gpu_linker.cc File Reference

#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 <basic/options/option_macros.hh>
#include <basic/Tracer.hh>
#include <core/chemical/ChemicalManager.hh>
#include <core/chemical/ResidueTypeSet.hh>
#include <core/chemical/util.hh>
#include <core/chemical/VariantType.hh>
#include <core/conformation/Conformation.hh>
#include <core/conformation/Residue.hh>
#include <core/conformation/ResidueFactory.hh>
#include <core/import_pose/import_pose.hh>
#include <devel/init.hh>
#include <core/io/pdb/pdb_writer.hh>
#include <core/io/silent/ScoreFileSilentStruct.hh>
#include <core/io/silent/SilentFileData.hh>
#include <core/kinematics/FoldTree.hh>
#include <core/kinematics/MoveMap.hh>
#include <core/kinematics/Stub.hh>
#include <core/pack/optimizeH.hh>
#include <core/pack/task/PackerTask.hh>
#include <core/pack/task/RotamerSampleOptions.hh>
#include <core/pack/task/TaskFactory.hh>
#include <core/pose/annotated_sequence.hh>
#include <core/pose/Pose.hh>
#include <core/pose/util.hh>
#include <core/scoring/rms_util.hh>
#include <core/scoring/ScoreFunction.hh>
#include <core/scoring/ScoreFunctionFactory.hh>
#include <core/scoring/ScoringManager.hh>
#include <core/util/SwitchResidueTypeSet.hh>
#include <numeric/conversions.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 <sstream>
#include <utility/io/izstream.hh>
#include <utility/io/ozstream.hh>
#include <apps/pilot/will/will_util.ihh>
#include <apps/pilot/will/mynamespaces.ihh>
#include <apps/pilot/will/gpu/CL.hh>
#include <apps/pilot/will/gpu/set_pose_to_ideal.ihh>

Typedefs
typedef numeric::xyzVector< float >	Vecf
typedef numeric::xyzMatrix< float >	Matf
typedef cl_float16	float16
typedef cl_float8	float8
typedef cl_float4	float4
typedef cl_float3	float3
typedef cl_float2	float2
typedef cl_ushort2	ushort2
typedef cl_uint8	uint8

Functions
void	register_options ()
void	dump_points_pdb (float const *p, int n, string fn)
void	dump_points_pdb (Pose const &p, string fn)
utility::vector1< numeric::xyzVector< Real > >	array2vecs (float const *xyz, int N)
void	fere_torsions (int N, float *tor)
void	random_torsions (int N, float *tor)
void	refold_ros (core::pose::Pose &p, float const *tor, float *crd)
void	refold_gpu (float const *tor, int N, float *crd, CL &cl, cl_mem &clmtor, cl_mem &clmout)
void	test_refold ()
int	main (int argc, char *argv[])

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

Typedef Documentation

float16

typedef cl_float16 float16

float2

typedef cl_float2 float2

float3

typedef cl_float3 float3

float4

typedef cl_float4 float4

float8

typedef cl_float8 float8

Matf

typedef numeric::xyzMatrix<float> Matf

uint8

typedef cl_uint8 uint8

ushort2

typedef cl_ushort2 ushort2

Vecf

typedef numeric::xyzVector<float> Vecf

Function Documentation

array2vecs()

utility::vector1<numeric::xyzVector<Real> > array2vecs	(	float const *	xyz,
		int	N
	)

References create_a3b_hbs::i, N, kmeans_adaptive_kernel_density_bb_dependent_rotlib::v, and basic::options::OptionKeys::in::file::xyz.

Referenced by test_refold().

dump_points_pdb() [1/2]

void dump_points_pdb	(	float const *	p,
		int	n,
		string	fn
	)

References ObjexxFCL::format::F(), kmeans_adaptive_kernel_density_bb_dependent_rotlib::fn, create_a3b_hbs::i, test.T110_numeric::I, kmeans_adaptive_kernel_density_bb_dependent_rotlib::n, basic::options::OptionKeys::out::file::o, and kmeans_adaptive_kernel_density_bb_dependent_rotlib::p.

Referenced by test_refold().

dump_points_pdb() [2/2]

void dump_points_pdb	(	Pose const &	p,
		string	fn
	)

References ObjexxFCL::format::F(), kmeans_adaptive_kernel_density_bb_dependent_rotlib::fn, create_a3b_hbs::i, test.T110_numeric::I, basic::options::OptionKeys::out::file::o, kmeans_adaptive_kernel_density_bb_dependent_rotlib::p, x, predPRE::y, and predPRE::z.

fere_torsions()

void fere_torsions	(	int	N,
		float *	tor
	)

References create_a3b_hbs::i, N, pyrosetta.distributed.io::pose_from_file, and numeric::conversions::radians().

Referenced by test_refold().

main()

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

References argv, basic::init(), register_options(), and test_refold().

random_torsions()

void random_torsions	(	int	N,
		float *	tor
	)

References create_a3b_hbs::i, N, numeric::conversions::radians(), and numeric::random::uniform().

Referenced by test_refold().

refold_gpu()

void refold_gpu	(	float const *	tor,
		int	N,
		float *	crd,
		CL &	cl,
		cl_mem &	clmtor,
		cl_mem &	clmout
	)

References CL::cpu2gpu(), CL::finish(), CL::gpu2cpu(), N, and CL::q2d().

Referenced by test_refold().

refold_ros()

void refold_ros	(	core::pose::Pose &	p,
		float const *	tor,
		float *	crd
	)

References numeric::conversions::degrees(), create_a3b_hbs::i, and kmeans_adaptive_kernel_density_bb_dependent_rotlib::p.

Referenced by test_refold().

register_options()

void register_options

(

)

References kmeans_adaptive_kernel_density_bb_dependent_rotlib::kernel, and NEW_OPT.

Referenced by main().

test_refold()

void test_refold

(

)

References array2vecs(), numeric::model_quality::calc_rms(), utility::io::oc::cout, CL::cpu2gpu(), dump_points_pdb(), CL::errstr(), fere_torsions(), create_a3b_hbs::i, CL::kernels_, CL::make_kernel(), CL::makeROmem(), CL::makeRWmem(), CL::makeWOmem(), max(), min(), N, outs, kmeans_adaptive_kernel_density_bb_dependent_rotlib::p, random_torsions(), refold_gpu(), refold_ros(), loops_kic::rms, beta_sc_scan::seq, str(), and basic::options::TR.

Referenced by main().

Variable Documentation

TR

basic::Tracer TR("gpu_linker") ( "gpu_linker"  )

static