draw_gen_env_dep_pair_decompose.m File Reference

Functions
20, 2	zeros ()
end end get env	env_index (i)
	num_res_env (res_index(i), env_index(i))
	if (env_index(i)==1) if(env_index(j)
i, j, :	pair ()
end else	if (env_index(j)==1) %c-s core_surf(ai
id	beta ()
surf_surf	pre_fill_dfire ()
	surf_surf (i, j,:)
	surf_core (i, j,:)
	core_surf (i, j,:)
	core_core (i, j,:)
	if (i!=j) surf_surf(j
	surf_core (j, i,:)
	core_surf (j, i,:)
	core_core (j, i,:)
	N (ai, r)
	N (r)
	P (r)
	N (aa)
id	i: (i Sum_r_surf_surf)
	sr_surf_core (i,:)/
	sr_core_surf (i,:)/
	sr_core_core (i,:)/
cal i j if	exist ("ii", "var") ii else ii
	score (1:cutoff)=0
	score_w (1:cutoff)=0
	score_w2 (1:cutoff)=0
	score_w3 (1:cutoff)=0
	score_w (kk+20)
end	score_w2 (25:30)=0
	score_w (25:30)=0
draw	subplot (4, 5, jj)
	axis ([0 25 -1 0.6]) set(h(1)
	set (h(2), "linewidth", 2) %set(h(3)
	text (2, 0, t)
	fprintf (fp_pair, "PAIR: %s %s ", reslist(ii,:), reslist(jj,:))
	fprintf (fp_pair, "%.2f %.2f ", 0.25, 0.25+(range *2-1) *0.5)
	fprintf (fp_pair, "%d ", length(y2))
end	fprintf (fp_pair, "\n")
end	fprintf (fp_pair, "# END\n")
	fclose (fp_pair)

Variables
	cutoff =2
	range =12
	reslist
	CYS
	ASP
	GLU
	PHE
	GLY
	HIS
	ILE
	LYS
	LEU
	MET
	ASN
	PRO
	GLN
	ARG
	SER
	THR
	VAL
	TRP
	TYR
mark each table column row	res_index = zeros(40,1)
residue index	env_index = zeros(40,1)
env	__pad0__
residue number for surf &core for	i
	break
end split x4	surf_surf =zeros(20,20,30)
	surf_core =zeros(20,20,30)
	core_surf =zeros(20,20,30)
	core_core =zeros(20,20,30)
for	j
end else	aj
smooth data	L =5
	CONV1 = gausswin(2*L+1, 4)
	smoothed = conv(squeeze(surf_core(i,j,:)), CONV1)
	__pad1__
	__pad2__
end end end sum	aa_aa = (surf_surf+surf_core+core_surf+core_core)
to	pair_counts_symm = aa_aa
init	pair_sums_aan = squeeze(sum(pair_counts_symm))
	N
	sr_surf_core = squeeze(sum(surf_core, 2))
	sr_core_surf = squeeze(sum(core_surf, 2))
	sr_core_core = squeeze(sum(core_core, 2))
	Sum_r_surf_surf = squeeze(sum(sr_surf_surf,2))
	Sum_r_surf_core = squeeze(sum(sr_surf_core,2))
	Sum_r_core_surf = squeeze(sum(sr_core_surf,2))
	Sum_r_core_core = squeeze(sum(sr_core_core,2))
	Nr_surf_surf = sum(sr_surf_surf)
	Nr_core_surf = sum(sr_core_surf)
	Nr_surf_core = sum(sr_surf_core)
	Nr_core_core = sum(sr_core_core)
for	jj
	P_ii_jj = squeeze(pair_counts_symm(ii,jj,:)) ./ sum_ij
	P_ii = pair_sums_aan(ii, :) / sum_r_aa(ii)
	P_jj = pair_sums_aan(jj, :) / sum_r_aa(jj)
be careful	! wi = num_res_env(ii,1)/sum(num_res_env(ii,:))
	wj = num_res_env(jj,1)/sum(num_res_env(jj,:))
	P_ii_w = calc_Pi_sc(sr_surf_surf(ii,:), sr_surf_core(ii,:), sr_core_surf(ii,:), sr_core_core(ii,:), wi, wj)
	P_jj_w = calc_Pi_sc(sr_surf_surf(jj,:), sr_surf_core(jj,:), sr_core_surf(jj,:), sr_core_core(jj,:), wj, wi)
	P = P_ii_jj' .* P_r ./ (P_ii .* P_jj)
	Pr_w = calc_Pi_sc(Nr_surf_surf, Nr_surf_core, Nr_core_surf, Nr_core_core, num_res_env(ii,1)/sum(num_res_env(ii,:)), num_res_env(jj,1)/sum(num_res_env(jj,:)))
	P_w = P_ii_jj' .* P_r ./ (P_ii_w .* P_jj_w)
	P_w2 = P_ii_jj' .* Pr_w ./ (P_ii_w .* P_jj_w)
	P_w3 = P_ii_jj' ./ (P_ii_w .* P_jj_w) .* Pr_w .* Pr_w ./ P_r
score	score = -log(P)
	score_w = -log(P_w)
	score_w2 = -log(P_w2)
	score_w3 = -log(P_w3)
shift for	kk
	h =plot(1:30, score, 'r', 1:30, score_w, 'b', 1:30, score_w2, 'g', 1:30, score_w3, 'y')
	linewidth
	t = reslist(jj,:)
output	y2 = score_w2(1:range*2)
for	k

Function Documentation

axis()

axis

(

)

beta()

id beta ( )

virtual

core_core() [1/2]

core_core	(	i	,
		j	,
		:
	)

core_core() [2/2]

core_core	(	j	,
		i	,
		:
	)

core_surf() [1/2]

core_surf	(	i	,
		j	,
		:
	)

core_surf() [2/2]

core_surf	(	j	,
		i	,
		:
	)

env_index()

end end get env env_index

(

i

)

exist()

cal i j if exist	(	"ii"	,
		"var"
	)

fclose()

fclose

(

fp_pair

)

Referenced by buffered_file::close(), basic::get_usage_from_procfilesystem(), main(), output_PCA(), read_PCAfile(), svm_load_model(), svm_save_model(), test(), and buffered_file::~buffered_file().

fprintf() [1/5]

end fprintf	(	fp_pair	,
		"# END\n"
	)

fprintf() [2/5]

fprintf	(	fp_pair	,
		"%.2f %.2f "	,
		0.	25,
		0.25+(range *2-1) *0.	5
	)

fprintf() [3/5]

fprintf	(	fp_pair	,
		"%d "	,
		length(y2)
	)

fprintf() [4/5]

end fprintf	(	fp_pair	,
		"\n"
	)

fprintf() [5/5]

fprintf	(	fp_pair	,
		"PAIR: %s %s "	,
		reslist(ii,:)	,
		reslist(jj,:)
	)

i:()

id i: ( i  Sum_r_surf_surf )

virtual

if() [1/3]

if

(

env_index(i)

= =1

)

if() [2/3]

end else if

(

env_index(j)

= =1

)

if() [3/3]

if

(

i!

= j

)

N() [1/3]

N

(

aa

)

N() [2/3]

N	(	ai	,
		r
	)

N() [3/3]

N

(

r

)

num_res_env()

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

P()

P

(

r

)

pair()

i, j, : pair ( )

virtual

pre_fill_dfire()

core_core pre_fill_dfire ( )

staticvirtual

score()

score ( 1:cutoff  )

pure virtual

score_w() [1/3]

score_w ( 1:cutoff  )

pure virtual

score_w() [2/3]

score_w ( 25:30  )

pure virtual

score_w() [3/3]

score_w

(

kk+

20

)

score_w2() [1/2]

score_w2 ( 1:cutoff  )

pure virtual

score_w2() [2/2]

end score_w2 ( 25:30  )

pure virtual

score_w3()

score_w3 ( 1:cutoff  )

pure virtual

set()

set	(	h(2)	,
		"linewidth"	,
		2
	)

sr_core_core()

sr_core_core	(	i	,
		:
	)

sr_core_surf()

sr_core_surf	(	i	,
		:
	)

sr_surf_core()

sr_surf_core	(	i	,
		:
	)

subplot()

draw subplot	(	4	,
		5	,
		jj
	)

surf_core() [1/2]

surf_core	(	i	,
		j	,
		:
	)

surf_core() [2/2]

surf_core	(	j	,
		i	,
		:
	)

surf_surf()

surf_surf	(	i	,
		j	,
		:
	)

text()

text	(	2	,
		0	,
		t
	)

zeros()

20,2 zeros ( )

virtual

Variable Documentation

! wi

be careful ! wi = num_res_env(ii,1)/sum(num_res_env(ii,:))

__pad0__

env __pad0__

__pad1__

__pad1__

__pad2__

__pad2__

aa_aa

end end end sum aa_aa = (surf_surf+surf_core+core_surf+core_core)

aj

end else aj

ARG

ARG

ASN

ASN

ASP

ASP

break

break

CONV1

CONV1 = gausswin(2*L+1, 4)

core_core

core_core =zeros(20,20,30)

core_surf

core_surf =zeros(20,20,30)

cutoff

cutoff =2

CYS

CYS

env_index

residue index env_index = zeros(40,1)

GLN

GLN

GLU

GLU

GLY

GLY

h

h =plot(1:30, score, 'r', 1:30, score_w, 'b', 1:30, score_w2, 'g', 1:30, score_w3, 'y')

HIS

HIS

i

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

j

Initial value:

= 1:40
    aj = res_index(j)

jj

for jj

Initial value:

= 4:4
  sum_ij = sum(pair_counts_symm(ii,jj,:))

k

for k

Initial value:

=1:length(y2)
  %  fprintf(fp_pair, "%f ", y2(k))

kk

shift for kk

Initial value:

= 1:4
  %  score_w2(kk+20) = score_w2(20)*(4-kk)/4

L

smooth data L =5

LEU

LEU

linewidth

linewidth

LYS

LYS

MET

MET

N

N

Initial value:

= sum_r N(r)
P_r = pair_sums_tot / totalsum

Nr_core_core

Nr_core_core = sum(sr_core_core)

Nr_core_surf

Nr_core_surf = sum(sr_core_surf)

Nr_surf_core

Nr_surf_core = sum(sr_surf_core)

Nr_surf_surf

end Nr_surf_surf = sum(sr_surf_surf)

P

P = P_ii_jj' .* P_r ./ (P_ii .* P_jj)

P_ii

P_ii = pair_sums_aan(ii, :) / sum_r_aa(ii)

P_ii_jj

P_ii_jj = squeeze(pair_counts_symm(ii,jj,:)) ./ sum_ij

P_ii_w

P_ii_w = calc_Pi_sc(sr_surf_surf(ii,:), sr_surf_core(ii,:), sr_core_surf(ii,:), sr_core_core(ii,:), wi, wj)

P_jj

P_jj = pair_sums_aan(jj, :) / sum_r_aa(jj)

P_jj_w

P_jj_w = calc_Pi_sc(sr_surf_surf(jj,:), sr_surf_core(jj,:), sr_core_surf(jj,:), sr_core_core(jj,:), wj, wi)

P_w

P_w = P_ii_jj' .* P_r ./ (P_ii_w .* P_jj_w)

P_w2

P_w2 = P_ii_jj' .* Pr_w ./ (P_ii_w .* P_jj_w)

P_w3

P_w3 = P_ii_jj' ./ (P_ii_w .* P_jj_w) .* Pr_w .* Pr_w ./ P_r

pair_counts_symm

to pair_counts_symm = aa_aa

pair_sums_aan

init pair_sums_aan = squeeze(sum(pair_counts_symm))

PHE

PHE

Pr_w

Pr_w = calc_Pi_sc(Nr_surf_surf, Nr_surf_core, Nr_core_surf, Nr_core_core, num_res_env(ii,1)/sum(num_res_env(ii,:)), num_res_env(jj,1)/sum(num_res_env(jj,:)))

PRO

PRO

range

range =12

Referenced by pyrosetta.bindings.pose.PoseResidueAccessor::__getitem__(), pyrosetta.bindings.pose.PoseResidueLabelAccessor::__getitem__(), mutant_modeler.MutantModeler::__init__(), PyMOL-Rosetta-relay-client.Matrix::__init__(), PyMOL-RosettaServer.Matrix::__init__(), pyrosetta.bindings.pose.PoseResidueAccessor::__iter__(), pyrosetta.bindings.pose.PoseResidueLabelAccessor::__iter__(), pyrosetta.bindings.pose.PoseResidueAccessor::__reversed__(), pyrosetta.bindings.pose.PoseResidueLabelAccessor::__reversed__(), pyrosetta.toolbox.atom_pair_energy::_atom_pair_energy_table(), PyMOL-Rosetta-relay-client.PR_PyMOLServer::_color_model(), PyMOL-RosettaServer.PR_PyMOLServer::_color_model(), pyrosetta.PyMOLRosettaServer.PR_PyMOLServer::_color_model(), pyrosetta.distributed.cluster.initialization::_get_residue_type_set_name3(), pyrosetta.distributed.cluster.io.IO::_process_kwargs(), pyrosetta.toolbox.atom_pair_energy::_reisude_pair_energies(), basic_memory_buffer< T, SIZE, Allocator >::append(), TestQuickRelaxMover::apply(), pyrosetta.distributed.viewer.modules.setHydrogenBonds::apply(), pyrosetta.distributed.viewer.modules.setHydrogens::apply(), auto-DRRAFTER_setup::auto_setup_helices(), bin_torsions::bin_histograms(), demo.D090_Ala_scan::calc_binding_energy(), pyrosetta.toolbox.cleaning::cleanCRYS(), PyMOL_demo::coloring_demo(), compute_intrinsic_deviation(), PyMOL-Rosetta-relay-client::compute_plane_positions(), PyMOL-RosettaServer::compute_plane_positions(), pyrosetta.PyMOLRosettaServer::compute_plane_positions(), PyMOL-Rosetta-relay-client::connect_points(), PyMOL-RosettaServer::connect_points(), pyrosetta.PyMOLRosettaServer::connect_points(), detail::copy(), pyrosetta.bindings.pose::display_secstruct(), pyrosetta.distributed.cluster.core.PyRosettaCluster::distribute(), test.T500_Packing::elim_everything_except_G(), erraser_wrapper::erraser(), erraser_wrapper::erraser_single_res(), auto-DRRAFTER_setup_next_round::figure_out_next_round(), finalize_models::finalize(), autocorrelation::find_autocorrelation(), erraser_util::find_nearby_res(), setup_for_complex_scoring_general::find_offset(), mutant_modeler::find_pairs(), setup_for_complex_scoring_general::find_pairs(), DRRAFTER::find_pairs(), DRRAFTER_util::find_pairs(), demo.D030_Fold_tree::fold_tree(), pyrosetta.tests.protocols.indexed_structure_store.test_search::fragment_start_indicies_from_residue_array(), pyrosetta.tests.protocols.indexed_structure_store.test_search::fragments_from_source_residues(), pyrosetta.bindings.homogeneous_transform::from_array(), enumerate_junctions::generate_all_dhr_attach_permutations(), enumerate_junctions::generate_all_junction_attach_permutations(), enumerate_junctions::generate_all_terminal_pdb_permutations(), update_ui_project::generate_rosetta_project_files(), get_all_1helix_docks(), get_all_2helix_docks(), DRRAFTER::get_coord_csts(), auto-DRRAFTER_setup::get_density_btwn_points(), mutant_modeler.MutantModeler::get_high_res_command_lines(), DRRAFTER_util::get_ints(), mutant_modeler.MutantModeler::get_med_res_command_lines(), mutant_modeler.MutantModeler::get_mut_positions(), setup_for_complex_scoring_general::get_mut_string(), DRRAFTER::get_near_residues(), pyrosetta.distributed.cluster.tools::get_protocols(), DRRAFTER_util::get_resnum_chain(), auto-DRRAFTER_setup_next_round::get_results(), auto-DRRAFTER_setup_next_round::get_silent_file_subset(), make_templates::getMapFunction(), make_templates::getVectorFunction(), DRRAFTER_util::graph_from_ss(), demo.D060_Folding::guess_disulfides(), is_loop_neighbor(), join(), pyrosetta.protocols.structure_search.alignment::length_grouped_broadcast_metric(), pyrosetta.protocols.structure_search.alignment::length_grouped_pairwise_metric(), mutant_modeler::list_mutated_BPs(), setup_for_complex_scoring_general::list_mutated_BPs(), mutant_modeler::list_NC_BPs(), setup_for_complex_scoring_general::list_NC_BPs(), setup_for_complex_scoring_general::list_NC_BPs_noGU(), 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(), setup_for_complex_scoring_general::main(), relax_starting_structure::main(), options::main(), PyMOL-Rosetta-relay-client::make_axis(), PyMOL-RosettaServer::make_axis(), pyrosetta.PyMOLRosettaServer::make_axis(), PyMOL-Rosetta-relay-client::make_data(), PyMOL-RosettaServer::make_data(), pyrosetta.PyMOLRosettaServer::make_data(), mutant_modeler.MutantModeler::make_high_res_subsets_and_cmd_lines(), submit_jobs::make_job_files_and_submit(), DRRAFTER_util::make_tag_with_dashes(), util::make_tag_with_dashes(), make_templates::makeFile(), margin(), DRRAFTER_util::matches(), dummy-distribution::move_all_torsions(), pyrosetta.mpi::MPIJobDistributor(), pyrosetta.toolbox.mutants::mutate_residue(), mp_ddG::mutate_residue(), demo.D090_Ala_scan::mutate_residue(), demo.D050_Packer_task::packer_task(), formatter< std::chrono::duration< Rep, Period >, Char >::parse(), erraser_util::parse_option_chain_res_list(), erraser_util::parse_option_int_list(), erraser_util::parse_option_string_list(), DRRAFTER_util::parse_tag(), erraser_util::pdb_slice(), erraser_util::pdb_slice_into_chunks(), bin_torsions::plot_histograms(), pyrosetta.toolbox.extract_coords_pose::pose_coords_as_rows(), pyrosetta.io::pose_from_sequence(), demo.D020_Pose_scoring::pose_scoring(), demo.D010_Pose_structure::pose_structure(), mp_ddG::print_ddG_breakdown(), mp_ddG::print_score_labels_to_file(), PyMOL-Rosetta-relay-client.PR_PyMOLServer::process_packet(), PyMOL-RosettaServer.PR_PyMOLServer::process_packet(), pyrosetta.PyMOLRosettaServer.PR_PyMOLServer::process_packet(), numeric::random::RandomGenerator::random_range(), read_list_pose_range(), read_master_pose_range(), erraser_util::res_wise_rmsd(), DRRAFTER_util::residue_graph_from_ss(), pyrosetta.bindings.energies::residue_onebody_energies_array(), pyrosetta.bindings.energies::residue_pair_energies_array(), pyrosetta.bindings.energies::residue_total_energies_array(), pyrosetta.toolbox.mutants::restrict_non_nbrs_from_repacking(), demo.D060_Folding::sample_folding(), demo.D070_Refinement::sample_refinement(), demo.D080_Loop_modeling::sample_single_loop_modeling(), demo.D090_Ala_scan::scanning(), demo.D090_Ala_scan::scanning_analysis(), PyMOL-Rosetta-relay-client::set_spectrum(), PyMOL-RosettaServer::set_spectrum(), pyrosetta.PyMOLRosettaServer::set_spectrum(), pyrosetta.tests.distributed.test_viewer.TestViewer::setUp(), DRRAFTER::setup_job(), drrafter_rna::setup_next_round(), submit_jobs::setup_out_dir(), PyMOL-Rosetta-relay-client::start_rosetta_server(), PyMOL-RosettaServer::start_rosetta_server(), pyrosetta.PyMOLRosettaServer::start_rosetta_server(), ui::task::Updater::subscribe(), numeric::geometry::hashing::SixDOffsetTree::sum_radius(), erraser_wrapper::SWA_rebuild_erraser(), erraser_wrapper::SWA_rebuild_erraser_postproc(), PyMOL_demo::test(), pyrosetta.tests.distributed.cluster.test_smoke.MultipleClientsTest::test_clients(), pyrosetta.tests.distributed.cluster.test_logging.LoggingTest::test_logging(), pyrosetta.tests.bindings.core.test_pose.TestPoseIO::test_pose_io(), pyrosetta.tests.bindings.core.test_pose.TestPosesToSilent::test_poses_to_silent(), pyrosetta.tests.protocols.indexed_structure_store.test_search.TestStructureSearch::test_rep_search(), pyrosetta.tests.distributed.cluster.test_smoke.ResourcesTest::test_resources(), pyrosetta.tests.distributed.cluster.test_smoke.ResourcesTest::test_resources_clients(), pyrosetta.tests.distributed.cluster.test_smoke.SaveAllTest::test_save_all(), pyrosetta.tests.distributed.cluster.test_smoke.SaveAllTest::test_save_all_dry_run(), pyrosetta.tests.distributed.cluster.test_smoke.SerializationTest::test_serialization(), pyrosetta.tests.distributed.test_smoke.SmokeTestDistributed::test_silent_io(), pyrosetta.tests.distributed.cluster.test_smoke.SmokeTest::test_smoke(), pyrosetta.tests.distributed.cluster.test_smoke.SmokeTestMulti::test_smoke_multi(), pyrosetta.tests.distributed.cluster.test_smoke.SmokeTestMulti::test_smoke_multi_from_instance(), pyrosetta.tests.numeric.test_alignment.TestAlignment::test_superimpose(), pyrosetta.tests.distributed.test_viewer.TestViewer::test_viewer_with_poses(), pyrosetta.utility.array::to_structured_array(), ui::task::Updater::update_data_ready(), and FragMonteCarlo::updated_covered_rsds().

res_index

mark each table column row res_index = zeros(40,1)

reslist

reslist

Initial value:

= 

score

score score = -log(P)

score_w

score_w = -log(P_w)

score_w2

score_w2 = -log(P_w2)

score_w3

score_w3 = -log(P_w3)

SER

SER

smoothed

smoothed = conv(squeeze(surf_core(i,j,:)), CONV1)

sr_core_core

sr_core_core = squeeze(sum(core_core, 2))

sr_core_surf

sr_core_surf = squeeze(sum(core_surf, 2))

sr_surf_core

sr_surf_core = squeeze(sum(surf_core, 2))

Sum_r_core_core

Sum_r_core_core = squeeze(sum(sr_core_core,2))

Sum_r_core_surf

Sum_r_core_surf = squeeze(sum(sr_core_surf,2))

Sum_r_surf_core

Sum_r_surf_core = squeeze(sum(sr_surf_core,2))

Sum_r_surf_surf

Sum_r_surf_surf = squeeze(sum(sr_surf_surf,2))

surf_core

surf_core =zeros(20,20,30)

surf_surf

end split x4 surf_surf =zeros(20,20,30)

t

t = reslist(jj,:)

THR

THR

TRP

TRP

TYR

TYR

VAL

VAL

wj

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

y2

output y2 = score_w2(1:range*2)

Referenced by CrystFFTDock::apply(), base_doublet_rmsd_test(), numeric::interpolation::bilinearly_interpolated(), numeric::alignment::QCPKernel< Real >::calc_rmsd_Theobald_method(), coarse_to_full_test(), numeric::statistics::Dawson(), numeric::statistics::errf(), CrystFFTDock::get_transform_distance(), numeric::alignment::QCPKernel< Real >::inner_product(), and numeric::interpolation::spline::spline_second_derivative().