sicdock.cc File Reference

#include <basic/options/keys/in.OptionKeys.gen.hh>
#include <basic/options/keys/out.OptionKeys.gen.hh>
#include <basic/options/keys/mh.OptionKeys.gen.hh>
#include <basic/options/keys/sicdock.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/pose/symmetry/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 <protocols/sic_dock/xyzStripeHashPose.hh>
#include <protocols/sic_dock/scores/MotifHashRigidScore.hh>
#include <protocols/sic_dock/scores/TrisBpyScore.hh>
#include <protocols/motif_hash/motif_hash_stuff.hh>
#include <numeric/xyzTransform.hh>
#include <basic/sampling/orientations/QuaternionGrid.hh>
#include <core/scoring/constraints/ConstraintSet.hh>
#include <core/scoring/constraints/AtomPairConstraint.hh>

Classes
struct	Hit

Functions
void	register_options ()
bool	cmpscore (Hit i, Hit j)
bool	cmprmsd (Hit i, Hit j)
Vec	get_rot_center (Xform const &xsym, int sym)
Vec	get_rot_center (Xform const &x1, Xform const &x2, int sym)
Xform	get_cx_xform (Xform const &x1, Xform const &x2, int sym)
Real	get_rmsd (utility::vector1< Vec > const &native_ca, utility::vector1< Vec > const &init_ca, Hit const &h)
void	dock (Pose const &init_pose, std::string const &fn, basic::sampling::orientations::QuaternionGridCOP qgrid, Pose const &, int native_nfold=1, Vec cen=Vec(0, 0, 0))
utility::vector1< Vec >	align_native_state (core::pose::Pose &pose, int nfold)
void	get_tasks_from_command_line (utility::vector1< std::pair< string, int > > &tasks)
int	main (int argc, char *argv[])

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

Function Documentation

align_native_state()

utility::vector1<Vec> align_native_state	(	core::pose::Pose &	pose,
		int	nfold
	)

References numeric::dihedral_degrees(), beta_nonlocal::pose, and rot_pose().

cmprmsd()

bool cmprmsd	(	Hit	i,
		Hit	j
	)

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

cmpscore()

bool cmpscore	(	Hit	i,
		Hit	j
	)

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

Referenced by dock().

dock()

void dock	(	Pose const &	init_pose,
		std::string const &	fn,
		basic::sampling::orientations::QuaternionGridCOP	qgrid,
		Pose const &	,
		int	native_nfold = 1,
		Vec	cen = Vec(0,0,0)
	)

References kmeans_adaptive_kernel_density_bb_dependent_rotlib::ang, begin, sicdock::clash_dis(), cmpscore(), basic::options::OptionKeys::constraints::constraints, sicdock::contact_dis(), utility::io::oc::cout, kmeans_adaptive_kernel_density_bb_dependent_rotlib::dang, numeric::conversions::degrees(), numeric::dihedral(), kmeans_adaptive_kernel_density_bb_dependent_rotlib::dis, end, ObjexxFCL::format::F(), utility::file_basename(), detail::find(), kmeans_adaptive_kernel_density_bb_dependent_rotlib::fn, get_cx_xform(), h, create_a3b_hbs::i, ObjexxFCL::format::I(), test.T110_numeric::I, numeric::xyzMatrix< Real >::identity(), enumerate_junctions::int, create_a3b_hbs::j, numeric::xyzVector< T >::length(), ObjexxFCL::format::LJ(), max(), min(), SmotifHasher::min_score, surface_app::native, local::nstruct, basic::options::OptionKeys::out::nstruct, basic::options::OptionKeys::out::file::o, basic::options::option, option, erraser_single_res_analysis::out, test.G203_Module_SQLPDB::outdir, docking::R, numeric::xyzTransform< T >::R, loops_kic::rms, numeric::rotation_axis(), numeric::rotation_matrix_degrees(), Hit::rscore, ObjexxFCL::string_of(), predPRE::t, numeric::xyzTransform< T >::t, tag, td, TR, basic::options::OptionKeys::inout::dbms::user, x, Hit::x1, Hit::x2, xform_pose(), numeric::y_rotation_matrix_degrees(), numeric::xyzVector< T >::z(), numeric::z_rotation_matrix(), and numeric::z_rotation_matrix_degrees().

Referenced by main().

get_cx_xform()

Xform get_cx_xform ( Xform const &  x1, Xform const &  x2, int  sym  )

inline

References get_rot_center(), and numeric::xyzTransform< T >::R.

Referenced by dock().

get_rmsd()

Real get_rmsd ( utility::vector1< Vec > const &  native_ca, utility::vector1< Vec > const &  init_ca, Hit const &  h  )

inline

References kmeans_adaptive_kernel_density_bb_dependent_rotlib::ang, numeric::dihedral_degrees(), h, create_a3b_hbs::i, create_a3b_hbs::j, oop_conformations::length, numeric::constants::d::pi, create_a3b_hbs::r, docking::R, average_rmsds::rmsd, tan, kmeans_adaptive_kernel_density_bb_dependent_rotlib::v, x, numeric::x_rotation_matrix_degrees(), and numeric::z_rotation_matrix_degrees().

get_rot_center() [1/2]

Vec get_rot_center ( Xform const &  x1, Xform const &  x2, int  sym  )

inline

References get_rot_center().

get_rot_center() [2/2]

Vec get_rot_center ( Xform const &  xsym, int  sym  )

inline

References create_a3b_hbs::i.

Referenced by get_cx_xform(), and get_rot_center().

get_tasks_from_command_line()

void get_tasks_from_command_line

(

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

tasks

)

References option, in::file::s(), subloop_histogram::size, make_templates::tasks, and basic::options::OptionKeys::inout::dbms::user.

Referenced by main().

main()

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

References argv, utility::io::oc::cout, dock(), basic::options::OptionKeys::in::file::dssp, test.T009_Exceptions::e, kmeans_adaptive_kernel_density_bb_dependent_rotlib::fn, utility::SingletonBase< QuaternionGridManager >::get_instance(), get_tasks_from_command_line(), create_a3b_hbs::i, basic::init(), kmeans_adaptive_kernel_density_bb_dependent_rotlib::m, basic::options::OptionKeys::mh::harvest::max_res, option, pyrosetta.distributed.io::pose_from_file, register_options(), make_templates::tasks, TR, trans_pose(), basic::options::OptionKeys::inout::dbms::user, utility_exit_with_message, numeric::xyzVector< T >::x(), numeric::xyzVector< T >::y(), and numeric::xyzVector< T >::z().

register_options()

void register_options

(

)

References numeric::dihedral(), basic::options::OptionKeys::mh::harvest::max_res, SmotifHasher::min_score, and NEW_OPT.

Referenced by main().

Variable Documentation

sfd

core::io::silent::SilentFileData sfd

static

TR

basic::Tracer TR("sicdock") ( "sicdock"  )

static

Referenced by dock(), and main().