heterodock.cc File Reference

#include <basic/options/keys/in.OptionKeys.gen.hh>
#include <basic/options/keys/out.OptionKeys.gen.hh>
#include <basic/options/option_macros.hh>
#include <basic/Tracer.hh>
#include <basic/database/open.hh>
#include <core/chemical/AtomType.hh>
#include <core/conformation/symmetry/util.hh>
#include <core/import_pose/import_pose.hh>
#include <devel/init.hh>
#include <core/io/silent/SilentFileData.hh>
#include <core/pose/Pose.hh>
#include <core/pose/util.hh>
#include <core/scoring/dssp/Dssp.hh>
#include <core/scoring/ScoreFunction.hh>
#include <core/scoring/ScoreFunctionFactory.hh>
#include <core/scoring/symmetry/SymmetricScoreFunction.hh>
#include <core/scoring/packing/compute_holes_score.hh>
#include <core/scoring/rms_util.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 <utility/io/izstream.hh>
#include <utility/io/ozstream.hh>
#include <numeric/xyzVector.hh>
#include <protocols/sic_dock/SICFast.hh>
#include <protocols/sic_dock/RigidScore.hh>
#include <protocols/sic_dock/util.hh>
#include <apps/pilot/will/pick_normal_sampling.hh>
#include <apps/pilot/will/will_util.ihh>
#include <numeric/xyzTransform.hh>

Classes
struct	Hit

Typedefs
typedef numeric::xyzVector< core::Real >	Vec
typedef numeric::xyzMatrix< core::Real >	Mat
typedef numeric::xyzTransform< core::Real >	Xform

Functions
void	register_options ()
int	num_threads ()
int	thread_num ()
void	make_olig (core::pose::Pose const &pose1, core::pose::Pose const &pose2, Xform const &x1, Xform const &x2, core::pose::Pose &olig)
bool	cmpscore (Hit i, Hit j)
bool	cmprmsd (Hit i, Hit j)
Real	myxdis (Xform const &x1, Xform const &x2)
void	dock (Pose const &init_pose1, Pose const &init_pose2, std::string const &tag0, vector1< Vec > const &normals, Xform const &xnative)
void	read_sphere (vector1< Vec > &normals)
void	get_tasks_from_command_line (utility::vector1< std::pair< string, string > > &tasks)
Pose	get_centered_pose (string fname, Vec &cen)
int	main (int argc, char *argv[])

Variables
static basic::Tracer	TR ("heterodock")
static core::io::silent::SilentFileData	sfd

Typedef Documentation

Mat

typedef numeric::xyzMatrix<core::Real> Mat

Vec

typedef numeric::xyzVector<core::Real> Vec

Xform

typedef numeric::xyzTransform<core::Real> Xform

Function Documentation

cmprmsd()

bool cmprmsd	(	Hit	i,
		Hit	j
	)

References create_a3b_hbs::i, and create_a3b_hbs::j.

Referenced by dock().

cmpscore()

bool cmpscore	(	Hit	i,
		Hit	j
	)

References create_a3b_hbs::i, and create_a3b_hbs::j.

dock()

void dock	(	Pose const &	init_pose1,
		Pose const &	init_pose2,
		std::string const &	tag0,
		vector1< Vec > const &	normals,
		Xform const &	xnative
	)

References kmeans_adaptive_kernel_density_bb_dependent_rotlib::ang, basic::options::OptionKeys::crossmatch::clash_dis, cmprmsd(), basic::options::OptionKeys::sicdock::contact_dis, utility::io::oc::cout, numeric::conversions::degrees(), kmeans_adaptive_kernel_density_bb_dependent_rotlib::dis, h, create_a3b_hbs::i, enumerate_junctions::int, create_a3b_hbs::j, numeric::xyzVector< T >::length(), make_olig(), min(), myxdis(), local::nstruct, basic::options::OptionKeys::out::nstruct, basic::options::OptionKeys::out::file::o, basic::options::option, test.G203_Module_SQLPDB::outdir, numeric::xyzTransform< T >::R, numeric::rotation_axis(), numeric::rotation_matrix_degrees(), ObjexxFCL::string_of(), numeric::xyzTransform< T >::t, tag, basic::options::TR, numeric::random::uniform(), and basic::options::OptionKeys::inout::dbms::user.

Referenced by main().

get_centered_pose()

Pose get_centered_pose	(	string	fname,
		Vec &	cen
	)

References basic::options::OptionKeys::in::file::dssp, PREcst::fname, pyrosetta.distributed.io::pose_from_file, and trans_pose().

Referenced by main().

get_tasks_from_command_line()

void get_tasks_from_command_line

(

utility::vector1< std::pair< string, string > > &

tasks

)

References utility::io::oc::cerr, basic::options::option, make_templates::tasks, basic::options::OptionKeys::inout::dbms::user, and utility_exit_with_message.

Referenced by main().

main()

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

References argv, dock(), utility::file_basename(), get_centered_pose(), get_tasks_from_command_line(), create_a3b_hbs::i, basic::init(), basic::options::OptionKeys::mh::harvest::max_res, basic::options::option, read_sphere(), register_options(), numeric::xyzTransform< T >::t, tag, make_templates::tasks, and basic::options::TR.

make_olig()

void make_olig	(	core::pose::Pose const &	pose1,
		core::pose::Pose const &	pose2,
		Xform const &	x1,
		Xform const &	x2,
		core::pose::Pose &	olig
	)

References create_a3b_hbs::i, test.T008_Serialization::pose1, test.T008_Serialization::pose2, and xform_pose().

Referenced by dock().

myxdis()

Real myxdis	(	Xform const &	x1,
		Xform const &	x2
	)

References numeric::xyzMatrix< T >::col_x(), numeric::xyzMatrix< T >::col_y(), numeric::xyzMatrix< T >::col_z(), numeric::xyzVector< T >::distance_squared(), numeric::xyzTransform< T >::R, and numeric::xyzTransform< T >::t.

Referenced by dock().

num_threads()

int num_threads

(

)

read_sphere()

void read_sphere

(

vector1< Vec > &

normals

)

References kmeans_adaptive_kernel_density_bb_dependent_rotlib::ang, utility::io::izstream::close(), create_a3b_hbs::i, basic::database::open(), basic::options::option, pick_normal_sampling(), str(), basic::options::TR, utility_exit_with_message, x, predPRE::y, and predPRE::z.

Referenced by main().

register_options()

void register_options

(

)

References basic::options::OptionKeys::crossmatch::clash_dis, basic::options::OptionKeys::sicdock::contact_dis, basic::options::OptionKeys::mh::harvest::max_res, and NEW_OPT.

Referenced by main().

thread_num()

int thread_num

(

)

Variable Documentation

sfd

core::io::silent::SilentFileData sfd

static

TR

basic::Tracer TR("heterodock") ( "heterodock"  )

static