gen_env_dep_orient_draw.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)
	surf_surf_th2 (ai, aj, :, :)+
i, j, :, :	th1_table ()
	surf_core_th2 (ai, aj, :, :)+
end else	if (env_index(j)==1) %c-s core_surf_th1(ai
end else	core_surf_th2 (ai, aj, :, :)+
	core_core_th2 (ai, aj, :, :)+
surf_surf_th2(:, i,:,:	squeeze ()
end don t smooth with zero	dat_a_a_r_ang (aa, bb,:,:)
	dat_a_a_r_ang (aa, bb, cc:30,:)
end	p_a_r_ang1 (ii, kk,:)
	p_a_r_ang2 (ii, kk,:)
end	p_r_ang (kk,:)
	aa_surf_p_r_ang (kk,:)
	aa_core_p_r_ang (kk,:)
	surf_surf_p_r_ang (kk,:)
	surf_core_p_r_ang (kk,:)
	core_surf_p_r_ang (kk,:)
	core_core_p_r_ang (kk,:)
	contourf (xx, yy, score)

Variables
	reslist
	CYS
	ASP
	GLU
	PHE
	GLY
	HIS
	ILE
	LYS
	LEU
	MET
	ASN
	PRO
	GLN
	ARG
	SER
	THR
	VAL
	TRP
	TYR
buildlist	res_index = zeros(40,1)
	env_index = zeros(40,1)
	num_res_env = zeros(20,2)
for	i
	break
end split	surf_surf_th1 =zeros(20,20,30,16)
	surf_core_th1 =zeros(20,20,30,16)
	core_surf_th1 =zeros(20,20,30,16)
	core_core_th1 =zeros(20,20,30,16)
	surf_surf_th2 =zeros(20,20,30,16)
	surf_core_th2 =zeros(20,20,30,16)
	core_surf_th2 =zeros(20,20,30,16)
	core_core_th2 =zeros(20,20,30,16)
for	j
end else	aj
end end end end smooth sum	aa_surf =zeros(20,30,16)
	aa_core =zeros(20,30,16)
	surf_surf =zeros(20,30,16)
	surf_core =zeros(20,30,16)
	core_surf =zeros(20,30,16)
	core_core =zeros(20,30,16)
end	aa_aa_th1 = (surf_surf_th1 + surf_core_th1 + core_surf_th1 + core_core_th1)+0.1
to	aa_aa_th2 = (surf_surf_th2 + surf_core_th2 + core_surf_th2 + core_core_th2)+0.1
to cal	ntype = 20
	dat_ang = aa_aa_th1
	dat_a_a_r_ang = zeros(ntype, ntype, 30, 16)
for	aa
for	kk
end end	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)
	aa_surf_dat_r_ang = squeeze(sum(aa_surf))
	aa_core_dat_r_ang = squeeze(sum(aa_core))
	surf_surf_dat_r_ang = squeeze(sum(surf_surf))
	surf_core_dat_r_ang = squeeze(sum(surf_core))
	core_surf_dat_r_ang = squeeze(sum(core_surf))
	core_core_dat_r_ang = squeeze(sum(core_core))
	aa_surf_sum_r = sum(aa_surf_dat_r_ang, 2)
	aa_core_sum_r = sum(aa_core_dat_r_ang, 2)
	surf_surf_sum_r = sum(surf_surf_dat_r_ang, 2)
	surf_core_sum_r = sum(surf_core_dat_r_ang, 2)
	core_surf_sum_r = sum(core_surf_dat_r_ang, 2)
	core_core_sum_r = sum(core_core_dat_r_ang, 2)
	aa_surf_p_r_ang = zeros(30,16)
	aa_core_p_r_ang = zeros(30,16)
	surf_surf_p_r_ang = zeros(30,16)
	surf_core_p_r_ang = zeros(30,16)
	core_surf_p_r_ang = zeros(30,16)
	core_core_p_r_ang = zeros(30,16)
	end [xx, yy] = meshgrid(1:16, 1:30)
	SS = smooth_2D(surf_surf_p_r_ang, [15,1,2], [2,0.1,2])
	SC = smooth_2D(surf_core_p_r_ang, [15,1,2], [2,0.1,2])
	CS = smooth_2D(core_surf_p_r_ang, [15,1,2], [2,0.1,2])
	CC = smooth_2D(core_core_p_r_ang, [15,1,2], [2,0.1,2])

Function Documentation

aa_core_p_r_ang()

aa_core_p_r_ang	(	kk	,
		:
	)

aa_surf_p_r_ang()

aa_surf_p_r_ang	(	kk	,
		:
	)

contourf()

contourf	(	xx	,
		yy	,
		score
	)

core_core_p_r_ang()

core_core_p_r_ang	(	kk	,
		:
	)

core_core_th2()

core_core_th2	(	ai	,
		aj	,
		:	,
		:
	)

core_surf_p_r_ang()

core_surf_p_r_ang	(	kk	,
		:
	)

core_surf_th2()

end else core_surf_th2	(	ai	,
		aj	,
		:	,
		:
	)

dat_a_a_r_ang() [1/2]

dat_a_a_r_ang	(	aa	,
		bb	,
		cc:30	,
		:
	)

dat_a_a_r_ang() [2/2]

end don t smooth with zero dat_a_a_r_ang	(	aa	,
		bb	,
		:	,
		:
	)

env_index()

end end get env env_index

(

i

)

if() [1/2]

if

(

env_index(i)

= =1

)

if() [2/2]

end else if

(

env_index(j)

= =1

)

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	,
		:
	)

squeeze()

surf_surf_th2(:,i,:,: squeeze ( )

staticvirtual

surf_core_p_r_ang()

surf_core_p_r_ang	(	kk	,
		:
	)

surf_core_th2()

surf_core_th2	(	ai	,
		aj	,
		:	,
		:
	)

surf_surf_p_r_ang()

surf_surf_p_r_ang	(	kk	,
		:
	)

surf_surf_th2()

surf_surf_th2	(	ai	,
		aj	,
		:	,
		:
	)

th1_table()

i, j, :, : th1_table ( )

virtual

Referenced by my_main().

Variable Documentation

aa

for aa

Initial value:

= 1:ntype
  for bb = 1:ntype
    dat_ang(aa,bb,:,:) += aa_aa_th2(bb,aa,:,:)

aa_aa_th1

end aa_aa_th1 = (surf_surf_th1 + surf_core_th1 + core_surf_th1 + core_core_th1)+0.1

aa_aa_th2

to aa_aa_th2 = (surf_surf_th2 + surf_core_th2 + core_surf_th2 + core_core_th2)+0.1

aa_core

aa_core =zeros(20,30,16)

aa_core_dat_r_ang

aa_core_dat_r_ang = squeeze(sum(aa_core))

aa_core_p_r_ang

aa_core_p_r_ang = zeros(30,16)

aa_core_sum_r

aa_core_sum_r = sum(aa_core_dat_r_ang, 2)

aa_surf

end end end end smooth sum aa_surf =zeros(20,30,16)

aa_surf_dat_r_ang

aa_surf_dat_r_ang = squeeze(sum(aa_surf))

aa_surf_p_r_ang

aa_surf_p_r_ang = zeros(30,16)

aa_surf_sum_r

aa_surf_sum_r = sum(aa_surf_dat_r_ang, 2)

aj

end else aj

ARG

ARG

ASN

ASN

ASP

ASP

break

break

CC

CC = smooth_2D(core_core_p_r_ang, [15,1,2], [2,0.1,2])

core_core

core_core =zeros(20,30,16)

core_core_dat_r_ang

core_core_dat_r_ang = squeeze(sum(core_core))

core_core_p_r_ang

core_core_p_r_ang = zeros(30,16)

core_core_sum_r

core_core_sum_r = sum(core_core_dat_r_ang, 2)

core_core_th1

core_core_th1 =zeros(20,20,30,16)

core_core_th2

core_core_th2 =zeros(20,20,30,16)

core_surf

core_surf =zeros(20,30,16)

core_surf_dat_r_ang

core_surf_dat_r_ang = squeeze(sum(core_surf))

core_surf_p_r_ang

core_surf_p_r_ang = zeros(30,16)

core_surf_sum_r

core_surf_sum_r = sum(core_surf_dat_r_ang, 2)

core_surf_th1

core_surf_th1 =zeros(20,20,30,16)

core_surf_th2

core_surf_th2 =zeros(20,20,30,16)

CS

CS = smooth_2D(core_surf_p_r_ang, [15,1,2], [2,0.1,2])

CYS

CYS

dat_a_a_r_ang

dat_a_a_r_ang = zeros(ntype, ntype, 30, 16)

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_ang

dat_ang = aa_aa_th1

dat_r_ang

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

end

end[xx, yy] = meshgrid(1:16, 1:30)

Referenced by PoseWrap::add_apcs_local(), utility::json_spirit::add_esc_chars(), apps::public1::scenarios::chemically_conjugated_docking::add_extra_bodies(), utility::json_spirit::add_posn_iter_and_read_range_or_throw(), PoseWrap::align_orig_pose(), detail::buffer< T >::append(), utility::vectorL< L, T, A >::append(), utility::vectorL< L, bool, A >::append(), utility::json_spirit::append_esc_char_and_incr_iter(), zinc_helix_cap::apply(), xtal_water_bunsat::apply(), LocalRmsd::apply(), DeleteSegments::apply(), FloppyTailMover::apply(), MPFindInterfaceTestMover::apply(), apply_filter_base_stack_direction(), base_name(), benzene_pair_score_test(), bind_std_array(), bind_std_forward_list(), bind_std_stl_vector(), bind_std_stl_vector_1(), bind_T20_template_variadic(), blosum_score_alignment(), bunsats(), calc_dgaps(), calc_scores(), cartesian_product(), utility::options::OptionCollection::check_specs(), utility::options::OptionCollection::check_values(), ClashCheck::clash_check(), MatchSet::clash_check(), cleanup_dna_chains(), compare_chi1_2_angles(), compare_residues_and_chi1_2_angles(), utility::vectorL< L, T, A >::contains(), detail::copy(), detail::copy_str(), ChallengeMover::count_alignment(), count_backbone_atoms(), delete_protein_from_pose(), delete_RNA_from_pose(), DeleteSegments::DeleteSegments(), numeric::interpolation::spline::CubicSpline::dF(), dna_motif_matcher(), formatter< std::chrono::duration< Rep, Period >, Char >::do_parse(), protocols::abinitio::JumpSpecificAbrelax::do_rerun(), dock(), DomainDescription::DomainDescription(), TCDock::dump_pdb(), expand_chi_for_silent_structs(), extract_pdbs_test(), numeric::interpolation::spline::CubicSpline::F(), utility::file::file_size(), basic::sampling::orientations::QuaternionGridManager::fill_metadata(), find_clusters(), utility::graph::Node::find_edge(), utility::graph::DirectedNode::find_edge_from(), utility::graph::DirectedNode::find_edge_to(), utility::options::OptionCollection::find_key_cl(), HbondZinc::find_neighbors(), HbondZincBackbone::find_neighbors(), basic_printf_context< OutputIt, Char >::format(), formatter< std::chrono::duration< Rep, Period >, Char >::format(), formatter< T, Char, enable_if_t< fmt::is_range< T, Char >::value &&(has_formatter< detail::value_type< T >, format_context >::value||detail::has_fallback_formatter< detail::value_type< T >, format_context >::value) > >::format(), detail::format_decimal(), detail::format_uint(), ga_main(), get_disulfides_from_aln(), get_filename(), get_helix_axis(), get_helix_center(), utility::json_spirit::get_str(), utility::json_spirit::get_str_(), numeric::VoxelGrid< T >::GetNeighborsMultiDimensional(), harvest_scores(), utility::vectorL< L, bool, A >::has_value(), utility::vector1< T, A >::has_value(), numeric::VoxelGrid< T >::HasNeighborsMultiDimensional(), utility::vector1< bool, A >::index(), utility::vector1< T, A >::index(), utility::vectorL< L, T, A >::index_of(), UBQ_E2Mover::init_on_new_input(), UBQ_GTPase_disulfide_Mover::init_on_new_input(), FloppyTailMover::init_on_new_input(), input_coordCstsMapped(), numeric::geometry::hashing::SixDOffsetTree::insert(), protocols::abinitio::JumpSpecificAbrelax::insert_template_frags(), numeric::IntervalSet< T >::IntervalSet(), binder::Config::is_function_binding_requested(), binder::Config::is_function_skipping_requested(), join(), load_coordinates_from_database(), main(), make_frag_set(), mean(), measure_sequence_recovery(), numeric::kinematic_closure::modp(), MSA_design(), my_main(), utility::json_spirit::Semantic_actions< Value_type, Iter_type >::new_false(), utility::json_spirit::Semantic_actions< Value_type, Iter_type >::new_name(), utility::json_spirit::Semantic_actions< Value_type, Iter_type >::new_null(), utility::json_spirit::Semantic_actions< Value_type, Iter_type >::new_str(), utility::json_spirit::Semantic_actions< Value_type, Iter_type >::new_true(), detail::format_handler< OutputIt, Char, Context >::on_format_specs(), detail::part_counter< Char >::on_format_specs(), detail::format_string_compiler< Char, PartHandler >::on_format_specs(), detail::part_counter< Char >::on_text(), detail::format_string_compiler< Char, PartHandler >::on_text(), detail::format_handler< OutputIt, Char, Context >::on_text(), detail::chrono_formatter< FormatContext, OutputIt, Rep, Period >::on_text(), SleepForATenthOfASecond::operator()(), detail::iterator_buffer< T *, T >::out(), apps::public1::scenarios::chemically_conjugated_docking::pack_extra_bodies(), formatter< std::tm, Char >::parse(), detail::parse_align(), detail::parse_arg_id(), detail::parse_chrono_format(), basic_printf_context< OutputIt, Char >::parse_flags(), detail::parse_format_specs(), detail::parse_format_string(), basic_printf_context< OutputIt, Char >::parse_header(), detail::parse_nonnegative_int(), detail::parse_precision(), detail::parse_replacement_field(), detail::parse_width(), protocols::jd2::RECONMPIJobDistributor::pick_consensus_AA(), utility::vectorL< L, T, A >::pop(), poses_from_cmd_line(), poses_from_cmd_line_noPDBtag(), PoseWrap::PoseWrap(), prepare_full_length_start_model(), print_internal_coord_test(), print_seq_map(), PrintSequenceMover::print_seqs(), SuperDeviationMover::print_stats(), process_for_motifs(), process_ss_str(), processChildren(), processChildrenIntensification(), numeric::IntervalSet< T >::push_back(), utility::tag::Tag::read(), read_list_pose_range(), read_master_pose_range(), utility::json_spirit::read_range(), utility::json_spirit::read_range_or_throw(), utility::replace_environment_variables(), numeric::random::reservoir_sample(), detail::reset_color(), reverse_doublet_test(), utility::graph::RingSizeVisitor< Graph, DistanceMap, LabelMap >::RingSizeVisitor(), rna_fullatom_minimize_silent_test(), rna_lores_score_silent_test(), rot_pose(), run_pep_prep(), sasa_bunsats(), CapriTotalEnergy::score_experimental_constraints(), sd(), sequence_tolerance_main(), sequence_tolerance_mf_main(), sequences_from_cmd_line(), numeric::IntervalSet< T >::set(), protocols::abinitio::JumpSpecificAbrelax::setup(), PDB_IOBenchmark::setUp(), protocols::abinitio::JumpSpecificAbrelax::setup_fold(), BBG_Cyclic_Mover::setup_locker(), setup_rhiju_fold_tree(), utility::options::OptionCollection::show_all(), utility::options::OptionCollection::show_all_hier(), utility::options::OptionCollection::show_help(), utility::options::OptionCollection::show_help_hier(), utility::options::OptionCollection::show_inaccessed_user_options(), utility::options::OptionCollection::show_table_text(), utility::options::OptionCollection::show_table_Wiki(), utility::options::OptionCollection::show_user(), sicdock_thread_num(), detail::snprintf_float(), split_silent_file_data(), DomainDescription::ss_match(), utility::strip(), utility::json_spirit::substitute_esc_chars(), superimpose_via_alignment(), svm_binary_svc_probability(), svm_cross_validation(), basic::database::schema_generator::Schema::table_schema_statements(), myspace::GraftTester::test_rb_min_graft(), numeric::kdtree::KDPoint::to_string(), trans_pose(), binder::trim(), detail::utf8_to_utf16::utf8_to_utf16(), detail::cf::vformat_to(), vsasa_bunsats(), XMLprinterMover::write_output_file(), and detail::write_significand().

env_index

env_index = zeros(40,1)

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

Initial value:

= 1:40
    aj = res_index(j)

kk

for kk

Initial value:

= 1:30
      dat_ang(aa,bb,kk,:) = squeeze(dat_ang(aa,bb,kk,:))

LEU

LEU

LYS

LYS

MET

MET

ntype

to cal ntype = 20

num_res_env

num_res_env = zeros(20,2)

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_r_ang

p_r_ang = zeros(30, 16)

PHE

PHE

PRO

PRO

res_index

buildlist res_index = zeros(40,1)

reslist

reslist

Initial value:

= 

SC

SC = smooth_2D(surf_core_p_r_ang, [15,1,2], [2,0.1,2])

SER

SER

SS

SS = smooth_2D(surf_surf_p_r_ang, [15,1,2], [2,0.1,2])

Referenced by basic::options::int2afteroption(), basic::options::intafteroption(), main(), make_rand_ss(), basic::options::optional_positive_intafteroption(), basic::options::real2afteroption(), basic::options::real3afteroption(), and basic::options::realafteroption().

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

end end 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

surf_core =zeros(20,30,16)

surf_core_dat_r_ang

surf_core_dat_r_ang = squeeze(sum(surf_core))

surf_core_p_r_ang

surf_core_p_r_ang = zeros(30,16)

surf_core_sum_r

surf_core_sum_r = sum(surf_core_dat_r_ang, 2)

surf_core_th1

surf_core_th1 =zeros(20,20,30,16)

surf_core_th2

surf_core_th2 =zeros(20,20,30,16)

surf_surf

surf_surf =zeros(20,30,16)

surf_surf_dat_r_ang

surf_surf_dat_r_ang = squeeze(sum(surf_surf))

surf_surf_p_r_ang

surf_surf_p_r_ang = zeros(30,16)

surf_surf_sum_r

surf_surf_sum_r = sum(surf_surf_dat_r_ang, 2)

surf_surf_th1

end split surf_surf_th1 =zeros(20,20,30,16)

surf_surf_th2

surf_surf_th2 =zeros(20,20,30,16)

THR

THR

TRP

TRP

TYR

TYR

VAL

VAL