cryst_design.cc File Reference

@Author Frank Dimaio More...

#include <protocols/cryst/spacegroup.hh>
#include <protocols/cryst/refinable_lattice.hh>
#include <apps/pilot/frank/cryst_reporters.hh>
#include <core/chemical/ChemicalManager.hh>
#include <core/chemical/ResidueTypeSet.hh>
#include <core/conformation/Residue.hh>
#include <core/conformation/ResidueFactory.hh>
#include <core/conformation/Conformation.hh>
#include <core/conformation/symmetry/SymmetricConformation.hh>
#include <core/pose/Pose.hh>
#include <core/pose/PDBInfo.hh>
#include <core/io/Remarks.hh>
#include <core/io/CrystInfo.hh>
#include <core/id/AtomID.hh>
#include <core/import_pose/import_pose.hh>
#include <devel/init.hh>
#include <core/types.hh>
#include <core/pack/task/ResfileReader.hh>
#include <core/pack/task/TaskFactory.hh>
#include <core/scoring/dssp/Dssp.hh>
#include <core/scoring/EnergyGraph.hh>
#include <core/scoring/methods/EnergyMethodOptions.hh>
#include <core/scoring/constraints/ResidueTypeConstraint.hh>
#include <protocols/jd2/JobDistributor.hh>
#include <protocols/jd2/JobDistributorFactory.hh>
#include <protocols/jd2/util.hh>
#include <protocols/jd2/SilentFileJobOutputter.hh>
#include <protocols/viewer/viewers.hh>
#include <protocols/moves/Mover.hh>
#include <protocols/moves/MoverContainer.hh>
#include <protocols/minimization_packing/PackRotamersMover.hh>
#include <protocols/minimization_packing/symmetry/SymPackRotamersMover.hh>
#include <protocols/cryst/cryst_rms.hh>
#include <protocols/relax/FastRelax.hh>
#include <protocols/cryst/util.hh>
#include <utility/vector1.hh>
#include <utility/string_util.hh>
#include <utility/file/FileName.hh>
#include <utility/file/file_sys_util.hh>
#include <numeric/random/random.hh>
#include <numeric/fourier/FFT.hh>
#include <numeric/xyzMatrix.hh>
#include <numeric/xyzVector.hh>
#include <numeric/xyz.functions.hh>
#include <numeric/UniformRotationSampler.hh>
#include <numeric/random/random_permutation.hh>
#include <ObjexxFCL/FArray2D.hh>
#include <ObjexxFCL/FArray3D.hh>
#include <utility/excn/Exceptions.hh>
#include <basic/Tracer.hh>
#include <basic/options/option.hh>
#include <basic/options/option_macros.hh>
#include <basic/options/keys/in.OptionKeys.gen.hh>
#include <basic/options/keys/out.OptionKeys.gen.hh>
#include <basic/options/keys/packing.OptionKeys.gen.hh>
#include <basic/options/keys/symmetry.OptionKeys.gen.hh>
#include <fstream>
#include <cmath>
#include <string>
#include <queue>
#include <core/optimization/MinimizerOptions.hh>
#include <core/optimization/symmetry/SymAtomTreeMinimizer.hh>
#include <core/scoring/ScoreFunctionFactory.hh>
#include <core/pack/task/PackerTask.hh>
#include <core/pack/task/ResidueLevelTask.hh>

Classes
struct	SpacegroupHit
struct	InterfaceHit
class	InterfaceHitComparitor
class	InterfaceHitDatabase
class	CrystDesign
class	CrystRelax
class	CrystCluster
class	CrystFFTDock

Macros
#define	DEG2RAD   0.0174532925199433
#define	RAD2DEG   57.295779513082323

Functions
double	sign (double x)
double	norm4 (double a, double b, double c, double d)
void	adjust_ref_weights (core::scoring::ScoreFunction &scorefxn)
template<class S >
core::Real	interp_linear (ObjexxFCL::FArray3D< S > const &data, numeric::xyzVector< core::Real > const &idxX)
void	euler2rot (core::Real a, core::Real b, core::Real g, numeric::xyzMatrix< Real > &R)
numeric::xyzVector< Real >	center_pose_at_origin (Pose &pose)
void	add_crystinfo_to_pose (Pose &pose, Spacegroup const &sg)
void *	my_main (void *)
int	main (int argc, char *argv[])

Variables
static basic::Tracer	TR ("cryst.design")

Detailed Description

@Author Frank Dimaio

Macro Definition Documentation

DEG2RAD

#define DEG2RAD   0.0174532925199433

RAD2DEG

#define RAD2DEG   57.295779513082323

Function Documentation

add_crystinfo_to_pose()

void add_crystinfo_to_pose	(	Pose &	pose,
		Spacegroup const &	sg
	)

References beta_nonlocal::pose.

Referenced by CrystCluster::transform_pdb().

adjust_ref_weights()

void adjust_ref_weights

(

core::scoring::ScoreFunction &

scorefxn

)

References aa, ObjexxFCL::float_of(), create_a3b_hbs::ii, extract_by_sidechain_sasa_score::l, option, options, runtime_assert, oop_conformations::scorefxn, basic::TR, and basic::options::OptionKeys::inout::dbms::user.

Referenced by CrystDesign::apply(), and main().

center_pose_at_origin()

numeric::xyzVector<Real> center_pose_at_origin

(

Pose &

pose

)

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

Referenced by CrystFFTDock::apply().

euler2rot()

void euler2rot	(	core::Real	a,
		core::Real	b,
		core::Real	g,
		numeric::xyzMatrix< Real > &	R
	)

References a, compute_difference::b, DEG2RAD, g(), and docking::R.

interp_linear()

template<class S >

core::Real interp_linear	(	ObjexxFCL::FArray3D< S > const &	data,
		numeric::xyzVector< core::Real > const &	idxX
	)

backward interpolation (unrotated->rotated) used to generate grids

References data, test.T009_Exceptions::e, and enumerate_junctions::int.

Referenced by CrystFFTDock::resample_maps_and_get_self().

main()

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

References spectral_cluster_kmeans_adaptive_kernel_density_bb_dependent_rotlib::A, adjust_ref_weights(), compute_difference::alpha, argv, basic::options::OptionKeys::corrections::beta, C, basic::options::OptionKeys::corrections::water::cluster_cutoff, basic::options::OptionKeys::msd::debug, test.T009_Exceptions::e, loops::gamma, basic::init(), PREcst::K, SmotifHasher::mode, my_main(), NEW_OPT, basic::options::OptionKeys::mp::mutate_relax::nmodels, and viewer_main().

my_main()

void* my_main

(

void *

)

References SmotifHasher::mode, out::nooutput(), option, basic::options::OptionKeys::in::preserve_crystinfo, beta_sc_scan::seq, strategy, basic::options::OptionKeys::symmetry::symmetry_definition, and utility_exit_with_message.

Referenced by main().

norm4()

double norm4 ( double  a, double  b, double  c, double  d  )

inline

References a, compute_difference::b, and kmeans_adaptive_kernel_density_bb_dependent_rotlib::c.

sign()

double sign ( double  x )

inline

References x.

Referenced by detail::write_float().

Variable Documentation

TR

basic::Tracer TR("cryst.design") ( "cryst.design"  )

static