, PoseWrap::pose, repack(), basic::options::OptionKeys::out::sf, and vancomycin::task.

Referenced by cen_fold().

cen_fold()

core::scoring::ScoreFunctionOP cen_fold	(	PoseWrap &	pw,
		Size	NCYCLES,
		core::fragment::FragSetOP	frags0,
		core::fragment::FragSetOP	frags3
	)

References cen_design(), pyrosetta::create_score_function, PoseWrap::debug, PoseWrap::dump_pdb(), filter, PoseWrap::floating_scs_, PoseWrap::has_floating_sc, create_a3b_hbs::i, basic::init(), basic::options::OptionKeys::edensity::mapfile, basic::options::OptionKeys::MonteCarlo::MonteCarlo, PoseWrap::nres, basic::options::option, option, PoseWrap::pose, basic::options::OptionKeys::smhybrid::rb_mag, basic::options::OptionKeys::remodel::rg, rot, basic::options::OptionKeys::frags::scoring::scoring, subloop_histogram::size, test.Workshop7test::slide, basic::options::OptionKeys::smhybrid::switch_concert_sub, PoseWrap::switch_to_cen(), erraser_analysis::temp, basic::options::OptionKeys::smhybrid::temperature, TR, trans, and basic::options::OptionKeys::inout::dbms::user.

Referenced by doit().

change_floating_sc_geometry()

void change_floating_sc_geometry	(	Pose &	pose,
		Size	rsd_in,
		Size	nres
	)

References job_manager::app, measure_params::cross(), build_jacobian::distance, ObjexxFCL::format::F(), test.T020_Pose_Bindings::ft, create_a3b_hbs::i, create_a3b_hbs::j, kmeans_adaptive_kernel_density_bb_dependent_rotlib::m, metal, natoms(), numeric::xyzVector< T >::normalized(), create_a3b_hbs::nres, erraser_single_res_analysis::out, beta_nonlocal::pose, numeric::rotation_matrix_degrees(), utility_exit_with_message, x, predPRE::y, and predPRE::z.

Referenced by FloatScRotMover::apply(), ScMinMover::apply(), and change_floating_sc_geometry_reverse().

change_floating_sc_geometry_reverse()

void change_floating_sc_geometry_reverse	(	Pose &	pose,
		Size	rsd,
		Size	nres
	)

References change_floating_sc_geometry(), create_a3b_hbs::nres, and beta_nonlocal::pose.

design()

void design	(	PoseWrap &	pw,
		ScoreFunctionOP	sf,
		bool	do_trp = false
	)

References PoseWrap::attached_scattach_res_, PoseWrap::check_scattach_res(), basic::options::OptionKeys::smhybrid::design_hydrophobic, create_a3b_hbs::i, PoseWrap::is_rsd_designable(), PoseWrap::is_rsd_repackable(), PoseWrap::nres, basic::options::option, PoseWrap::pose, repack(), basic::options::OptionKeys::out::sf, vancomycin::task, TR, PoseWrap::update_designable_packable(), and utility_exit_with_message.

Referenced by fa_refine_and_design(), and get_frags_map().

doit()

void* doit

(

void *

)

References basic::options::OptionKeys::smhybrid::abinitio_cycles, cen_fold(), basic::options::OptionKeys::smhybrid::fa_refine, fa_refine_and_design(), filter, get_frags_map(), local::nstruct, option, test.T008_Serialization::oss, PoseWrap::pose, posewrap_from_command_line(), report(), basic::options::OptionKeys::in::file::silent_energy_cut, ObjexxFCL::string_of(), PoseWrap::switch_to_fa(), PoseWrap::tag(), TR, numeric::random::uniform(), and basic::options::OptionKeys::inout::dbms::user.

Referenced by main().

doit_refine()

void* doit_refine

(

void *

)

References PoseWrap::check_scattach_res(), PoseWrap::dump_pdb(), create_a3b_hbs::f, fa_refine_and_design(), PoseWrap::floating_scs_, PREcst::fname, natoms(), local::nstruct, option, test.T008_Serialization::oss, PoseWrap::pose, pyrosetta.distributed.io::pose_from_file, posewrap_from_command_line(), kic_runner::refine, report(), PoseWrap::switch_to_fa(), TR, and numeric::random::uniform().

Referenced by main().

fa_refine_and_design()

core::scoring::ScoreFunctionOP fa_refine_and_design	(	PoseWrap &	pw,
		Size	NCYCLE
	)

References utility::io::oc::cerr, PoseWrap::check(), PoseWrap::check_scattach_res(), PoseWrap::debug, design(), PoseWrap::dump_pdb(), create_a3b_hbs::i, basic::options::OptionKeys::smhybrid::minbb, minimize(), basic::options::OptionKeys::AnchoredDesign::filters::omega, basic::options::option, option, PoseWrap::pose, basic::options::OptionKeys::smhybrid::refine, repack(), basic::options::OptionKeys::frags::scoring::scoring, ObjexxFCL::string_of(), TR, numeric::random::uniform(), and basic::options::OptionKeys::inout::dbms::user.

Referenced by doit(), and doit_refine().

find_clashes()

std::map< std::pair<Size,Size>, Real > find_clashes

(

PoseWrap &

pw

)

References utility::graph::Node::const_upper_edge_list_end(), utility::graph::Edge::get_node(), create_a3b_hbs::i, create_a3b_hbs::j, PoseWrap::nres, PoseWrap::pose, basic::options::OptionKeys::frags::scoring::scoring, and basic::options::OptionKeys::symmetry::symmetry.

Referenced by report().

flxbb_nobu()

ScoreFunctionOP flxbb_nobu

(

PoseWrap &

pw

)

References basic::options::OptionKeys::smhybrid::fa_refine, basic::options::OptionKeys::flxbb::flxbb, basic::options::option, PoseWrap::pose, and basic::options::OptionKeys::frags::scoring::scoring.

get_frags_map()

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

(

bool

design = false

)

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

Referenced by doit().

get_res_downstream_of_jump()

void get_res_downstream_of_jump	(	FoldTree const &	ft,
		Size	j,
		vector1< Size > &	resout
	)

References test.T020_Pose_Bindings::ft, create_a3b_hbs::i, and create_a3b_hbs::j.

Referenced by MyRotMover::MyRotMover().

interface_energy_ratio()

vector1<Real> interface_energy_ratio	(	core::pose::Pose const &	pose,
		ScoreFunctionOP	sf
	)

References utility::graph::Node::const_upper_edge_list_end(), utility::graph::Edge::get_node(), create_a3b_hbs::i, create_a3b_hbs::j, PoseWrap::pose, basic::options::OptionKeys::frags::scoring::scoring, basic::options::OptionKeys::out::sf, and basic::options::OptionKeys::symmetry::symmetry.

Referenced by report().

jumps_to_root()

void jumps_to_root	(	Pose &	pose,
		Size	rsd,
		vector1< Size > &	jumps
	)

References test.T020_Pose_Bindings::ft, create_a3b_hbs::i, PoseWrap::pose, and utility_exit_with_message.

Referenced by make_float_sc_min_mover(), and minimize().

main()

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

References argv, doit(), doit_refine(), test.T009_Exceptions::e, func, basic::init(), basic::options::option, option, basic::options::OptionKeys::smhybrid::refine, basic::options::OptionKeys::inout::dbms::user, basic::options::OptionKeys::parser::view, and viewer_main().

make_float_sc_min_mover()

MoverOP make_float_sc_min_mover	(	core::pose::Pose &	pose,
		vector1< Size >	rsd_,
		Real	tol
	)

References create_a3b_hbs::i, docking::jumps, jumps_to_root(), basic::options::OptionKeys::in::file::movemap, PoseWrap::pose, and loops_kic::tol.

Referenced by ScMinMover::ScMinMover().

make_frag_set()

core::fragment::FragSetOP make_frag_set	(	PoseWrap const &	pw,
		std::map< string, vector1< core::fragment::FragDataOP > >	fds
	)

References kmeans_adaptive_kernel_density_bb_dependent_rotlib::c, PoseWrap::cuts_, 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, PoseWrap::nres, PoseWrap::ss(), basic::options::OptionKeys::mh::match::ss1, basic::options::OptionKeys::mh::match::ss2, and TR.

make_frag_set_9mers()

core::fragment::FragSetOP make_frag_set_9mers

(

Size

nres

)

References fi(), basic::options::OptionKeys::frags::frags, numeric::kinematic_closure::frame(), create_a3b_hbs::i, basic::options::OptionKeys::in::in, subloop_histogram::iterator, PoseWrap::nres, and read_fragdata().

make_rand_ss_h()

string make_rand_ss_h

(

core::Size

len

)

References create_a3b_hbs::i, ObjexxFCL::len(), PoseWrap::ss(), and numeric::random::uniform().

make_rand_ss_hs()

string make_rand_ss_hs

(

core::Size

)

References create_a3b_hbs::i, basic::options::OptionKeys::dna::specificity::nloop, PoseWrap::ss(), and numeric::random::uniform().

minimize()

void minimize	(	PoseWrap &	pw,
		ScoreFunctionOP	sf,
		int	bb = 0,
		bool	jmp = true,
		bool	chi1 = false
	)

References PoseWrap::check_scattach_res(), test.T009_Exceptions::e, PoseWrap::floating_scs_, create_a3b_hbs::i, docking::jumps, jumps_to_root(), kmeans_adaptive_kernel_density_bb_dependent_rotlib::m, basic::options::OptionKeys::in::file::movemap, PoseWrap::nres, PoseWrap::pose, print_movemap(), basic::options::OptionKeys::out::sf, and TR.

Referenced by fa_refine_and_design().

posewrap_from_command_line()

PoseWrap posewrap_from_command_line	(	string	symm_def_template = "",
		string	symm_def_template_reduced = ""
	)

References smhybrid::add_res_after(), smhybrid::add_res_before(), smhybrid::add_ss_after(), smhybrid::add_ss_before(), smhybrid::attach_as_sc(), basic::options::OptionKeys::smhybrid::attach_as_sc, smhybrid::attach_atom(), basic::options::OptionKeys::smhybrid::attach_atom, smhybrid::attach_rsd(), basic::options::OptionKeys::smhybrid::attach_rsd, cal_vdw_radius_pool::buf, smhybrid::chainbreaks(), basic::options::OptionKeys::smhybrid::chainbreaks, smhybrid::cst_sub_files(), basic::options::OptionKeys::smhybrid::cst_sub_files, smhybrid::design_res_files(), utility::file_basename(), basic::options::OptionKeys::rna::erraser::fixed_res, smhybrid::fixed_res_files(), PREcst::fname, evaluate_beta_mutants::fp, smhybrid::frag_res_files(), create_a3b_hbs::i, basic::options::OptionKeys::in::in, smhybrid::jumpcut_files(), option, pdbs, pyrosetta.distributed.io::pose_from_file, basic::options::OptionKeys::mp::assembly::poses, PoseWrap::PoseWrap(), process_ss_str(), read_jumpcut_file(), read_res_list(), smhybrid::rep_edge_files(), in::file::s(), smhybrid::scattach_res_files(), select_string(), subloop_histogram::size, smhybrid::symm_def_template(), basic::options::OptionKeys::smhybrid::symm_def_template, smhybrid::symm_def_template_reduced(), basic::options::OptionKeys::smhybrid::symm_def_template_reduced, PoseWrap::tag(), to_integer(), basic::options::OptionKeys::inout::dbms::user, utility_exit_with_message, basic::options::OptionKeys::full_model::virtual_res, and smhybrid::virtual_res_files().

Referenced by doit(), and doit_refine().

print_movemap()

void print_movemap

(

core::kinematics::MoveMap const &

movemap

)

References create_a3b_hbs::i, basic::options::OptionKeys::in::file::movemap, and TR.

Referenced by minimize().

process_ss_str()

string process_ss_str

(

string

in

)

References end, create_a3b_hbs::i, create_a3b_hbs::j, max(), kmeans_adaptive_kernel_density_bb_dependent_rotlib::n, utility::string2int(), TR, numeric::random::uniform(), and utility_exit_with_message.

Referenced by posewrap_from_command_line().

read_fragdata()

void read_fragdata	(	vector1< core::fragment::FragDataOP > &	fds,
		std::istream &	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(), and make_frag_set_9mers().

read_jumpcut_file()

vector1<xyzVector<Size> > read_jumpcut_file

(

string

fn

)

References kmeans_adaptive_kernel_density_bb_dependent_rotlib::fn, basic::options::OptionKeys::in::in, extract_by_sidechain_sasa_score::l, utility_exit_with_message, x, predPRE::y, and predPRE::z.

Referenced by posewrap_from_command_line().

read_res_list()

vector1<Size> read_res_list

(

string

fn

)

References kmeans_adaptive_kernel_density_bb_dependent_rotlib::fn, basic::options::OptionKeys::in::in, extract_by_sidechain_sasa_score::l, create_a3b_hbs::r, and utility_exit_with_message.

Referenced by posewrap_from_command_line().

repack()

void repack	(	PoseWrap &	pw,
		ScoreFunctionOP	sf,
		bool	fsc_only = false
	)

References PoseWrap::attached_scattach_res_, detail::find(), create_a3b_hbs::i, PoseWrap::is_rsd_repackable(), PoseWrap::nres, PoseWrap::pose, basic::options::OptionKeys::out::sf, vancomycin::task, TR, and PoseWrap::update_designable_packable().

Referenced by cen_design(), design(), and fa_refine_and_design().

replace_string()

string& replace_string	(	string &	s,
		string const &	f,
		string const &	r
	)

References create_a3b_hbs::f, create_a3b_hbs::i, create_a3b_hbs::r, docking::s, and utility_exit_with_message.

Referenced by PoseWrap::PoseWrap(), utility::replace_first_in(), and utility::replace_in().

report()

void report	(	PoseWrap &	pw,
		ScoreFunctionOP	sf_fa,
		std::ostringstream &	oss,
		Real	censcore
	)

References PoseWrap::absrms_to_orig_subsubs(), PoseWrap::attach_atom_, PoseWrap::attach_rsd_, basic::options::OptionKeys::constraints::constraints, utility::io::oc::cout, lactamize::cs, PoseWrap::dump_pdb(), ObjexxFCL::format::F(), find_clashes(), PoseWrap::floating_scs_, utility::io::ocstream::flush(), kmeans_adaptive_kernel_density_bb_dependent_rotlib::fn, create_a3b_hbs::i, test.T110_numeric::I, interface_energy_ratio(), subloop_histogram::iterator, ObjexxFCL::format::LJ(), PoseWrap::nres, basic::options::OptionKeys::smhybrid::nres_mono, basic::options::OptionKeys::out::file::o, option, test.T008_Serialization::oss, test.G203_Module_SQLPDB::outdir, basic::options::OptionKeys::out::file::output_virtual, basic::options::OptionKeys::corrections::score::p_aa_pp, basic::options::OptionKeys::out::pdb_gz, PoseWrap::pose, basic::options::OptionKeys::remodel::rg, PoseWrap::rms_to_orig_subsubs(), basic::options::OptionKeys::in::file::silent_energy_cut, ObjexxFCL::string_of(), surface, symm_self_rep(), PoseWrap::tag(), TR, numeric::random::uniform(), and basic::options::OptionKeys::inout::dbms::user.

Referenced by doit(), and doit_refine().

select_string()

string select_string	(	string	in,
		Size &	fp
	)

References evaluate_beta_mutants::fp, create_a3b_hbs::i, and numeric::random::uniform().

Referenced by posewrap_from_command_line(), and setup_roc_curve().

symm_self_rep()

Real symm_self_rep	(	PoseWrap &	pw,
		ScoreFunctionOP	sf,
		Size	rsd
	)

References utility::graph::Node::const_upper_edge_list_end(), utility::graph::Edge::get_node(), create_a3b_hbs::i, create_a3b_hbs::j, PoseWrap::nres, PoseWrap::pose, basic::options::OptionKeys::frags::scoring::scoring, basic::options::OptionKeys::out::sf, and basic::options::OptionKeys::symmetry::symmetry.

Referenced by report().

to_integer()

Size to_integer

(

string

s

)

References create_a3b_hbs::i, test.T008_Serialization::iss, and docking::s.

Referenced by posewrap_from_command_line().

up_jump_tree()

int up_jump_tree	(	Pose &	pose,
		int	rsd
	)

References create_a3b_hbs::i, enumerate_junctions::int, and beta_nonlocal::pose.

Referenced by PoseWrap::check_scattach_res().

Variable Documentation

TR

basic::Tracer TR("smhybrid") ( "smhybrid"  )

static

Referenced by PoseWrap::add_apcs_local(), PoseWrap::add_floating_sc_csts(), MyTransMover::apply(), MyRotMover::apply(), ScMinMover::apply(), FloatScMonteCarlo::apply(), cen_fold(), PoseWrap::check_scattach_res(), design(), doit(), doit_refine(), fa_refine_and_design(), PoseWrap::get_closest_res_for_sc_attach(), get_frags_map(), make_frag_set(), minimize(), PoseWrap::PoseWrap(), print_movemap(), process_ss_str(), repack(), PoseWrap::replace_scattach_res(), report(), PoseWrap::switch_to_cen(), PoseWrap::switch_to_fa(), and PoseWrap::update_designable_packable().