loodo.cc File Reference

#include <devel/init.hh>
#include <basic/Tracer.hh>
#include <basic/options/option.hh>
#include <basic/options/keys/loodo.OptionKeys.gen.hh>
#include <basic/citation_manager/CitationManager.hh>
#include <basic/citation_manager/CitationCollection.hh>
#include <core/conformation/Residue.hh>
#include <core/fragment/ConstantLengthFragSet.hh>
#include <core/fragment/FrameIterator.hh>
#include <core/fragment/Frame.hh>
#include <core/id/AtomID.hh>
#include <core/import_pose/import_pose.hh>
#include <core/kinematics/Stub.hh>
#include <core/kinematics/RT.hh>
#include <core/chemical/ChemicalManager.hh>
#include <core/pose/Pose.hh>
#include <core/scoring/rms_util.hh>
#include <core/scoring/dssp/Dssp.hh>
#include <protocols/forge/components/VarLengthBuild.hh>
#include <protocols/forge/build/Interval.hh>
#include <protocols/match/BumpGrid.hh>
#include <protocols/match/downstream/ActiveSiteGrid.hh>
#include <protocols/sic_dock/util.hh>
#include <numeric/geometry/hashing/SixDHasher.fwd.hh>
#include <numeric/HomogeneousTransform.hh>
#include <numeric/xyzVector.hh>
#include <utility/vector1.hh>
#include <utility/io/izstream.hh>
#include <map>
#include <iostream>
#include <string>
#include <fstream>

Classes
class	VarLengthBuildKristin

Functions
core::fragment::ConstantLengthFragSetOP	get_vallfrags (int round, core::Size fraglength, std::string cap_pose_ss, std::string cap_pose_aa, std::string bot_pose_ss, std::string bot_pose_aa, int ins_begin, int ins_end)
core::fragment::ConstantLengthFragSetOP	molten_get_vallfrags (core::Size fraglength, std::string frag_ss, std::string frag_aa, int known)
core::pose::Pose	perturb (std::string round, std::string pair, core::pose::Pose &stationary_pose, core::pose::Pose &moving_pose, int ins_begin, int ins_end)
protocols::match::BumpGrid	make_bb_grid (core::pose::Pose &bot_pose)
protocols::match::downstream::ActiveSiteGrid	make_active_site_grid ()
core::Size	find_centerest_residue (core::pose::Pose &cap_pose)
bool	containment_and_clash_checks (protocols::match::BumpGrid &bb_grid, protocols::match::downstream::ActiveSiteGrid &active_site_grid, core::pose::Pose &cap_pose, core::Size &COM, core::Size &clash_fail, core::Size &cont_fail)
numeric::geometry::hashing::Real6	real6_from_rt (core::kinematics::RT &rt)
numeric::geometry::hashing::Real6	six_coords_to_real6 (numeric::xyzVector< core::Real > bot_ca_1, numeric::xyzVector< core::Real > bot_ca_2, numeric::xyzVector< core::Real > bot_ca_3, numeric::xyzVector< core::Real > cap_ca_1, numeric::xyzVector< core::Real > cap_ca_2, numeric::xyzVector< core::Real > cap_ca_3)
bool	real6_similarity (numeric::geometry::hashing::Real6 &first_real6, numeric::geometry::hashing::Real6 &second_real6, core::Real dist_tolerance, core::Real euler_tolerance)
int	main (int argc, char *argv[])
	Main method. More...

Variables
static basic::Tracer	TR ("apps.public.loop_modeling.loodo")

Function Documentation

containment_and_clash_checks()

bool containment_and_clash_checks	(	protocols::match::BumpGrid &	bb_grid,
		protocols::match::downstream::ActiveSiteGrid &	active_site_grid,
		core::pose::Pose &	cap_pose,
		core::Size &	COM,
		core::Size &	clash_fail,
		core::Size &	cont_fail
	)

References basic::options::OptionKeys::loodo::ca_ratio, basic::options::OptionKeys::loodo::com_in_grid, count, create_a3b_hbs::ii, basic::options::option, and PREcst::ratio.

Referenced by main().

find_centerest_residue()

core::Size find_centerest_residue

(

core::pose::Pose &

cap_pose

)

References utility::io::oc::cerr, numeric::xyzVector< T >::distance(), utility::exit(), create_a3b_hbs::ii, beta_nonlocal::jj, and natoms().

Referenced by main().

get_vallfrags()

core::fragment::ConstantLengthFragSetOP get_vallfrags	(	int	round,
		core::Size	fraglength,
		std::string	cap_pose_ss,
		std::string	cap_pose_aa,
		std::string	bot_pose_ss,
		std::string	bot_pose_aa,
		int	ins_begin,
		int	ins_end
	)

References aa, basic::options::OptionKeys::loodo::ins_begin, basic::options::OptionKeys::ms::checkpoint::interval, create_a3b_hbs::j, create_a3b_hbs::k, basic::options::OptionKeys::loodo::num_frags, basic::options::option, VarLengthBuildKristin::public_pick_fragments(), round(), docking::s, challenge::ss, predPRE::t, TR, basic::options::OptionKeys::loodo::use_fraglib, and basic::options::OptionKeys::inout::dbms::user.

Referenced by main().

main()

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

Main method.

References basic::citation_manager::Application, argv, basic::options::OptionKeys::loodo::bot, basic::options::OptionKeys::loodo::ca_ratio, basic::options::OptionKeys::loodo::cap, utility::io::oc::cerr, basic::options::OptionKeys::cm::cm, basic::options::OptionKeys::loodo::com_in_grid, containment_and_clash_checks(), data, basic::options::OptionKeys::loodo::debug, basic::options::OptionKeys::loodo::distance_tolerance, basic::options::OptionKeys::loodo::dump_all_As, basic::options::OptionKeys::loodo::dump_all_Bs, test.T009_Exceptions::e, basic::options::OptionKeys::loodo::euler_tolerance, utility::exit(), lactamize::filename, find_centerest_residue(), demo.D080_Loop_modeling::frag_length, basic::options::OptionKeys::loodo::fragAlength, basic::options::OptionKeys::loodo::fragAnative, basic::options::OptionKeys::loodo::fragBlength, basic::options::OptionKeys::loodo::fragBnative, numeric::kinematic_closure::frame(), utility::SingletonBase< CitationManager >::get_instance(), get_vallfrags(), getline(), getxform(), h, hist2d::H, create_a3b_hbs::i, test.T110_numeric::I, basic::init(), basic::options::OptionKeys::loodo::ins_begin, create_a3b_hbs::j, basic::options::OptionKeys::loodo::known, spectral_cluster_kmeans_adaptive_kernel_density_bb_dependent_rotlib::L, line, basic::options::OptionKeys::loodo::loud, make_active_site_grid(), make_bb_grid(), molten_get_vallfrags(), basic::options::option, perturb(), pyrosetta.distributed.io::pose_from_file, real6_similarity(), round(), six_coords_to_real6(), basic::options::TR, basic::options::OptionKeys::loodo::use_fraglib, and basic::options::OptionKeys::inout::dbms::user.

make_active_site_grid()

protocols::match::downstream::ActiveSiteGrid make_active_site_grid

(

)

References basic::options::OptionKeys::loodo::gridligpath, basic::options::option, and TR.

Referenced by main().

make_bb_grid()

protocols::match::BumpGrid make_bb_grid

(

core::pose::Pose &

bot_pose

)

References create_a3b_hbs::ii.

Referenced by main().

molten_get_vallfrags()

core::fragment::ConstantLengthFragSetOP molten_get_vallfrags	(	core::Size	fraglength,
		std::string	frag_ss,
		std::string	frag_aa,
		int	known
	)

References aa, create_a3b_hbs::i, basic::options::OptionKeys::ms::checkpoint::interval, create_a3b_hbs::j, create_a3b_hbs::k, basic::options::OptionKeys::loodo::known, basic::options::OptionKeys::loodo::num_frags, basic::options::option, VarLengthBuildKristin::public_pick_fragments(), docking::s, challenge::ss, TR, basic::options::OptionKeys::loodo::use_fraglib, and basic::options::OptionKeys::inout::dbms::user.

Referenced by main().

perturb()

core::pose::Pose perturb	(	std::string	round,
		std::string	pair,
		core::pose::Pose &	stationary_pose,
		core::pose::Pose &	moving_pose,
		int	ins_begin,
		int	ins_end
	)

References basic::options::OptionKeys::loodo::ins_begin, pair, round(), and superimpose_pose().

Referenced by protocols::abinitio::JumpSpecificAbrelax::fold(), main(), and protocols::abinitio::JumpSpecificAbrelax::register_options().

real6_from_rt()

numeric::geometry::hashing::Real6 real6_from_rt

(

core::kinematics::RT &

rt

)

References numeric::HomogeneousTransform< T >::euler_angles_deg(), numeric::xyzVector< T >::x(), numeric::xyzVector< T >::y(), and numeric::xyzVector< T >::z().

Referenced by six_coords_to_real6().

real6_similarity()

bool real6_similarity	(	numeric::geometry::hashing::Real6 &	first_real6,
		numeric::geometry::hashing::Real6 &	second_real6,
		core::Real	dist_tolerance,
		core::Real	euler_tolerance
	)

References ObjexxFCL::abs(), and basic::options::OptionKeys::loodo::euler_tolerance.

Referenced by main().

six_coords_to_real6()

numeric::geometry::hashing::Real6 six_coords_to_real6	(	numeric::xyzVector< core::Real >	bot_ca_1,
		numeric::xyzVector< core::Real >	bot_ca_2,
		numeric::xyzVector< core::Real >	bot_ca_3,
		numeric::xyzVector< core::Real >	cap_ca_1,
		numeric::xyzVector< core::Real >	cap_ca_2,
		numeric::xyzVector< core::Real >	cap_ca_3
	)

References real6_from_rt().

Referenced by main().

Variable Documentation

TR

basic::Tracer TR("apps.public.loop_modeling.loodo") ( "apps.public.loop_modeling.loodo"  )

static

Referenced by get_vallfrags(), make_active_site_grid(), and molten_get_vallfrags().