gen_vdw_radius_soft.m File Reference

Functions
clean the clash	nonidcen_counts (:,:, 1:6)=0
	Nint (ndx)
	printf ("%.3f ", rvdw *rvdw)
	Pvdw (rx >rvdw)
draw the	g (r) picture h
	text (0, Nall/100000, t)
	set (h(1), "linewidth", 2) set(h(2)
end	printf ("\n")

Variables
	dic = [ "Nbb"
	CAbb
	CB
	CObb
	OCbb
	CEN_ALA
	CEN_CYS
	CEN_ASP
	CEN_GLU
	CEN_PHE
	CEN_GLY
	CEN_HIS
	CEN_ILE
	CEN_LYS
	CEN_LEU
	CEN_MET
	CEN_ASN
	CEN_PRO
	CEN_GLN
	CEN_ARG
	CEN_SER
	CEN_THR
	CEN_VAL
	CEN_TRP
	CEN_TYR
	cutoff = 0.001
for	aandx
for	ii
	r = 0.25:0.5:15
	shell = (4.0*pi*r.*r)'
	Nr = squeeze(nonidcen_counts(ii, aandx, :))
	Nint = Nr
	Pr = Nr ./ shell / 0.2
	Nall = 0
for	ndx
end	Nc = Nall*cutoff
	rm = 0:0.001:10
	sm = 4.0*pi*rm.*rm
	Nrm = interp1( r, Nint, rm, 'linear')
	Prm = interp1( r, Pr, rm, 'linear')
	p_end = Pr(50)/3
	rx = 0:0.1:10
	Px = interp1( r, Pr, rx, 'linear')
	Pvdw = exp(-(rvdw**2-rx.*rx).**2/rvdw)
	t = dic(ii,:)
	linewidth

Function Documentation

g()

draw the g

(

r

)

Referenced by SymRBMover::apply(), numeric::VoxelArray< _Float, _Value >::at(), utility::graph::RingEdgeAnnotationVisitor< Graph, EdgeMap, PathMap >::back_edge(), utility::graph::breadth_first_search_prune(), utility::graph::breadth_first_visit_prune(), utility::graph::delete_all_intragroup_edges(), deleteEdge(), utility::graph::depth_first_search_sort(), utility::graph::depth_first_visit(), utility::graph::depth_first_visit_sort_impl(), utility::graph::digraph_is_a_DAG(), do_two(), euler2rot(), utility::graph::find_connected_components(), utility::graph::RingSizeVisitor< Graph, DistanceMap, LabelMap >::gray_target(), numeric::fourier::SHT::idx_to_rot(), jacobi(), main(), output_interface_graphviz(), print_graph(), utility::tag::Tag::read(), numeric::rgb_to_hsv(), basic::svd::SVD_Solver::svdcmp(), numeric::linear_algebra::svdcmp(), utility::graph::topological_sort(), PathFinder::tree_edge(), utility::graph::RingSizeVisitor< Graph, DistanceMap, LabelMap >::tree_edge(), RerootRestypeVisitor::tree_edge(), utility::graph::RingEdgeAnnotationVisitor< Graph, EdgeMap, PathMap >::tree_edge(), and utility::graph::visit().

Nint()

Nint

(

ndx

)

nonidcen_counts()

clean the clash nonidcen_counts ( :  , :  , 1:6    )

pure virtual

printf() [1/2]

printf	(	"%.3f "	,
		rvdw *	rvdw
	)

printf() [2/2]

end printf

(

"\n"

)

Pvdw()

Pvdw	(	rx	,
		rvdw
	)

set()

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

text()

text	(	0	,
		Nall/	100000,
		t
	)

Variable Documentation

aandx

for aandx

Initial value:

= aaa
printf("%s ",dic(aandx,:))

CAbb

CAbb

CB

CB

CEN_ALA

CEN_ALA

CEN_ARG

CEN_ARG

CEN_ASN

CEN_ASN

CEN_ASP

CEN_ASP

CEN_CYS

CEN_CYS

CEN_GLN

CEN_GLN

CEN_GLU

CEN_GLU

CEN_GLY

CEN_GLY

CEN_HIS

CEN_HIS

CEN_ILE

CEN_ILE

CEN_LEU

CEN_LEU

CEN_LYS

CEN_LYS

CEN_MET

CEN_MET

CEN_PHE

CEN_PHE

CEN_PRO

CEN_PRO

CEN_SER

CEN_SER

CEN_THR

CEN_THR

CEN_TRP

CEN_TRP

CEN_TYR

CEN_TYR

CEN_VAL

CEN_VAL

CObb

CObb

cutoff

cutoff = 0.001

dic

dic = [ "Nbb"

ii

for ii

Initial value:

=1:25
  subplot(5,5,ii)

linewidth

linewidth

Nall

Nall = 0

Nc

end Nc = Nall*cutoff

ndx

for ndx

Initial value:

= 1:50
    Nall = Nall+Nr(ndx)

Nint

Nint = Nr

Nr

Nr = squeeze(nonidcen_counts(ii, aandx, :))

Nrm

Nrm = interp1( r, Nint, rm, 'linear')

OCbb

OCbb

p_end

p_end = Pr(50)/3

Referenced by numeric::kdtree::HyperRectangle::extend(), numeric::kdtree::get_percentile_bounds(), numeric::statistics::kl_divergence(), numeric::kdtree::make_points(), numeric::kdtree::transform_percentile(), and numeric::kdtree::transform_percentile_single_pt().

Pr

Pr = Nr ./ shell / 0.2

Prm

Prm = interp1( r, Pr, rm, 'linear')

Pvdw

Pvdw = exp(-(rvdw**2-rx.*rx).**2/rvdw)

Px

Px = interp1( r, Pr, rx, 'linear')

r

r = 0.25:0.5:15

rm

rm = 0:0.001:10

rx

rx = 0:0.1:10

Referenced by main(), CrystFFTDock::resample_maps_and_get_self(), CrystFFTDock::transform_map(), and CrystFFTDock::transform_map_offset0().

shell

shell = (4.0*pi*r.*r)'

sm

sm = 4.0*pi*rm.*rm

Referenced by calc_ddg(), RelaxJobQueen::complete_larval_job_maturation(), binder::generate_documentation_string_for_declaration(), header(), binder::Binder::is_in_system_header(), jacobi(), binder::line_number(), main(), binder::relevant_include(), and sicdock_thread_num().

t

t = dic(ii,:)