draw_gen_env_dep_pair.m File Reference

Functions
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
	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,:)
	aa_core (:,:)+
	N (ai, r)
	N (r)
	P (r)
	N (aa)
cal i j if	exist ("ii", "var") % ii %else % ii
	score (1:8)
	score_w (1:8)
	subplot (4, 5, jj)
	set (h(2), "linewidth", 2) axis([0 25 -1 0.6]) t
	text (2, score(10), t)

Variables
	reslist
	CYS
	ASP
	GLU
	PHE
	GLY
	HIS
	ILE
	LYS
	LEU
	MET
	ASN
	PRO
	GLN
	ARG
	SER
	THR
	VAL
	TRP
	TYR
	res_index = zeros(40,1)
	env_index = zeros(40,1)
	num_res_env = zeros(20,2)
for	i
	break
end split	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
end end end end smooth data	L =6
	CONV1 = gausswin(2*L+1, 6)
	smoothed = conv(squeeze(surf_core(i,j,:)), CONV1)
	__pad0__
	__pad1__
end end end sum	aa_surf =zeros(20,30)
	aa_core =zeros(20,30)
end	aa_aa = (surf_surf+surf_core+core_surf+core_core)
to	pair_counts_symm = aa_aa
	aa_all = aa_surf+aa_core
to all init	pair_sums_aan = squeeze(sum(pair_counts_symm))
	N
	sum_r_aa_core = sum(aa_core, 2)
	P_ii_jj = squeeze(pair_counts_symm(ii,jj,:)) ./ sum_ij
	P_ii_surf_func = calc_Pi(aa_surf, aa_core, ii, 1.0)
	P_ii_core_func = calc_Pi(aa_surf, aa_core, ii, 0.0)
	P_ii = pair_sums_aan(ii, :) / sum_r_aa(ii)
	P_ii_w = calc_Pi(aa_surf, aa_core, ii, num_res_env(jj,1)/sum(num_res_env(jj,:)))
	P_jj = pair_sums_aan(jj, :) / sum_r_aa(jj)
	P_jj_w = calc_Pi(aa_surf, aa_core, jj, num_res_env(ii,1)/sum(num_res_env(ii,:)))
	P = P_ii_jj' .* P_r ./ (P_ii .* P_jj)
	P_w = P_ii_jj' .* P_r ./ (P_ii_w .* P_jj_w)
	score = -log(P)
	score_w = -log(P_w)
	h =plot(1:30, score, 'r', 1:30, score_w)

Function Documentation

aa_core()

aa_core	(	:	,
		:
	)

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"
	)

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

score()

score

(

1:8

)

score_w()

score_w

(

1:8

)

set()

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

subplot()

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	,
		score(10)	,
		t
	)

Variable Documentation

__pad0__

__pad0__

__pad1__

__pad1__

aa_aa

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

aa_all

aa_all = aa_surf+aa_core

aa_core

aa_core =zeros(20,30)

aa_surf

end end end sum aa_surf =zeros(20,30)

aj

end else aj

ARG

ARG

ASN

ASN

ASP

ASP

break

break

CONV1

CONV1 = gausswin(2*L+1, 6)

core_core

core_core =zeros(20,20,30)

core_surf

core_surf =zeros(20,20,30)

CYS

CYS

env_index

env_index = zeros(40,1)

GLN

GLN

GLU

GLU

GLY

GLY

h

h =plot(1:30, score, 'r', 1:30, score_w)

Referenced by PairDistance::apply(), LoopHashRelax_Sampler::apply(), xtal_water_bunsat::apply(), numeric::VoxelArray< _Float, _Value >::at(), bunsats(), calc_ddg(), ui::task::NetworkCall::call(), clash(), pointGroupHit::construct_from_basis(), contacts(), design_hits(), dock(), download_url(), TCDock::dump_top_hits(), hbond_energy_strat::evaluate(), hbond_geom_strat::evaluate(), find_dsf(), fixH(), get_cx_xform(), Cache::get_data(), get_rmsd(), get_rmsd_debug(), numeric::hsv_to_rgb(), ik_lys_ctp_asp(), ik_lys_ctp_glu(), jacobi(), TCDock::justone(), Cache::lru_delete(), Cache::lru_insert(), main(), make_dock_olig(), numeric::linear_algebra::minimum_bounding_ellipse(), detail::stringifier::operator()(), numeric::interpolation::InterpolatedPotential< N >::operator()(), detail::custom_formatter< Context >::operator()(), operator<<(), operator>>(), KinFunGroupTK::place_c(), numeric::linear_algebra::point_in_ellipse(), PoseWrap::PoseWrap(), print_header(), MainWindow::resizeGL(), TCDock::run(), run(), sasa_bunsats(), numeric::interpolation::spline::spline_interpolate(), basic::svd::SVD_Solver::svdcmp(), numeric::linear_algebra::svdcmp(), Cache::swap_index(), TEST(), detail::vformat_to(), detail::cf::vformat_to(), vsasa_bunsats(), and Cache::~Cache().

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

j

Initial value:

= 1:40
    aj = res_index(j)

L

end end end end smooth data L =6

LEU

LEU

LYS

LYS

MET

MET

N

N

Initial value:

= sum_r N(r)
P_r = pair_sums_tot / totalsum

Referenced by dsRNA_grow::apply(), array2vecs(), numeric::kinematic_closure::radians::bridge_objects(), numeric::kinematic_closure::bridgeObjects(), Link::c_anchor(), calculate_helical_parameters(), detail::dragonbox::check_divisibility_and_divide_by_pow5(), clash_check_bb(), Link::clashes(), cnl_print(), cnl_store_hbs(), detail::compile(), detail::compile_string_to_view(), detail::compile_to_parts(), contact_model_prediction(), cyclize_pose(), numeric::interpolation::spline::PolycubicSpline< N >::dFdall(), numeric::interpolation::spline::PolycubicSpline< N >::dFdxi(), numeric::interpolation::InterpolatedPotential< N >::dimension(), numeric::interpolation::spline::PolycubicSpline< N >::dimensionality(), doit(), Link::dump_pdb(), PoseWrap::dump_pdb(), TCDock::dump_top_hits(), ObjexxFCL::end(), numeric::expand_xforms(), numeric::interpolation::spline::PolycubicSpline< N >::F(), numeric::factorial(), fere_torsions(), fitfun(), numeric::fourier::SHT::forwardS2(), generate_disulfide_conformations(), numeric::fourier::SO3coeffs::genWigner_ds(), numeric::interpolation::spline::PolycubicSpline< N >::get_all_derivs(), get_dm(), get_dm_features(), get_dots_area(), numeric::interpolation::InterpolatedPotential< N >::get_indices(), numeric::MathNTensor< T, N >::get_mathmatrix(), get_N(), numeric::interpolation::get_patch(), get_repl_xyz(), numeric::interpolation::get_val(), gpu_refold_test(), gpu_score_test(), in_cnl(), in_set(), numeric::fourier::SHT::inverseS2(), numeric::MathNTensor< T, N >::is_valid_position(), TCDock::justone(), Link::Link(), main(), make_two_trimers(), numeric::MathNTensor< T, N >::MathNTensor(), numeric::linear_algebra::minimum_bounding_ellipse(), motif_deviation(), numeric::interpolation::multilinear_interpolation(), Link::nres(), numeric::MathNTensor< T, N >::num_dimensions(), numeric::interpolation::InterpolatedPotential< N >::operator()(), numeric::MathNTensor< T, N >::operator()(), numeric::interpolation::TempStruct< T, N >::operator()(), numeric::interpolation::polycubic_interpolate_catmull_rom(), numeric::interpolation::polycubic_interpolation(), pseudoTraceRecords::pseudoTraceRecords(), pymol(), random_torsions(), numeric::read_tensor_from_file(), refine(), refold_first(), refold_gpu(), refold_second(), repackmin(), numeric::MathNTensor< T, N >::replace_layer(), basic::sampling::orientations::QuaternionGridManager::request_by_size(), Link::rotate(), run(), TCDock::run(), set_disulf(), numeric::MathNTensor< T, N >::set_value(), setup_segment_insert(), numeric::fourier::SHT::setup_Wig(), detail::dragonbox::small_division_by_pow10(), stat_output(), str(), Tensor::sum_to(), basic::svd::SVD_Solver::SVD_Solver(), utility::swap4_aligned(), test(), test_bridgeObjects(), numeric::kinematic_closure::test_bridgeObjects(), test_gpu_speed(), test_MAT_VEC(), test_numerical_deriv(), test_pack14(), test_refold(), testone(), numeric::interpolation::spline::PolycubicSpline< N >::train(), numeric::kinematic_closure::radians::triaxialCoefficients(), numeric::kinematic_closure::triaxialCoefficients(), numeric::MathNTensor< T, N >::value(), visualize(), which_subsub(), and write_cluster_frags().

num_res_env

num_res_env = zeros(20,2)

P

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

Referenced by Link::align_c(), Link::align_n(), numeric::deriv::angle_p1_deriv(), numeric::deriv::angle_p1_p2_p3_deriv(), numeric::deriv::angle_p2_deriv(), Link::c_anchor(), Link::clashes(), numeric::deriv::dihedral_deriv_second(), numeric::deriv::dihedral_p1_cosine_deriv(), numeric::deriv::dihedral_p1_cosine_deriv_first(), numeric::deriv::dihedral_p2_cosine_deriv(), numeric::deriv::dihedral_p2_cosine_deriv_first(), numeric::deriv::distance_f1_f2_deriv(), Link::dump_pdb(), get_boltzmann_probabilities(), Link::get_phi(), Link::get_psi(), Link::is_connected(), Link::Link(), main(), numeric::linear_algebra::minimum_bounding_ellipse(), motif_column_deviation(), motif_deviation(), Link::n_anchor(), numeric::geometry::hashing::bin_index_hasher::operator()(), numeric::deriv::p1_theta_deriv(), CrystFFTDock::project_along_axis(), Bola::random_close_phipsi_from_rama(), Link::rotate(), Link::set_phi(), Link::set_psi(), stat_output(), Tensor::sum_to(), and numeric::deriv::x_and_dtheta_dx().

P_ii

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

P_ii_core_func

P_ii_core_func = calc_Pi(aa_surf, aa_core, ii, 0.0)

P_ii_jj

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

P_ii_surf_func

P_ii_surf_func = calc_Pi(aa_surf, aa_core, ii, 1.0)

P_ii_w

P_ii_w = calc_Pi(aa_surf, aa_core, ii, num_res_env(jj,1)/sum(num_res_env(jj,:)))

P_jj

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

P_jj_w

P_jj_w = calc_Pi(aa_surf, aa_core, jj, num_res_env(ii,1)/sum(num_res_env(ii,:)))

P_w

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

pair_counts_symm

to pair_counts_symm = aa_aa

pair_sums_aan

to all init pair_sums_aan = squeeze(sum(pair_counts_symm))

PHE

PHE

PRO

PRO

res_index

res_index = zeros(40,1)

reslist

reslist

Initial value:

= 

score

score = -log(P)

score_w

score_w = -log(P_w)

SER

SER

smoothed

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

sum_r_aa_core

sum_r_aa_core = sum(aa_core, 2)

surf_core

surf_core =zeros(20,20,30)

surf_surf

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

THR

THR

TRP

TRP

TYR

TYR

VAL

VAL