bpy.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/ConstantLengthFragSet.hh>
#include <core/fragment/FragData.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/FoldTree.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/keys/smhybrid.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/pack/optimizeH.hh>
#include <core/pose/Pose.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/pack/dunbrack/DunbrackRotamer.fwd.hh>
#include <core/pack/dunbrack/RotamerLibrary.hh>
#include <core/pack/dunbrack/RotamerLibraryScratchSpace.hh>
#include <core/scoring/Energies.hh>
#include <core/scoring/packstat/compute_sasa.hh>
#include <core/scoring/rms_util.hh>
#include <core/scoring/ScoreFunction.hh>
#include <core/scoring/ScoreFunctionFactory.hh>
#include <core/scoring/ScoringManager.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/simple_moves/FragmentMover.hh>
#include <protocols/flxbb/FlxbbDesign.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/annotated_sequence.hh>
#include <core/pose/util.hh>
#include <core/util/SwitchResidueTypeSet.hh>

Classes
struct	PoseWrap
class	ChiMover

Functions
void	switch_to_fa (PoseWrap &pw)
void	switch_to_cen (PoseWrap &pw)
void	add_apc (core::pose::Pose &pose, core::id::AtomID aid1, core::id::AtomID aid2, core::Real mean, core::Real sd)
void	read_fragdata (FragDataCOPs &fds, utility::io::izstream &in, bool)
std::map< std::string, FragDataCOPs >	get_frags_map (bool design=false)
core::fragment::FragSetOP	make_frag_set (Size start, std::string ss, std::map< std::string, FragDataCOPs > const &fds)
void	design (PoseWrap &pw, ScoreFunctionOP sf)
void	minimize (PoseWrap &pw, ScoreFunctionOP sf)
core::scoring::ScoreFunctionOP	cen_fold (PoseWrap &pw, Size NCYCLES, core::fragment::FragSetOP frags, Real temp=2.0)
PoseWrap	make_pose (Size Nprev, Size Npost)
ScoreFunctionOP	flxbb_nobu (PoseWrap &pw)
void	report (PoseWrap &pw, ScoreFunctionOP sf_fa, std::ostringstream &oss, Real censcore)
std::string	make_rand_ss (core::Size len)
int	main (int argc, char *argv[])

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

Function Documentation

add_apc()

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

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

cen_fold()

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

References basic::options::OptionKeys::smhybrid::abinitio_design, PoseWrap::attach, ChiMover::ChiMover(), pyrosetta::create_score_function, design(), basic::options::OptionKeys::frags::frags, create_a3b_hbs::i, basic::init(), basic::options::OptionKeys::MonteCarlo::MonteCarlo, basic::options::option, beta_nonlocal::pose, PoseWrap::pose, basic::options::OptionKeys::frags::scoring::scoring, switch_to_cen(), erraser_analysis::temp, and TR.

Referenced by main(), and HubDenovo::run().

design()

void design	(	PoseWrap &	pw,
		ScoreFunctionOP	sf
	)

References PoseWrap::attach, create_a3b_hbs::i, beta_nonlocal::pose, PoseWrap::pose, basic::options::OptionKeys::casp::repack, basic::options::OptionKeys::out::sf, and vancomycin::task.

Referenced by cen_fold(), and get_frags_map().

flxbb_nobu()

ScoreFunctionOP flxbb_nobu

(

PoseWrap &

pw

)

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

Referenced by main().

get_frags_map()

std::map<std::string, FragDataCOPs > get_frags_map

(

bool

design = false

)

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

Referenced by HubDenovo::HubDenovo(), and main().

main()

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

References basic::options::OptionKeys::smhybrid::abinitio_cycles, argv, basic::options::OptionKeys::smhybrid::attach_rsd, cen_fold(), test.T009_Exceptions::e, flxbb_nobu(), get_frags_map(), basic::init(), make_frag_set(), make_pose(), make_rand_ss(), min(), N, basic::options::OptionKeys::smhybrid::nres_mono, basic::options::option, test.T008_Serialization::oss, beta_nonlocal::pose, PoseWrap::pose, report(), SS, switch_to_fa(), TR, and numeric::random::uniform().

make_frag_set()

core::fragment::FragSetOP make_frag_set	(	Size	start,
		std::string	ss,
		std::map< std::string, FragDataCOPs > const &	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 HubDenovo::HubDenovo(), and main().

make_pose()

PoseWrap make_pose	(	Size	Nprev,
		Size	Npost
	)

References PoseWrap::attach, test.T020_Pose_Bindings::ft, create_a3b_hbs::i, beta_sc_scan::name3, PoseWrap::nres, PoseWrap::nsub, basic::options::option, option, PoseWrap::pose, pyrosetta.distributed.io::pose_from_file, basic::options::OptionKeys::in::file::residue_type_set, and docking::s.

Referenced by main().

make_rand_ss()

std::string make_rand_ss

(

core::Size

len

)

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

Referenced by main().

minimize()

void minimize	(	PoseWrap &	pw,
		ScoreFunctionOP	sf
	)

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

read_fragdata()

void read_fragdata	(	FragDataCOPs &	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().

report()

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

References utility::io::oc::cout, PoseWrap::dump_pdb(), ObjexxFCL::format::F(), utility::io::ocstream::flush(), test.T110_numeric::I, ObjexxFCL::format::LJ(), PoseWrap::nres, 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, PoseWrap::pose, basic::options::OptionKeys::in::file::silent_energy_cut, ObjexxFCL::string_of(), surface, tag, and numeric::random::uniform().

Referenced by CrystDesign::filter_and_report(), main(), and basic::Reporter::Reporter().

switch_to_cen()

void switch_to_cen

(

PoseWrap &

pw

)

References PoseWrap::attach, create_a3b_hbs::i, natoms(), PoseWrap::nres, PoseWrap::nsub, and PoseWrap::pose.

Referenced by cen_fold().

switch_to_fa()

void switch_to_fa

(

PoseWrap &

pw

)

References PoseWrap::attach, create_a3b_hbs::i, natoms(), PoseWrap::nres, PoseWrap::nsub, and PoseWrap::pose.

Referenced by main().

Variable Documentation

TR

basic::Tracer TR("bpy") ( "bpy"  )

static

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