draw_gen_env_dep_orient_decompose.m File Reference

Functions
end end get env	env_index (i)
	num_res_env (res_index(i), env_index(i))
	if (ai >NAA) continue end for j
	if (aj >NAA) continue end if(env_index(i)
	surf_surf_th1 (ai, aj, :, :)+
i, j, :, :	th1_table ()
	surf_core_th1 (ai, aj, :, :)+
end else	if (env_index(j)==1) %c-s core_surf_th1(ai
end else	core_surf_th1 (ai, aj, :, :)+
	core_core_th1 (ai, aj, :, :)+
id	beta ()
surf_surf_th1, NAA	pre_fill_dfire_2D ()
	surf_surf_th1 (i, j,:,:)
	surf_core_th1 (i, j,:,:)
	core_surf_th1 (i, j,:,:)
	core_core_th1 (i, j,:,:)
	if (i!=j) % surf_surf_th1(j
	surf_core_th1 (j, i,:,:)
	core_surf_th1 (j, i,:,:)
	core_core_th1 (j, i,:,:)
NAA, 30, 16	zeros ()
sum(surf_surf_th1, 2	squeeze ()
id	i: (aasurf_surf_da1(i,:,:) calc_NtoP)
	aasurf_core_da1 (i,:,:)
	aacore_surf_da1 (i,:,:)
	aacore_core_da1 (i,:,:)
	aasurf_surf_da2 (i,:,:)
	aacore_surf_da2 (i,:,:)
	aasurf_core_da2 (i,:,:)
	aacore_core_da2 (i,:,:)
end	p_a_r_ang1 (ii, kk,:)
	p_a_r_ang2 (ii, kk,:)
end	p_r_ang (kk,:)
	set (f, "visible", "off") else fp_ang
end if	exist ("iii", "var") % iii %else % iii
debug if debug	printf ("score_w(%d,%d): max=%f, min=%f\n", iii, jjj, max(max(score)), min(min(score)))
	contourf (xx, yy, score)
	print (fname, "-dpng") else fprintf(fp_ang
ANGLE1	reslist (iii,:)
ANGLE1	reslist (jjj,:))
end	fprintf (fp_ang, "\n")
end	fprintf (fp_ang, "%.6f ", score(xx, 16))
end end end if debug	printf ("Done!\n")
	set (f, "visible", "on") else fclose(fp_ang)
end debug	subplot (2, 1, 1) %[xx
	contourf (xx, yy, score_w)
	plot (1:16, p_ii_w(30,:), 1:16, squeeze(p_ii(1, 30,:)), 1:16, squeeze(aa_surf_da1(4, 30,:))/sum(squeeze(aa_surf_da1(4, 30,:))), 1:16, squeeze(aa_core_da1(4, 30,:))/sum(squeeze(aa_core_da1(4, 30,:)))) %subplot(2
plot(1:16, score(24,:),"r", 1:16, score_w(24,:),"b") %axis([1 16 -0.2 0.2]) %plot(1	contourf (xx, yy, Na1_r_surf_surf) %subplot(4
plot(1:16, score(24,:),"r", 1:16, score_w(24,:),"b") %axis([1 16 -0.2 0.2]) %plot(1	contourf (xx, yy, Na2_r_surf_surf) %subplot(4
plot(1:16, score(24,:),"r", 1:16, score_w(24,:),"b") %axis([1 16 -0.2 0.2]) %plot(1	contourf (xx, yy, Na1_r_core_surf) %subplot(4
plot(1:16, score(24,:),"r", 1:16, score_w(24,:),"b") %axis([1 16 -0.2 0.2]) %plot(1	contourf (xx, yy, Na2_r_surf_core) %subplot(4
plot(1:16, score(24,:),"r", 1:16, score_w(24,:),"b") %axis([1 16 -0.2 0.2]) %plot(1	contourf (xx, yy, Na1_r_surf_core) %subplot(4
plot(1:16, score(24,:),"r", 1:16, score_w(24,:),"b") %axis([1 16 -0.2 0.2]) %plot(1	contourf (xx, yy, Na2_r_core_surf) %subplot(4
plot(1:16, score(24,:),"r", 1:16, score_w(24,:),"b") %axis([1 16 -0.2 0.2]) %plot(1	contourf (xx, yy, Na1_r_core_core) %subplot(4

Variables
	debug = 1
	reslist
	CYS
	ASP
	GLU
	PHE
	TRP
	HIS
	ILE
	LYS
	LEU
	MET
	ASN
	VAL
	GLN
	ARG
	SER
	THR
	PRO
	ALA
	GLY
should not contain ALA GLY PRO	NAA = 17
	Rcut = 12
	Bcut = 24
buildlist	res_index = zeros(40,1)
	env_index = zeros(40,1)
	num_res_env = zeros(NAA,2)
for	i
	break
end split	surf_surf_th1 =zeros(NAA,NAA,30,16)
	surf_core_th1 =zeros(NAA,NAA,30,16)
	core_surf_th1 =zeros(NAA,NAA,30,16)
	core_core_th1 =zeros(NAA,NAA,30,16)
end else	aj
end else	j
	smoothed = smooth_2D(surf_core_th1(i,j,:,:), [15, 0.1, 2], [360, 40, 2])
	__pad0__
	__pad1__
	__pad2__
	__pad3__
end end end sum symm	aasurf_surf_da1 =zeros(NAA,30,16)
	aacore_surf_da1 =squeeze(sum(core_surf_th1,2))
	aasurf_core_da1 =squeeze(sum(surf_core_th1,2))
	aacore_core_da1 =squeeze(sum(core_core_th1,2))
	aasurf_surf_da2 =squeeze(sum(surf_surf_th1))
	aacore_surf_da2 =squeeze(sum(surf_core_th1))
	aasurf_core_da2 =squeeze(sum(core_surf_th1))
	aacore_core_da2 =squeeze(sum(core_core_th1))
	Na1_r_surf_surf = squeeze(sum(aasurf_surf_da1))
	Na1_r_surf_core = squeeze(sum(aasurf_core_da1))
	Na1_r_core_surf = squeeze(sum(aacore_surf_da1))
	Na1_r_core_core = squeeze(sum(aacore_core_da1))
	Na2_r_surf_surf = squeeze(sum(aasurf_surf_da2))
	Na2_r_surf_core = squeeze(sum(aasurf_core_da2))
	Na2_r_core_surf = squeeze(sum(aacore_surf_da2))
	Na2_r_core_core = squeeze(sum(aacore_core_da2))
	aa_aa_th1 = (surf_surf_th1 + surf_core_th1 + core_surf_th1 + core_core_th1)
NAAaa to NAAaa cal	ntype = NAA
	dat_a_a_r_ang = aa_aa_th1
old way	sum_a_a_r = sum(dat_a_a_r_ang,4)
sum over ang	dat_a_r_ang1 = squeeze(sum(dat_a_a_r_ang, 2))
sum over the second aa	sum_a1_r = sum(dat_a_r_ang1, 3)
sum over ang	dat_a_r_ang2 = squeeze(sum(dat_a_a_r_ang))
sum over the first aa	sum_a2_r = sum(dat_a_r_ang2, 3)
sum over ang	dat_r_ang = squeeze(sum(dat_a_r_ang1))
sum over all aa	sum_r = sum(dat_r_ang,2)
sum over ang	p_a_a_r_ang = zeros(ntype, ntype, 30, 16)
	p_a_r_ang1 = zeros(ntype, 30, 16)
	p_a_r_ang2 = zeros(ntype, 30, 16)
	p_r_ang = zeros(30, 16)
for	kk
end shift	shift = zeros(30,16)
end debug if debug	f = figure()
	wj = num_res_env(jjj,1)/sum(num_res_env(jjj,:))
	p_ii_jj = squeeze(p_a_a_r_ang( iii, jjj, :, : ))
	p_ii = p_a_r_ang1(iii, :, :)
	p_ii_w = calc_Pi_ang_sc(aasurf_surf_da1(iii,:,:), aasurf_core_da1(iii,:,:), aacore_surf_da1(iii,:,:), aacore_core_da1(iii,:,:), wi, wj)
	p_jj = p_a_r_ang2(jjj, :, :)
	p_jj_w = calc_Pi_ang_sc(aasurf_surf_da2(jjj,:,:), aasurf_core_da2(jjj,:,:), aacore_surf_da2(jjj,:,:), aacore_core_da2(jjj,:,:), wj, wi)
	p_ii_p_jj = squeeze(p_ii .* p_jj)
	p_ii_p_jj_w = squeeze(p_ii_w .* p_jj_w)
	p = (p_ii_jj .* p_r_ang) ./ (p_ii_p_jj)
	p_r_ang_w = calc_Pi_ang_sc(Na1_r_surf_surf, Na1_r_surf_core, Na1_r_core_surf, Na1_r_core_core, wi, wj)
	p_w = (p_ii_jj .* p_r_ang_w + shift) ./ (p_ii_p_jj_w + shift)
	p_w0 = (p_ii_jj .* p_r_ang + shift) ./ (p_ii_p_jj_w + shift)
	score0 = -log(p)
	score_w = -log(p_w)
	score_w0 = -log(p_w0)
	score = score_w(1:Bcut,:)
	fname = [ "score_", int2str(iii), "_", int2str(jjj), ".png" ]
ANGLE1	__pad4__
for	yy
for	xx

Function Documentation

aacore_core_da1()

aacore_core_da1	(	i	,
		:	,
		:
	)

aacore_core_da2()

aacore_core_da2	(	i	,
		:	,
		:
	)

aacore_surf_da1()

aacore_surf_da1	(	i	,
		:	,
		:
	)

aacore_surf_da2()

aacore_surf_da2	(	i	,
		:	,
		:
	)

aasurf_core_da1()

aasurf_core_da1	(	i	,
		:	,
		:
	)

aasurf_core_da2()

aasurf_core_da2	(	i	,
		:	,
		:
	)

aasurf_surf_da2()

aasurf_surf_da2	(	i	,
		:	,
		:
	)

beta()

id beta ( )

virtual

contourf() [1/9]

plot (1:16,score(24,:),"r",1:16,score_w(24,:),"b") %axis([1 16 -0.2 0.2]) %plot(1 contourf	(	xx	,
		yy	,
		Na1_r_core_core
	)

contourf() [2/9]

plot (1:16,score(24,:),"r",1:16,score_w(24,:),"b") %axis([1 16 -0.2 0.2]) %plot(1 contourf	(	xx	,
		yy	,
		Na1_r_core_surf
	)

contourf() [3/9]

plot (1:16,score(24,:),"r",1:16,score_w(24,:),"b") %axis([1 16 -0.2 0.2]) %plot(1 contourf	(	xx	,
		yy	,
		Na1_r_surf_core
	)

contourf() [4/9]

plot (1:16,score(24,:),"r",1:16,score_w(24,:),"b") %axis([1 16 -0.2 0.2]) %plot(1 contourf	(	xx	,
		yy	,
		Na1_r_surf_surf
	)

contourf() [5/9]

plot (1:16,score(24,:),"r",1:16,score_w(24,:),"b") %axis([1 16 -0.2 0.2]) %plot(1 contourf	(	xx	,
		yy	,
		Na2_r_core_surf
	)

contourf() [6/9]

plot (1:16,score(24,:),"r",1:16,score_w(24,:),"b") %axis([1 16 -0.2 0.2]) %plot(1 contourf	(	xx	,
		yy	,
		Na2_r_surf_core
	)

contourf() [7/9]

plot (1:16,score(24,:),"r",1:16,score_w(24,:),"b") %axis([1 16 -0.2 0.2]) %plot(1 contourf	(	xx	,
		yy	,
		Na2_r_surf_surf
	)

contourf() [8/9]

contourf	(	xx	,
		yy	,
		score
	)

contourf() [9/9]

contourf	(	xx	,
		yy	,
		score_w
	)

core_core_th1() [1/3]

core_core_th1	(	ai	,
		aj	,
		:	,
		:
	)

core_core_th1() [2/3]

core_core_th1	(	i	,
		j	,
		:	,
		:
	)

core_core_th1() [3/3]

core_core_th1	(	j	,
		i	,
		:	,
		:
	)

core_surf_th1() [1/3]

end else core_surf_th1	(	ai	,
		aj	,
		:	,
		:
	)

core_surf_th1() [2/3]

core_surf_th1	(	i	,
		j	,
		:	,
		:
	)

core_surf_th1() [3/3]

core_surf_th1	(	j	,
		i	,
		:	,
		:
	)

env_index()

end end get env env_index

(

i

)

exist()

end if exist	(	"iii"	,
		"var"
	)

fprintf() [1/2]

end fprintf	(	fp_ang	,
		"%.6f "	,
		score(xx, 16)
	)

fprintf() [2/2]

end fprintf	(	fp_ang	,
		"\n"
	)

Referenced by detail::assert_fail(), assure(), main(), output_PCA(), Solver::Solve(), svm_get_svr_probability(), svm_load_model(), svm_save_model(), and svm_train().

i:()

id i: ( aasurf_surf_da1(i,:,:)  calc_NtoP )

virtual

if() [1/4]

if	(	ai	,
		NAA
	)

if() [2/4]

if	(	aj	,
		NAA
	)

if() [3/4]

end else if

(

env_index(j)

= =1

)

if() [4/4]

if

(

i!

= j

)

num_res_env()

num_res_env	(	res_index(i)	,
		env_index(i)
	)

p_a_r_ang1()

end p_a_r_ang1	(	ii	,
		kk	,
		:
	)

p_a_r_ang2()

p_a_r_ang2	(	ii	,
		kk	,
		:
	)

p_r_ang()

end p_r_ang	(	kk	,
		:
	)

plot()

plot	(	1:16	,
		p_ii_w(30,:)	,
		1:16	,
		squeeze(p_ii(1, 30,:))	,
		1:16	,
		squeeze(aa_surf_da1(4, 30,:))/sum(squeeze(aa_surf_da1(4, 30,:)))	,
		1:16	,
		squeeze(aa_core_da1(4, 30,:))/sum(squeeze(aa_core_da1(4, 30,:)))
	)

pre_fill_dfire_2D()

core_core_th1 NAA pre_fill_dfire_2D ( )

staticvirtual

print()

print	(	fname	,
		"-dpng"
	)

Referenced by test.T850_SubClassing.A::__init__(), test.T850_SubClassing.My_New_Mover::__init__(), test.T850_SubClassing.MyNewCI1B::__init__(), options_class.Option::__init__(), PyMOL-Rosetta-relay-client.Matrix::__init__(), PyMOL-RosettaServer.Matrix::__init__(), test.T850_SubClassing.PyValue::__init__(), pyrosetta.toolbox.atom_pair_energy::_atom_pair_energy_table(), pyrosetta.distributed.cluster.tools::_print_conda_warnings(), test.T850_SubClassing.My_New_Mover::apply(), test.Workshop9_my_shapes.PhiNByXDegreesMover::apply(), auto-DRRAFTER_setup::auto_setup_helices(), build_jacobian(), options.KeepSameFile::close(), get_junctions_from_legos::collect_junctions(), make_bindings_via_cmake::compile_sources(), PyMOL-Rosetta-relay-client::connect_to_rosetta_tcp_server(), build::create_package(), build::create_wheel(), pyrosetta.bindings.pose::display_secstruct(), test.T900_distributed::e(), DRRAFTER::estimate_error(), test.T870_SubClassing_EnergyMethods2.CI2B_Method::eval_intrares_energy(), test.T870_SubClassing_EnergyMethods2.CD2B_Method::eval_intrares_energy(), self-test::execute(), update_ui_project::execute(), build::execute(), DRRAFTER_util::extract_lowscore_decoys(), auto-DRRAFTER_setup_next_round::figure_out_next_round(), finalize_models::finalize(), find_jacobian(), demo.D030_Fold_tree::fold_tree(), update_ui_project::generate_app_project_files(), update_ui_project::generate_app_shell_scripts(), build::generate_bindings(), build::generate_documentation(), enumerate_junctions::generate_structures_wrapper(), DRRAFTER::get_coord_csts(), build::get_defines(), mutant_modeler.MutantModeler::get_high_res_command_lines(), auto-DRRAFTER_setup_next_round::get_results(), auto-DRRAFTER_setup_next_round::get_results_and_setup_next_round(), auto-DRRAFTER_setup_next_round::get_silent_file_subset(), util::get_surrounding_res(), demo.D060_Folding::guess_disulfides(), pyrosetta::init(), build::install_llvm_tool(), build::install_pybind11(), PyMOL-Rosetta-relay-client.PR_UDPServer::listen(), PyMOL-RosettaServer.PR_UDPServer::listen(), pyrosetta.network.rosetta_udp_to_tcp_bridge.PR_UDPServer::listen(), pyrosetta.PyMOLRosettaServer.PR_UDPServer::listen(), enumerate_junctions::listener(), pyrosetta.toolbox.load_ligand::load_from_pubchem(), setup_for_complex_scoring_general::main(), dbscan_adaptive_kernel_density_bb_dependent_rotlib::main(), dbscan_cluster_rotamer::main(), self-test::main(), get_lowest_scoring_relaxed_models::main(), options::main(), build::main(), sphinx-doc-generator::main(), update_ui_project::main(), PyMOL-Rosetta-relay-client::main(), PyMOL-RosettaServer::main(), pyrosetta.PyMOLRosettaServer::main(), make_bindings_via_cmake::make_bindings_code(), submit_jobs::make_job_files_and_submit(), self-test::mfork(), demo.D040_Movemap::movemap(), test.T007_TracerIO.MyPyTracer::output_callback(), add_xyz_to_pose::output_lego_names(), demo.D050_Packer_task::packer_task(), DRRAFTER::parse_fasta(), DRRAFTER_util::pdbslice(), demo.D020_Pose_scoring::pose_scoring(), demo.D010_Pose_structure::pose_structure(), pyrosetta.toolbox.atom_pair_energy::print_atom_pair_energy_table(), pyrosetta.toolbox.atom_pair_energy::print_residue_pair_energies(), PyMOL-Rosetta-relay-client.PR_PyMOLServer::process_packet(), PyMOL-RosettaServer.PR_PyMOLServer::process_packet(), pyrosetta.PyMOLRosettaServer.PR_PyMOLServer::process_packet(), test.T850_SubClassing.PyOverloadTest::pure_test_ref(), DRRAFTER_util::renumber_pdb(), erraser_util::res_wise_rmsd(), pyrosetta.toolbox.numpy_utils::rigid_transform_3D(), DRRAFTER_util::rna_helix(), self-test::run_test(), demo.D070_Refinement::sample_refinement(), demo.D090_Ala_scan::scanning(), pyrosetta.toolbox.load_ligand::sdf2mdl(), add_xyz_to_pose::select_area(), PyMOL-Rosetta-relay-client::set_spectrum(), PyMOL-RosettaServer::set_spectrum(), pyrosetta.PyMOLRosettaServer::set_spectrum(), DRRAFTER::setup_job(), drrafter_rna::setup_next_round(), PyMOL-Rosetta-relay-client::start_rosetta_server(), PyMOL-RosettaServer::start_rosetta_server(), pyrosetta.PyMOLRosettaServer::start_rosetta_server(), PyMOL-Rosetta-relay-client.SecretInputDialog::start_server(), pyrosetta.network.rosetta_udp_to_tcp_bridge::start_udp_server(), pyrosetta.network.rosetta_udp_to_tcp_bridge::start_udp_to_tcp_bridge_daemon(), submit_jobs::submit_jobs(), PyMOL-Rosetta-relay-client::tcp_client_main(), pyrosetta.network.rosetta_udp_to_tcp_bridge::tcp_main(), pyrosetta.tests.distributed.cluster.test_logging.LoggingTest::test_logging(), pyrosetta.network.rosetta_udp_to_tcp_bridge::udp_main(), build::update_source_file(), and update_ui_project::update_source_file().

printf() [1/2]

end end end if debug printf

(

"Done!\n"

)

printf() [2/2]

debug if debug printf

(

"score_w(%d,%d):

max = %f

)

Referenced by myspace::Scheduler::accept_and_report(), Dog< I >::Breathe(), calc_dist(), myspace::check_clash(), decompose(), designloop(), do_initial_checks(), do_postload_checks(), Dog< I >::Eat(), myspace::evaluate_and_write(), good_geometry(), HBondedPairIterator::HBondedPairIterator(), jitterloop(), kinclose(), numeric::nls::lm_lmdif(), numeric::nls::lm_lmpar(), numeric::nls::lm_printout_std(), numeric::nls::lm_qrfac(), numeric::nls::lm_qrsolv(), main(), mutate_to_sequence(), noclash(), output_PCA(), parse_extra_atom_list(), read_covalent_connections_file(), relaxloop(), myspace::Scheduler::run_LHeval(), myspace::Scheduler::run_md(), myspace::Scheduler::run_NM_evalmodes(), scan_Evalue(), myspace::scan_Evalue(), scoreall(), set_up_pose(), shift_center_and_PCA(), superimposebb(), and wait_for_gdb().

reslist() [1/2]

ANGLE1 reslist	(	iii	,
		:
	)

reslist() [2/2]

ANGLE1 reslist	(	jjj	,
		:
	)

set() [1/2]

set	(	f	,
		"visible"	,
		"off"
	)

Referenced by pyrosetta.bindings.pose.ResidueLabelAccessor::__str__(), pyrosetta.distributed.cluster.initialization::_get_residue_type_set_name3(), pyrosetta.distributed.cluster.converters::_parse_target_results(), pyrosetta.bindings.pose.ResidueLabelAccessor::_repr_pretty_(), pyrosetta.distributed.cluster.validators::_validate_clients_indices(), detail::buffer< Container::value_type >::append(), pyrosetta.utility.array::assign_by_field_names(), auto-DRRAFTER_setup::auto_setup_helices(), bind_std_functional_hash(), bind_T42_stl_names_set(), bind_T43_stl_pybind11_include_stl(), bind_T60_pybind11(), cartesian_product(), apps::pilot::frankdt::check_motifs(), pyrosetta.toolbox.cleaning::cleanCRYS(), compare_times::compare_times(), count_numerically(), pyrosetta.bindings.pose.ResidueLabelAccessor::discard(), pyrosetta.utility.array::extend_structured_array(), mutant_modeler::figure_out_WT_seq(), erraser_util::find_error_res(), mutant_modeler.MutantModeler::get_high_res_command_lines(), mutant_modeler.MutantModeler::get_med_res_command_lines(), DRRAFTER_util::graph_from_ss(), enumerate_junctions::listener(), dbscan_adaptive_kernel_density_bb_dependent_rotlib::main(), dbscan_cluster_rotamer::main(), arls_impl::main(), prune_atdiff_top5pct::main(), main(), make_bindings_via_cmake::make_all_includes(), helpers::pick_torsions(), percent_subangstrom::plot_benchmark(), dbscan_adaptive_kernel_density_bb_dependent_rotlib::plot_cluster(), bin_torsions::plot_histograms(), read_occupancy_data(), job_manager.JobWindow::refresh(), DRRAFTER::setup_job(), drrafter_rna::setup_next_round(), pyrosetta.utility.array::structured_array_to_basic(), pyrosetta.tests.bindings.core.test_pose.TestPoseResidueLabelAccessor::test_labels(), pyrosetta.tests.protocols.indexed_structure_store.test_search.TestStructureSearch::test_pair_search(), pyrosetta.tests.distributed.cluster.test_smoke.SerializationTest::test_serialization(), pyrosetta.tests.protocols.indexed_structure_store.test_search.TestStructureSearch::test_single_search(), pyrosetta.distributed.cluster.serialization::update_scores(), ez_setup::use_setuptools(), arls_impl::write_common_flags(), arls_impl::write_rpkmin_script(), and arls_impl::write_setup_script().

set() [2/2]

set	(	f	,
		"visible"	,
		"on"
	)

squeeze()

sum(surf_surf_th1,2 squeeze ( )

virtual

Referenced by pyrosetta.utility.array::coordinate_array_to_atoms().

subplot()

end debug subplot	(	2	,
		1	,
		1
	)

surf_core_th1() [1/3]

surf_core_th1	(	ai	,
		aj	,
		:	,
		:
	)

surf_core_th1() [2/3]

surf_core_th1	(	i	,
		j	,
		:	,
		:
	)

surf_core_th1() [3/3]

surf_core_th1	(	j	,
		i	,
		:	,
		:
	)

surf_surf_th1() [1/2]

surf_surf_th1	(	ai	,
		aj	,
		:	,
		:
	)

surf_surf_th1() [2/2]

surf_surf_th1	(	i	,
		j	,
		:	,
		:
	)

th1_table()

i, j, :, : th1_table ( )

virtual

zeros()

NAA zeros ( )

virtual

Referenced by solve_nu_svc(), and solve_one_class().

Variable Documentation

__pad0__

__pad0__

__pad1__

__pad1__

__pad2__

__pad2__

__pad3__

__pad3__

__pad4__

ANGLE1 __pad4__

aa_aa_th1

aa_aa_th1 = (surf_surf_th1 + surf_core_th1 + core_surf_th1 + core_core_th1)

aacore_core_da1

aacore_core_da1 =squeeze(sum(core_core_th1,2))

aacore_core_da2

aacore_core_da2 =squeeze(sum(core_core_th1))

aacore_surf_da1

aacore_surf_da1 =squeeze(sum(core_surf_th1,2))

aacore_surf_da2

aacore_surf_da2 =squeeze(sum(surf_core_th1))

aasurf_core_da1

aasurf_core_da1 =squeeze(sum(surf_core_th1,2))

aasurf_core_da2

aasurf_core_da2 =squeeze(sum(core_surf_th1))

aasurf_surf_da1

end end end sum symm aasurf_surf_da1 =zeros(NAA,30,16)

aasurf_surf_da2

aasurf_surf_da2 =squeeze(sum(surf_surf_th1))

aj

end else aj

Referenced by atoms_have_bond_to_bonded_atoms(), atoms_have_mutual_bond_to_atom(), bump_check(), membrane_center_protein_core(), and refine().

ALA

ALA

Referenced by main().

ARG

ARG

ASN

ASN

ASP

ASP

Bcut

Bcut = 24

break

break

core_core_th1

i::: core_core_th1 =zeros(NAA,NAA,30,16)

core_surf_th1

core_surf_th1 =zeros(NAA,NAA,30,16)

CYS

CYS

dat_a_a_r_ang

dat_a_a_r_ang = aa_aa_th1

dat_a_r_ang1

sum over ang dat_a_r_ang1 = squeeze(sum(dat_a_a_r_ang, 2))

dat_a_r_ang2

sum over ang dat_a_r_ang2 = squeeze(sum(dat_a_a_r_ang))

dat_r_ang

sum over ang dat_r_ang = squeeze(sum(dat_a_r_ang1))

debug

debug = 1

env_index

env_index = zeros(40,1)

f

end debug if debug f = figure()

fname

fname = [ "score_", int2str(iii), "_", int2str(jjj), ".png" ]

GLN

GLN

GLU

GLU

GLY

GLY

HIS

HIS

i

for i

Initial value:

= 1:40
  %get aa
  for n = 1:20
    if (list(i,1:3)==reslist(n,:))
      res_index(i)=n

ILE

ILE

j

end else j

kk

for kk

Initial value:

= 1:30
  for ii = 1:ntype
    for jj = 1:ntype
      p_a_a_r_ang(ii,jj,kk,:) = dat_a_a_r_ang(ii,jj,kk,:) / sum_a_a_r(ii,jj,kk)

Referenced by utility::graph::Graph::all_pairs_shortest_paths(), analyze_poses_for_convergence(), ExposedStrandMover::apply(), CloseContactWithResidue::apply(), ScoreFunctionFingerprintMover::apply(), back_in_time_2d(), numeric::kinematic_closure::radians::bridge_objects(), numeric::kinematic_closure::bridgeObjects(), buns_for_pose(), calc_scores(), calculate_hASA_by_type_and_attractiveE(), calculate_hASA_by_type_and_exposure(), compare_gpu_result_against_cpu(), correct_dunbrack(), CrystFFTDock::fft2dslice(), InterfaceDDGBindJobInputter::fill_jobs(), gather_info_all_repeats(), gather_info_canonical_repeats(), gather_ss_pct(), get_all_2helix_docks(), get_helixCAInContact(), get_inflection_points(), CrystFFTDock::get_interfaces_allatom(), numeric::fourier::SHT::idx_to_euler(), numeric::fourier::SHT::idx_to_rot(), CrystFFTDock::ifft2dslice(), iterative_optE(), numeric::nls::lm_qrsolv(), main(), utility::nmers_of(), utility::nmers_worker(), output_all_repeats(), ScoreEachBenchmark::run_long_ranged_two_body_energy(), ScoreEachBenchmark::run_short_ranged_two_body_energy(), save_cluster_tree_lite(), and ship_coordinates_to_gpu().

LEU

LEU

LYS

LYS

MET

MET

Na1_r_core_core

Na1_r_core_core = squeeze(sum(aacore_core_da1))

Na1_r_core_surf

Na1_r_core_surf = squeeze(sum(aacore_surf_da1))

Na1_r_surf_core

Na1_r_surf_core = squeeze(sum(aasurf_core_da1))

Na1_r_surf_surf

end Na1_r_surf_surf = squeeze(sum(aasurf_surf_da1))

Na2_r_core_core

Na2_r_core_core = squeeze(sum(aacore_core_da2))

Na2_r_core_surf

Na2_r_core_surf = squeeze(sum(aacore_surf_da2))

Na2_r_surf_core

Na2_r_surf_core = squeeze(sum(aasurf_core_da2))

Na2_r_surf_surf

Na2_r_surf_surf = squeeze(sum(aasurf_surf_da2))

NAA

should not contain ALA GLY PRO NAA = 17

ntype

NAAaa to NAAaa cal ntype = NAA

num_res_env

num_res_env = zeros(NAA,2)

p

p = (p_ii_jj .* p_r_ang) ./ (p_ii_p_jj)

p_a_a_r_ang

sum over ang p_a_a_r_ang = zeros(ntype, ntype, 30, 16)

p_a_r_ang1

p_a_r_ang1 = zeros(ntype, 30, 16)

p_a_r_ang2

p_a_r_ang2 = zeros(ntype, 30, 16)

p_ii

p_ii = p_a_r_ang1(iii, :, :)

p_ii_jj

p_ii_jj = squeeze(p_a_a_r_ang( iii, jjj, :, : ))

p_ii_p_jj

p_ii_p_jj = squeeze(p_ii .* p_jj)

p_ii_p_jj_w

p_ii_p_jj_w = squeeze(p_ii_w .* p_jj_w)

p_ii_w

p_ii_w = calc_Pi_ang_sc(aasurf_surf_da1(iii,:,:), aasurf_core_da1(iii,:,:), aacore_surf_da1(iii,:,:), aacore_core_da1(iii,:,:), wi, wj)

p_jj

p_jj = p_a_r_ang2(jjj, :, :)

p_jj_w

p_jj_w = calc_Pi_ang_sc(aasurf_surf_da2(jjj,:,:), aasurf_core_da2(jjj,:,:), aacore_surf_da2(jjj,:,:), aacore_core_da2(jjj,:,:), wj, wi)

p_r_ang

p_r_ang = zeros(30, 16)

p_r_ang_w

p_r_ang_w = calc_Pi_ang_sc(Na1_r_surf_surf, Na1_r_surf_core, Na1_r_core_surf, Na1_r_core_core, wi, wj)

p_w

p_w = (p_ii_jj .* p_r_ang_w + shift) ./ (p_ii_p_jj_w + shift)

p_w0

p_w0 = (p_ii_jj .* p_r_ang + shift) ./ (p_ii_p_jj_w + shift)

PHE

PHE

PRO

PRO

Rcut

Rcut = 12

res_index

buildlist res_index = zeros(40,1)

reslist

reslist

Initial value:

= 

Referenced by register_options(), and run().

score

score = score_w(1:Bcut,:)

score0

score0 = -log(p)

Referenced by get_numeric_deriv(), and test_deriv_pose().

score_w

score_w = -log(p_w)

score_w0

score_w0 = -log(p_w0)

SER

SER

shift

end shift shift = zeros(30,16)

Referenced by PoseWrap::dump_pdb(), detail::fallback_format(), detail::dragonbox::floor_log10_pow2(), generate_from_point(), detail::get_cached_power(), latticeHit::latticeHit(), numeric::random::lshift128(), utility::graph::UEVertex< V, E >::make_edge_vector_current(), detail::bigint::operator<<=(), detail::accumulator::operator>>=(), myspace::Scheduler::pick_hashing_res(), myspace::Scheduler::run_LHeval(), and basic_format_args< Context >::type().

smoothed

smoothed = smooth_2D(surf_core_th1(i,j,:,:), [15, 0.1, 2], [360, 40, 2])

sum_a1_r

sum over the second aa sum_a1_r = sum(dat_a_r_ang1, 3)

sum_a2_r

sum over the first aa sum_a2_r = sum(dat_a_r_ang2, 3)

sum_a_a_r

old way sum_a_a_r = sum(dat_a_a_r_ang,4)

sum_r

sum over all aa sum_r = sum(dat_r_ang,2)

surf_core_th1

surf_core_th1 =zeros(NAA,NAA,30,16)

surf_surf_th1

end split surf_surf_th1 =zeros(NAA,NAA,30,16)

THR

THR

TRP

TRP

VAL

VAL

wj

wj = num_res_env(jjj,1)/sum(num_res_env(jjj,:))

xx

for xx

Initial value:

=1:Bcut
    fprintf(fp_ang, "%.6f ", score(xx,1))

Referenced by numeric::urs_Quat::asR(), numeric::model_quality::calc_rms_fast(), correlation_coefficient(), get_axis_angle(), kono_sarai_stats(), kono_sarai_zscore(), main(), numeric::kinematic_closure::operator<<(), numeric::quat2R(), numeric::model_quality::rms_fit(), numeric::model_quality::rmsfitca2(), numeric::model_quality::rmsfitca3(), numeric::model_quality::rsym_eigenval(), numeric::model_quality::rsym_evector(), run(), test_gpu_inlining(), and rosetta_binders::xyzMatrix_add_on_binder().

yy

end debug yy

Initial value:

=1:18
    fprintf(fp_ang, "%.6f ", 0)

Referenced by numeric::urs_Quat::asR(), numeric::model_quality::calc_rms_fast(), correlation_coefficient(), get_axis_angle(), kono_sarai_stats(), kono_sarai_zscore(), main(), numeric::quat2R(), numeric::model_quality::rms_fit(), numeric::model_quality::rmsfitca2(), numeric::model_quality::rmsfitca3(), numeric::model_quality::rsym_eigenval(), numeric::model_quality::rsym_evector(), test_gpu_inlining(), and rosetta_binders::xyzMatrix_add_on_binder().