dubois.cc File Reference

#include <core/chemical/ChemicalManager.hh>
#include <core/chemical/ResidueTypeSet.hh>
#include <core/chemical/VariantType.hh>
#include <core/conformation/Residue.hh>
#include <core/conformation/ResidueFactory.hh>
#include <core/conformation/symmetry/SymmData.hh>
#include <core/pose/symmetry/util.hh>
#include <core/conformation/symmetry/util.hh>
#include <core/fragment/FragmentIO.hh>
#include <core/fragment/BBTorsionSRFD.hh>
#include <core/fragment/FragSet.hh>
#include <devel/init.hh>
#include <basic/database/open.hh>
#include <core/io/pdb/pdb_writer.hh>
#include <core/kinematics/MoveMap.hh>
#include <basic/options/keys/in.OptionKeys.gen.hh>
#include <basic/options/keys/out.OptionKeys.gen.hh>
#include <basic/options/option.hh>
#include <basic/options/util.hh>
#include <core/pack/task/PackerTask.hh>
#include <core/pack/task/TaskFactory.hh>
#include <core/scoring/constraints/AmbiguousConstraint.hh>
#include <core/scoring/constraints/AngleConstraint.hh>
#include <core/scoring/constraints/AtomPairConstraint.hh>
#include <core/scoring/constraints/CoordinateConstraint.hh>
#include <core/scoring/constraints/DihedralConstraint.hh>
#include <core/scoring/func/HarmonicFunc.hh>
#include <core/scoring/constraints/util.hh>
#include <core/scoring/rms_util.hh>
#include <core/scoring/ScoreFunction.hh>
#include <core/scoring/ScoreFunctionFactory.hh>
#include <core/scoring/symmetry/SymmetricScoreFunction.hh>
#include <basic/Tracer.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/abinitio/FragmentMover.hh>
#include <protocols/moves/Mover.hh>
#include <protocols/moves/MonteCarlo.hh>
#include <protocols/moves/TrialMover.hh>
#include <protocols/moves/MoverContainer.hh>
#include <protocols/moves/RepeatMover.hh>
#include <protocols/minimization_packing/symmetry/SymMinMover.hh>
#include <protocols/minimization_packing/symmetry/SymPackRotamersMover.hh>
#include <protocols/symmetric_docking/SymDockingLowRes.hh>
#include <sstream>
#include <utility/io/izstream.hh>
#include <utility/io/ozstream.hh>
#include <core/import_pose/import_pose.hh>
#include <core/pose/util.hh>
#include <protocols/toolbox/SwitchResidueTypeSet.hh>

Classes
class	SeqBBTorSRFD
class	LigChiMover

Typedefs
typedef numeric::xyzVector< Real >	Vec
typedef utility::vector1< Vec >	Vecs
typedef numeric::xyzMatrix< Real >	Mat

Functions
void	switch_to_fa (core::pose::Pose &pose)
void	switch_to_cen (core::pose::Pose &pose)
void	minimize (core::pose::Pose &pose, ScoreFunctionOP sf)
void	read_fragdata (utility::vector1< core::fragment::FragDataOP > &fds, utility::io::izstream &in, bool design)
std::map< std::string, utility::vector1< core::fragment::FragDataOP > >	get_frags_map (bool design=true)
core::fragment::FragSetOP	make_frag_set (Size start, std::string ss, std::map< std::string, utility::vector1< core::fragment::FragDataOP > > fds)
void	test (core::pose::Pose &pose)
core::pose::Pose	make_pose (std::string seq)
void	repack (core::pose::Pose &pose, ScoreFunctionOP sf)
void	design (core::pose::Pose &pose, ScoreFunctionOP sf)
core::scoring::ScoreFunctionOP	cen_fold (core::pose::Pose &pose, Size NCYCLES, core::fragment::FragSetOP frags, Real temp=2.0)
core::scoring::ScoreFunctionOP	fa_refine_and_design (core::pose::Pose &pose, Size NCYCLE)
void	report (std::string tag, core::pose::Pose &pose, core::pose::Pose &cenpose, ScoreFunctionOP sf_fa, std::ostringstream &oss, Real censcore)
std::string	make_rand_ss ()
int	main (int argc, char *argv[])

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

Typedef Documentation

Mat

typedef numeric::xyzMatrix<Real> Mat

Vec

typedef numeric::xyzVector<Real> Vec

Vecs

typedef utility::vector1<Vec> Vecs

Function Documentation

cen_fold()

core::scoring::ScoreFunctionOP cen_fold	(	core::pose::Pose &	pose,
		Size	NCYCLES,
		core::fragment::FragSetOP	frags,
		Real	temp = 2.0
	)

References pyrosetta::create_score_function, create_a3b_hbs::i, basic::init(), basic::options::OptionKeys::MonteCarlo::MonteCarlo, beta_nonlocal::pose, basic::options::OptionKeys::remodel::rg, basic::options::OptionKeys::frags::scoring::scoring, erraser_analysis::temp, and TR.

Referenced by main().

design()

void design	(	core::pose::Pose &	pose,
		ScoreFunctionOP	sf
	)

References create_a3b_hbs::i, beta_nonlocal::pose, repack(), basic::options::OptionKeys::out::sf, and vancomycin::task.

Referenced by get_frags_map(), and read_fragdata().

fa_refine_and_design()

core::scoring::ScoreFunctionOP fa_refine_and_design	(	core::pose::Pose &	pose,
		Size	NCYCLE
	)

References ObjexxFCL::format::F(), create_a3b_hbs::i, test.T110_numeric::I, create_a3b_hbs::k, minimize(), basic::options::OptionKeys::smhybrid::nres_mono, beta_nonlocal::pose, repack(), basic::options::OptionKeys::frags::scoring::scoring, and TR.

Referenced by main().

get_frags_map()

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

(

bool

design = true

)

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

Referenced by main().

main()

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

References argv, cen_fold(), test.T009_Exceptions::e, fa_refine_and_design(), get_frags_map(), basic::init(), make_frag_set(), make_pose(), make_rand_ss(), test.T008_Serialization::oss, PHI, PI, numeric::NumericTraits< T >::pi(), beta_nonlocal::pose, report(), SS, ObjexxFCL::string_of(), switch_to_fa(), tag, THETA, and numeric::random::uniform().

make_frag_set()

core::fragment::FragSetOP make_frag_set	(	Size	start,
		std::string	ss,
		std::map< std::string, utility::vector1< core::fragment::FragDataOP > >	fds
	)

References end, fi(), basic::options::OptionKeys::frags::frags, numeric::kinematic_closure::frame(), create_a3b_hbs::i, challenge::ss, and basic::options::OptionKeys::cutoutdomain::start.

Referenced by main().

make_pose()

core::pose::Pose make_pose

(

std::string

seq

)

References test.T020_Pose_Bindings::ft, create_a3b_hbs::i, beta_sc_scan::name3, create_a3b_hbs::nres, PHI, PI, beta_nonlocal::pose, pyrosetta.distributed.io::pose_from_file, basic::options::OptionKeys::in::file::residue_type_set, beta_sc_scan::seq, switch_to_cen(), and THETA.

Referenced by main().

make_rand_ss()

std::string make_rand_ss

(

)

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

Referenced by main().

minimize()

void minimize	(	core::pose::Pose &	pose,
		ScoreFunctionOP	sf
	)

References test.T009_Exceptions::e, kmeans_adaptive_kernel_density_bb_dependent_rotlib::m, basic::options::OptionKeys::in::file::movemap, beta_nonlocal::pose, and basic::options::OptionKeys::out::sf.

Referenced by fa_refine_and_design(), and test().

read_fragdata()

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

References cal_vdw_radius_pool::buf, count, design(), 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().

repack()

void repack	(	core::pose::Pose &	pose,
		ScoreFunctionOP	sf
	)

References beta_nonlocal::pose, basic::options::OptionKeys::out::sf, and vancomycin::task.

Referenced by design(), and fa_refine_and_design().

report()

void report	(	std::string	tag,
		core::pose::Pose &	pose,
		core::pose::Pose &	cenpose,
		ScoreFunctionOP	sf_fa,
		std::ostringstream &	oss,
		Real	censcore
	)

References utility::io::oc::cout, ObjexxFCL::format::F(), utility::io::ocstream::flush(), test.T110_numeric::I, ObjexxFCL::format::LJ(), basic::options::OptionKeys::smhybrid::nres_mono, basic::options::OptionKeys::out::file::o, basic::options::option, option, test.T008_Serialization::oss, basic::options::OptionKeys::corrections::score::p_aa_pp, beta_nonlocal::pose, basic::options::OptionKeys::in::file::silent_energy_cut, and tag.

Referenced by main().

switch_to_cen()

void switch_to_cen

(

core::pose::Pose &

pose

)

References PHI, PI, beta_nonlocal::pose, and THETA.

Referenced by make_pose().

switch_to_fa()

void switch_to_fa

(

core::pose::Pose &

pose

)

References PHI, PI, beta_nonlocal::pose, and THETA.

Referenced by main().

test()

void test

(

core::pose::Pose &

pose

)

References utility::io::oc::cerr, create_a3b_hbs::i, minimize(), beta_nonlocal::pose, basic::options::OptionKeys::frags::scoring::scoring, basic::options::OptionKeys::out::sf, ObjexxFCL::string_of(), and numeric::random::uniform().

Variable Documentation

TR

basic::Tracer TR("dubois") ( "dubois"  )

static

Referenced by cen_fold(), fa_refine_and_design(), and get_frags_map().