zf_relax.cc File Reference

#include <devel/dna/ProteinDNA_Relax.hh>
#include <devel/dna/relax_util.hh>
#include <devel/dna/base_movers.hh>
#include <devel/cartesian_frags/DNA_FragLib.hh>
#include <protocols/loops/ccd_closure.hh>
#include <utility/excn/Exceptions.hh>
#include <protocols/viewer/viewers.hh>
#include <protocols/minimization_packing/PackRotamersMover.hh>
#include <protocols/minimization_packing/RotamerTrialsMover.hh>
#include <protocols/moves/TrialMover.hh>
#include <protocols/minimization_packing/MinMover.hh>
#include <protocols/moves/MonteCarlo.hh>
#include <core/scoring/methods/EnergyMethodOptions.hh>
#include <core/scoring/dna/setup.hh>
#include <core/scoring/func/Func.hh>
#include <core/scoring/rms_util.hh>
#include <core/scoring/ScoreFunction.hh>
#include <core/chemical/VariantType.hh>
#include <core/conformation/Residue.hh>
#include <core/pack/task/PackerTask.hh>
#include <core/pack/task/TaskFactory.hh>
#include <core/kinematics/MoveMap.hh>
#include <core/id/AtomID_Map.hh>
#include <core/pose/Pose.hh>
#include <basic/options/util.hh>
#include <basic/prof.hh>
#include <devel/init.hh>
#include <core/io/pdb/pdb_writer.hh>
#include <numeric/random/random.hh>
#include <ObjexxFCL/string.functions.hh>
#include <basic/Tracer.hh>
#include <basic/options/keys/out.OptionKeys.gen.hh>
#include <basic/options/keys/dna.OptionKeys.gen.hh>
#include <core/import_pose/import_pose.hh>
#include <core/kinematics/FoldTree.hh>
#include <core/pose/util.hh>
#include <core/scoring/constraints/Constraint.hh>
#include <ObjexxFCL/format.hh>

Classes
class	ZF_PatchupMover

Namespaces
	zf_relax_ns

Functions
Size const	zf_relax_ns::protein_root_mpos (3)
Size const	zf_relax_ns::dna_anchor_mpos (2)
Size const	zf_relax_ns::cutpoint_mpos (13)
Size const	zf_relax_ns::loop_begin_mpos (12)
Size const	zf_relax_ns::loop_end_mpos (17)
int	protein_motif_offset (Size const finger, pose::Pose const &pose)
Real	zf_chainbreak_distance (Size const finger, pose::Pose const &pose)
bool	ccd_close_zf_chainbreak (Size const finger, pose::Pose &pose)
void	setup_zf_pose (Size const nfinger, Size const dna_motif_offset, vector1< Size > const &prot_motif_offset, pose::Pose &pose)
void	zf_relax_test ()
void *	my_main (void *)
int	main (int argc, char *argv[])

Variables
static basic::Tracer	tt ("demo.phil.zf_relax", basic::t_trace)
static basic::Tracer	td ("demo.phil.zf_relax", basic::t_debug)
static basic::Tracer	ti ("demo.phil.zf_relax", basic::t_info)
static basic::Tracer	tw ("demo.phil.zf_relax", basic::t_warning)

Function Documentation

ccd_close_zf_chainbreak()

bool ccd_close_zf_chainbreak	(	Size const	finger,
		pose::Pose &	pose
	)

References loops::cutpoint, zf_relax_ns::cutpoint_mpos(), create_a3b_hbs::i, demo.D080_Loop_modeling::loop_begin, zf_relax_ns::loop_begin_mpos(), pivot_selection::loop_end, zf_relax_ns::loop_end_mpos(), basic::options::OptionKeys::loops::ccd::max_rama_score_increase, beta_nonlocal::mm, beta_nonlocal::pose, protein_motif_offset(), basic::options::OptionKeys::loops::ccd::tolerance, and tt.

Referenced by ZF_PatchupMover::apply().

main()

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

References argv, test.T009_Exceptions::e, basic::init(), my_main(), and viewer_main().

my_main()

void* my_main

(

void *

)

References utility::options::OptionKeys::options::exit, and zf_relax_test().

Referenced by main().

protein_motif_offset()

int protein_motif_offset	(	Size const	finger,
		pose::Pose const &	pose
	)

References beta_nonlocal::pose, and zf_relax_ns::protein_root_mpos().

Referenced by ccd_close_zf_chainbreak(), setup_zf_pose(), zf_chainbreak_distance(), and zf_relax_test().

setup_zf_pose()

void setup_zf_pose	(	Size const	nfinger,
		Size const	dna_motif_offset,
		vector1< Size > const &	prot_motif_offset,
		pose::Pose &	pose
	)

References loops::cutpoint, zf_relax_ns::cutpoint_mpos(), basic::options::OptionKeys::dna::dna, zf_relax_ns::dna_anchor_mpos(), create_a3b_hbs::f, create_a3b_hbs::i, create_a3b_hbs::nres, beta_nonlocal::pose, protein_motif_offset(), zf_relax_ns::protein_root_mpos(), and tt.

Referenced by zf_relax_test().

zf_chainbreak_distance()

Real zf_chainbreak_distance	(	Size const	finger,
		pose::Pose const &	pose
	)

References ObjexxFCL::abs(), loops::cutpoint, zf_relax_ns::cutpoint_mpos(), beta_nonlocal::pose, and protein_motif_offset().

Referenced by ZF_PatchupMover::apply().

zf_relax_test()

void zf_relax_test

(

)

Test zinc finger relaxation protocol.

for starters, hard code 1aay, later extend to other guys, read Zinc atoms, calculate motif positions...

setup a foldtree for DNA fragment insertions with jumps from triplet position 2 to each finger, and chainbreaks between the three fingers, after the glycine residue.

moves:

1. rigid-body perturbation of one of the fingers, followed by closure of the loop
2. internal dna flex-move followed by closure of one of the fingers, if necessary

experiment with ccd closure ? to close the finger chainbreaks, or fragment-based closure? or torsion/angle minimization as above?

References utility::io::oc::cout, basic::options::OptionKeys::dna::dna, basic::options::OptionKeys::relax::energycut, ObjexxFCL::format::F(), basic::options::OptionKeys::dna::specificity::frag_files, create_a3b_hbs::i, create_a3b_hbs::ii, test_terpenes::inner, ObjexxFCL::lead_zero_string_of(), zf_relax_ns::loop_begin_mpos(), zf_relax_ns::loop_end_mpos(), mc, pna::min_mm, vancomycin::min_mover, basic::options::OptionKeys::MonteCarlo::MonteCarlo, kmeans_adaptive_kernel_density_bb_dependent_rotlib::n, basic::options::OptionKeys::dna::specificity::n_inner, basic::options::OptionKeys::dna::specificity::n_outer, create_a3b_hbs::nres, local::nstruct, out::nstruct(), option, options, drrafter_rna::output_tag, out::output_tag(), test.Workshop6test::pack_mover, basic::options::OptionKeys::dna::specificity::params, beta_nonlocal::pose, pyrosetta.distributed.io::pose_from_file, basic::prof_reset(), basic::prof_show(), protein_motif_offset(), basic::options::OptionKeys::dna::specificity::score_function, oop_conformations::scorefxn, basic::options::OptionKeys::frags::scoring::scoring, setup_zf_pose(), basic::options::start_file(), ti, and basic::options::OptionKeys::inout::dbms::user.

Referenced by my_main().

Variable Documentation

td

basic::Tracer td("demo.phil.zf_relax", basic::t_debug) ( "demo.phil.zf_relax"  , basic::t_debug    )

static

Referenced by ZF_PatchupMover::apply().

ti

basic::Tracer ti("demo.phil.zf_relax", basic::t_info) ( "demo.phil.zf_relax"  , basic::t_info    )

static

Referenced by zf_relax_test().

tt

basic::Tracer tt("demo.phil.zf_relax", basic::t_trace) ( "demo.phil.zf_relax"  , basic::t_trace    )

static

Referenced by ccd_close_zf_chainbreak(), and setup_zf_pose().

tw

basic::Tracer tw("demo.phil.zf_relax", basic::t_warning) ( "demo.phil.zf_relax"  , basic::t_warning    )

static

Referenced by ZF_PatchupMover::apply().