cal_env.m File Reference

Functions
	env_counts_smoothed (i,:)
	env_counts_smoothed_ref (i,:)
	P_env_ref (:, i)
	P_env_ref (i,:)
	y1 (1:3)
	y1_ref (1:3)
	y1 (36:40)
	y1_ref (36:40)
	text (0, y1(1), t)
	set (h(1), "linewidth", 2) set(h(2)
	set (h(3), "linewidth", 2) set(gca
	if (ii >15) set(gca
end	printf ("\n")

Variables
	env_counts = load_env_table()
	env_ref = load_env_table_ref()
smooth data	env_counts_smoothed =zeros(20,40)
	env_counts_smoothed_ref =zeros(20,40)
	L =6
half window	CONV1 = gausswin(2*L+1, 3)
for	i
	smoothed_ref = conv(squeeze(env_ref(i,:)), CONV1)
end	env_sums_aa = sum(env_counts_smoothed, 2)
	env_sums_aa_ref = sum(env_counts_smoothed_ref, 2)
	P_env =zeros(20,40)
	P_env_ref =zeros(20,40)
end	env_sums_tot = squeeze(sum(P_env))
	env_sums_tot_ref = squeeze(sum(P_env_ref))
end	score = -log(P_env)
	score_ref = -log(P_env_ref)
	dic = [ "GLU"
	LYS
	SER
	ILE
	ASN
	CYS
	ASP
	LEU
	GLY
	VAL
	ARG
	PHE
	PRO
	THR
	TYR
	ALA
	MET
	HIS
	GLN
	TRP
	dic2 = [ "ALA"
	GLU
for	ii
	x = [1:40]
	y1 = score(ii,x)
	y1_ref = score_ref(ii,x)
for	jj
end end	h =plot(x, env(jj,x), 'b', x, y1_ref, 'g', x, y1, 'r')
	t = dic(ii,:)
	linewidth
	xtick
	xticklabel

Function Documentation

env_counts_smoothed()

env_counts_smoothed	(	i	,
		:
	)

env_counts_smoothed_ref()

env_counts_smoothed_ref	(	i	,
		:
	)

if()

if	(	ii	,
		15
	)

P_env_ref() [1/2]

P_env_ref	(	:	,
		i
	)

P_env_ref() [2/2]

P_env_ref	(	i	,
		:
	)

printf()

end printf

(

"\n"

)

set() [1/2]

set	(	h(1)	,
		"linewidth"	,
		2
	)

set() [2/2]

set	(	h(3)	,
		"linewidth"	,
		2
	)

text()

text	(	0	,
		y1(1)	,
		t
	)

y1() [1/2]

y1

(

1:3

)

y1() [2/2]

y1

(

36:40

)

y1_ref() [1/2]

y1_ref

(

1:3

)

y1_ref() [2/2]

y1_ref

(

36:40

)

Variable Documentation

ALA

ALA

ARG

ARG

ASN

ASN

ASP

ASP

CONV1

CONV1 = gausswin(2*L+1, 3)

CYS

CYS

dic

dic = [ "GLU"

dic2

dic2 = [ "ALA"

env_counts

env_counts = load_env_table()

env_counts_smoothed

smooth data env_counts_smoothed =zeros(20,40)

env_counts_smoothed_ref

env_counts_smoothed_ref =zeros(20,40)

env_ref

env_ref = load_env_table_ref()

env_sums_aa

end env_sums_aa = sum(env_counts_smoothed, 2)

env_sums_aa_ref

env_sums_aa_ref = sum(env_counts_smoothed_ref, 2)

env_sums_tot

end env_sums_tot = squeeze(sum(P_env))

env_sums_tot_ref

env_sums_tot_ref = squeeze(sum(P_env_ref))

GLN

GLN

GLU

GLU

GLY

GLY

h

end end h =plot(x, env(jj,x), 'b', x, y1_ref, 'g', x, y1, 'r')

HIS

HIS

i

for i

Initial value:

= 1:20
    smoothed = conv(squeeze(env_counts(i,:)), CONV1)

ii

for ii

Initial value:

=1:20
    subplot(4,5,ii)

ILE

ILE

jj

for jj

Initial value:

=1:20
    if (dic2(jj,:)==dic(ii,:))
      break

L

L =6

LEU

LEU

linewidth

linewidth

LYS

LYS

MET

MET

P_env

P_env =zeros(20,40)

P_env_ref

P_env_ref =zeros(20,40)

PHE

PHE

PRO

PRO

score

end score = -log(P_env)

score_ref

score_ref = -log(P_env_ref)

Referenced by generate_disulfide_conformations().

SER

SER

smoothed_ref

smoothed_ref = conv(squeeze(env_ref(i,:)), CONV1)

t

t = dic(ii,:)

THR

THR

TRP

TRP

TYR

TYR

VAL

VAL

x

x = [1:40]

Referenced by TCDock::__dock_base__(), PyMOL-Rosetta-relay-client.Matrix::__init__(), PyMOL-RosettaServer.Matrix::__init__(), ObjexxFCL::abs(), absfpart(), Tensor::add(), add_histograms_together(), numeric::interpolation::spline::SplineGenerator::add_known_value(), addvv(), Link::align_c(), Link::align_n(), LoopHash_Analyze::apply(), CrystFFTDock::apply(), apply_rigid_body_settings(), apply_rotation(), numeric::arccos(), argmax(), benzene_pair_score_test(), numeric::interpolation::bilinearly_interpolated(), numeric::interpolation::periodic_range::full::bin(), numeric::interpolation::periodic_range::half::bin(), numeric::interpolation::Histogram< X, Y >::bin_number(), ObjexxFCL::bit::bit_and(), ObjexxFCL::bit::bit_clr(), ObjexxFCL::bit::bit_not(), ObjexxFCL::bit::bit_or(), ObjexxFCL::bit::bit_set(), ObjexxFCL::bit::bit_test(), ObjexxFCL::bit::bit_xor(), calc_prob(), numeric::interpolation::catmull_rom_interpolate_basic(), ch_o_pdbstats_from_pose(), change_floating_sc_geometry(), check_6D_potential(), check_contact_and_output(), check_cubic_conv_test(), numeric::geometry::hashing::xyzStripeHash::clash(), numeric::geometry::hashing::xyzStripeHash::clash_amount(), numeric::geometry::hashing::xyzStripeHash::clash_check_ball(), numeric::geometry::hashing::xyzStripeHash::clash_not_resid(), numeric::geometry::hashing::xyzStripeHash::clash_raw(), comp(), compute_bb_motif_score(), numeric::interpolation::spline::Interpolator::compute_lb_function_solution(), numeric::interpolation::spline::Interpolator::compute_ub_function_solution(), numeric::geometry::BoundingBox< T >::contains(), convex_hull(), utility::copysign(), correct_dunbrack(), correct_rama(), correlation_coefficient(), numeric::cot(), ObjexxFCL::cross(), ObjexxFCL::cross_product(), numeric::csc(), numeric::cube(), ObjexxFCL::cube(), numeric::cubic_polynomial_deriv(), DockFragmentsMover::cut_from_map(), numeric::statistics::Dawson(), numeric::geometry::hashing::xyzStripeHash::debug_pdb(), denom(), numeric::interpolation::Histogram< X, Y >::derivative(), numeric::interpolation::Histogram< X, Y >::derivative_linear(), numeric::interpolation::spline::BicubicSpline::dFdx(), numeric::interpolation::spline::TricubicSpline::dFdx(), numeric::interpolation::spline::BicubicSpline::dFdy(), numeric::interpolation::spline::TricubicSpline::dFdy(), numeric::interpolation::spline::TricubicSpline::dFdz(), AbsFunc::dfunc(), RepFunc::dfunc(), 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::dihedral_radians(), detail::dragonbox::divisible_by_power_of_2(), detail::dragonbox::divisible_by_power_of_5(), numeric::random::do_recursion(), dock(), TCDock::dump_pdb(), dump_pdb_atom(), dump_points_pdb(), dump_points_pdb_contacts(), TCDock::dump_top_hits(), dump_unique_atoms(), numeric::linear_algebra::epslon(), numeric::eq_tol(), ObjexxFCL::eq_tol(), numeric::model_quality::erfcc(), numeric::statistics::errf(), numeric::statistics::errfc(), numeric::statistics::errfcx(), numeric::statistics::errfi(), basic::sampling::orientations::Quaternion::euler(), numeric::eval_cubic_polynomial(), numeric::kinematic_closure::evalpoly(), numeric::expand_xforms(), numeric::interpolation::spline::BicubicSpline::F(), ObjexxFCL::format::F(), numeric::interpolation::spline::TricubicSpline::F(), numeric::FArray_to_vector_of_xyzvectors(), numeric::FastRemainderSelector< T, bool >::fast_remainder(), numeric::FastRemainderSelector< T, true >::fast_remainder(), numeric::fast_remainder(), ObjexxFCL::FastRemainderSelector< T, bool >::fast_remainder(), ObjexxFCL::FastRemainderSelector< T, true >::fast_remainder(), ObjexxFCL::fast_remainder(), numeric::interpolation::spline::BicubicSpline::FdF(), numeric::geometry::hashing::xyzStripeHash::fill_pairs(), fitfun(), for(), HelixHit::frame(), AbsFunc::func(), RepFunc::func(), numeric::ge_tol(), ObjexxFCL::ge_tol(), get_axis_angle(), get_base_coordinate_system(), get_base_pair_coordinate_system(), protocols::antibody::design::AntibodyDesignMoverGenerator::get_cdrs_movemap_with_overhang(), CrystFFTDock::get_clash_score_exact(), Arch::get_disp_dofs(), ArchP6_32::get_disp_dofs(), ArchP4_42::get_disp_dofs(), get_element_coords(), get_hbond_rotation_samples(), numeric::interpolation::spline::SplineGenerator::get_interpolator(), get_localbfacs(), get_models(), get_phosphate_stub(), get_point_groups(), get_rmsd(), get_rmsd_debug(), Bola::get_target_xform(), get_zn_axes(), grid_matcher(), zinc1_homodimer_design::gridsearch_rollmove_angles(), numeric::gt_tol(), ObjexxFCL::gt_tol(), numeric::kinematic_closure::hyper_tan(), ik_his4(), numeric::in_sin_cos_range(), numeric::random::ini_func1(), numeric::random::ini_func2(), numeric::geometry::hashing::xyzStripeHash::init(), numeric::geometry::hashing::xyzStripeHashWithMeta< T >::init(), initialize_for_grid_matcher(), InterfaceHit::InterfaceHit(), numeric::interpolation::spline::CompoundInterpolator::interpolate(), numeric::interpolation::Histogram< X, Y >::interpolate(), basic::interpolate_2d_func_of_angles(), numeric::interpolation::Histogram< X, Y >::interpolate_flat(), basic::interpolate_get_angle_bins(), numeric::interpolation::Histogram< X, Y >::interpolate_linear(), numeric::interpolation::Histogram< X, Y >::interpolate_spline(), numeric::interpolation::periodic_range::full::interpolated(), numeric::interpolation::periodic_range::half::interpolated(), numeric::interpolation::interpolated(), intersecting_bpy_axes(), intersecting_disulfide_axes(), is_small(), numeric::fourier::kf_cexp(), kono_sarai_stats(), kono_sarai_zscore(), numeric::le_tol(), ObjexxFCL::le_tol(), numeric::xyzMatrix< T >::left_multiply_by(), numeric::xyzMatrix< T >::left_multiply_by_transpose(), length2f(), lengthf(), numeric::nls::lm_enorm(), numeric::nls::lm_lmdif(), numeric::nls::lm_lmpar(), numeric::nls::lm_qrsolv(), load_coordinates_from_database(), numeric::log(), numeric::lt_tol(), ObjexxFCL::lt_tol(), main(), make_dock_olig(), VallReader::make_fragment_lines(), make_fragments(), VallReader::make_nmer_profile(), map_morph(), max(), mg_pdbstats_from_pose(), min(), min_energy(), min_mod(), Mod(), numeric::ModSelector< T, bool >::mod(), numeric::ModSelector< T, true >::mod(), numeric::mod(), ObjexxFCL::ModSelector< T, bool >::mod(), ObjexxFCL::ModSelector< T, true >::mod(), ObjexxFCL::mod(), detail::mod(), mod360(), numeric::kinematic_closure::modrf(), numeric::ModuloSelector< T, bool >::modulo(), numeric::ModuloSelector< T, true >::modulo(), numeric::modulo(), ObjexxFCL::ModuloSelector< T, bool >::modulo(), ObjexxFCL::ModuloSelector< T, true >::modulo(), ObjexxFCL::modulo(), ui::ui_protocols::helical_bundle::HelicalBundlePoseDrawOpenGLWidget::mouseMoveEvent(), native_cos(), native_recip(), native_sin(), numeric::geometry::hashing::xyzStripeHash::nbcount(), numeric::geometry::hashing::xyzStripeHashWithMeta< T >::nbcount(), numeric::geometry::hashing::xyzStripeHash::nbcount_raw(), numeric::NearestSelector< R, T, bool >::nearest(), numeric::NearestSelector< R, T, true >::nearest(), numeric::nearest(), ObjexxFCL::NearestSelector< R, T, bool >::nearest(), ObjexxFCL::NearestSelector< R, T, true >::nearest(), ObjexxFCL::nearest(), numeric::nearest_int(), ObjexxFCL::nearest_int(), numeric::nearest_size(), ObjexxFCL::nearest_size(), numeric::nearest_ssize(), ObjexxFCL::nearest_ssize(), numeric::nint(), ObjexxFCL::nint(), ObjexxFCL::nlint(), norm_degrees(), basic::sampling::orientations::Quaternion::Normalize(), ObjexxFCL::nsint(), nucleobase_probe_score_test(), octree_test(), CheeseFunction::operator()(), numeric::kdtree::CompareKDPoints::operator()(), numeric::XformHash64::operator()(), numeric::XformHash32::operator()(), detail::operator*(), numeric::xyzMatrix< T >::operator*=(), operator<(), numeric::kinematic_closure::operator<<(), detail::operator==(), numeric::deriv::p1_theta_deriv(), pca_align_BROKEN(), JDmover::periodic_range(), periodic_range(), basic::periodic_range(), basic::sampling::orientations::Permute::Permute(), pos_mod(), PoseWrap::PoseWrap(), power_set(), utility::libsvm::Svm_rosetta::predict(), utility::libsvm::Svm_rosetta::predict_probability(), basic::sampling::orientations::Quaternion::Print(), printbits16(), printbits32(), DisulfideBondEnergy::probability(), CrystFFTDock::project_along_axis(), numeric::linear_algebra::qzvec(), randomly_shift_and_tilt_pose(), randomly_shift_and_tilt_poses(), read_embeddings(), read_jumpcut_file(), read_membrane(), read_parameters(), read_patchdock_entry(), read_penalties(), numeric::read_row(), read_sphere(), PickSSE::readSSE(), numeric::RemainderSelector< T, bool >::remainder(), numeric::RemainderSelector< T, true >::remainder(), numeric::remainder(), ObjexxFCL::RemainderSelector< T, bool >::remainder(), ObjexxFCL::RemainderSelector< T, true >::remainder(), ObjexxFCL::remainder(), CrystFFTDock::resample_maps_and_get_self(), return_zero(), numeric::xyzMatrix< T >::right_multiply_by(), numeric::xyzMatrix< T >::right_multiply_by_transpose(), rna_stack_pdbstats_from_pose(), rotatePoint(), basic::sampling::orientations::Quaternion::rotation_matrix(), run(), TCDock::run(), run_pep_prep(), run_sf4h(), numeric::sec(), numeric::serialize(), boost::unordered_object_pool< T, UserAllocator >::set_next_size(), PyMOL-Rosetta-relay-client::set_spectrum(), PyMOL-RosettaServer::set_spectrum(), pyrosetta.PyMOLRosettaServer::set_spectrum(), CrystFFTDock::setup_maps(), setup_symmetric_dimer(), numeric::VoxelGrid< T >::SetupGrid(), sicdock_thread_num(), sign(), numeric::sign(), ObjexxFCL::sign(), numeric::sign_transfered(), numeric::sin_cos_range(), numeric::statistics::sinc(), numeric::statistics::sinh_taylor(), sphere_coverage(), SphereSampler::SphereSampler(), numeric::interpolation::spline::spline_interpolate(), numeric::interpolation::spline::spline_second_derivative(), numeric::interpolation::spline::BicubicSpline::sqr(), numeric::interpolation::spline::CubicSpline::sqr(), numeric::statistics::sqr(), sqr(), numeric::interpolation::spline::sqr(), numeric::square(), ObjexxFCL::CArray< T >::square(), ObjexxFCL::CArrayP< T >::square(), ObjexxFCL::ChunkVector< T >::square(), ObjexxFCL::square(), utility::string2uint(), basic::svd::SVD_Solver::svdcmp(), numeric::linear_algebra::svdcmp(), svm_predict(), svm_predict_probability(), svm_predict_values(), svm_train(), swap(), utility::sys_sleep(), test_numerical_deriv(), test_real(), detail::dragonbox::to_decimal(), InterfaceHit::to_string(), CrystFFTDock::transform_map(), CrystFFTDock::transform_map_offset0(), detail::dragonbox::umul128(), detail::dragonbox::umul128_upper64(), detail::dragonbox::umul192_middle64(), detail::dragonbox::umul192_upper64(), detail::dragonbox::umul96_lower64(), detail::dragonbox::umul96_upper32(), numeric::UniformRotationSampler::UniformRotationSampler(), basic::unsigned_periodic_range(), ui::viewers::ScoreFileView::update_ui_from_file_data(), numeric::vector_of_xyzvectors_to_FArray(), numeric::geometry::hashing::xyzStripeHashWithMeta< T >::visit(), numeric::geometry::hashing::xyzStripeHash::visit(), numeric::geometry::hashing::xyzStripeHash::visit_lax(), numeric::geometry::hashing::xyzStripeHashWithMeta< T >::visit_lax(), numeric::statistics::w(), numeric::statistics::w_im(), numeric::statistics::w_im_y100(), write_for_resnum(), AbsFunc::x0(), and numeric::deriv::x_and_dtheta_dx().

xtick

xtick

xticklabel

xticklabel

y1

y1 = score(ii,x)

Referenced by base_doublet_rmsd_test(), numeric::interpolation::bilinearly_interpolated(), numeric::BodyPosition< T >::BodyPosition(), coarse_to_full_test(), CrystFFTDock::get_transform_distance(), and numeric::alignment::QCPKernel< Real >::inner_product().

y1_ref

y1_ref = score_ref(ii,x)