gen_env_dep_orient_decompose.m File Reference

Functions
end end get env	env_index (i)
	num_res_env (res_index(i), env_index(i))
	if (ai >NAA) continue end for j
	if (aj >NAA) continue end if(env_index(i)
	surf_surf_th1 (ai, aj, :, :)+
i, j, :, :	th1_table ()
	surf_core_th1 (ai, aj, :, :)+
end else	if (env_index(j)==1) %c-s core_surf_th1(ai
end else	core_surf_th1 (ai, aj, :, :)+
	core_core_th1 (ai, aj, :, :)+
id	beta ()
surf_surf_th1, NAA	pre_fill_dfire_2D ()
	surf_surf_th1 (i, j,:,:)
	surf_core_th1 (i, j,:,:)
	core_surf_th1 (i, j,:,:)
	core_core_th1 (i, j,:,:)
	if (i!=j) % surf_surf_th1(j
	surf_core_th1 (j, i,:,:)
	core_surf_th1 (j, i,:,:)
	core_core_th1 (j, i,:,:)
NAA, 30, 16	zeros ()
sum(surf_surf_th1, 2	squeeze ()
id	i: (aasurf_surf_da1(i,:,:) calc_NtoP)
	aasurf_core_da1 (i,:,:)
	aacore_surf_da1 (i,:,:)
	aacore_core_da1 (i,:,:)
	aasurf_surf_da2 (i,:,:)
	aacore_surf_da2 (i,:,:)
	aasurf_core_da2 (i,:,:)
	aacore_core_da2 (i,:,:)
end	p_a_r_ang1 (ii, kk,:)
	p_a_r_ang2 (ii, kk,:)
end	p_r_ang (kk,:)
	set (f, "visible", "off") else fp_ang
end if	exist ("iii", "var") % iii %else % iii
debug if debug	printf ("score_w(%d,%d): max=%f, min=%f\n", iii, jjj, max(max(score)), min(min(score)))
	contourf (xx, yy, score)
	print (fname, "-dpng") else fprintf(fp_ang
ANGLE1	reslist (iii,:)
ANGLE1	reslist (jjj,:))
end	fprintf (fp_ang, "\n")
end	fprintf (fp_ang, "%.6f ", score(xx, 16))
end end end if debug	printf ("Done!\n")
	set (f, "visible", "on") else fclose(fp_ang)
end debug	subplot (2, 1, 1) %[xx
	contourf (xx, yy, score_w)
	plot (1:16, p_ii_w(30,:), 1:16, squeeze(p_ii(1, 30,:)), 1:16, squeeze(aa_surf_da1(4, 30,:))/sum(squeeze(aa_surf_da1(4, 30,:))), 1:16, squeeze(aa_core_da1(4, 30,:))/sum(squeeze(aa_core_da1(4, 30,:)))) %subplot(2
plot(1:16, score(24,:),"r", 1:16, score_w(24,:),"b") %axis([1 16 -0.2 0.2]) %plot(1	contourf (xx, yy, Na1_r_surf_surf) %subplot(4
plot(1:16, score(24,:),"r", 1:16, score_w(24,:),"b") %axis([1 16 -0.2 0.2]) %plot(1	contourf (xx, yy, Na2_r_surf_surf) %subplot(4
plot(1:16, score(24,:),"r", 1:16, score_w(24,:),"b") %axis([1 16 -0.2 0.2]) %plot(1	contourf (xx, yy, Na1_r_core_surf) %subplot(4
plot(1:16, score(24,:),"r", 1:16, score_w(24,:),"b") %axis([1 16 -0.2 0.2]) %plot(1	contourf (xx, yy, Na2_r_surf_core) %subplot(4
plot(1:16, score(24,:),"r", 1:16, score_w(24,:),"b") %axis([1 16 -0.2 0.2]) %plot(1	contourf (xx, yy, Na1_r_surf_core) %subplot(4
plot(1:16, score(24,:),"r", 1:16, score_w(24,:),"b") %axis([1 16 -0.2 0.2]) %plot(1	contourf (xx, yy, Na2_r_core_surf) %subplot(4
plot(1:16, score(24,:),"r", 1:16, score_w(24,:),"b") %axis([1 16 -0.2 0.2]) %plot(1	contourf (xx, yy, Na1_r_core_core) %subplot(4

Variables
	debug = 0
	reslist
	CYS
	ASP
	GLU
	PHE
	TRP
	HIS
	ILE
	LYS
	LEU
	MET
	ASN
	VAL
	GLN
	ARG
	SER
	THR
	PRO
	ALA
	GLY
should not contain ALA GLY PRO	NAA = 17
	Rcut = 12
	Bcut = 24
buildlist	res_index = zeros(40,1)
	env_index = zeros(40,1)
	num_res_env = zeros(NAA,2)
for	i
	break
end split	surf_surf_th1 =zeros(NAA,NAA,30,16)
	surf_core_th1 =zeros(NAA,NAA,30,16)
	core_surf_th1 =zeros(NAA,NAA,30,16)
	core_core_th1 =zeros(NAA,NAA,30,16)
end else	aj
end else	j
	smoothed = smooth_2D(surf_core_th1(i,j,:,:), [15, 0.1, 2], [360, 40, 2])
	__pad0__
	__pad1__
	__pad2__
	__pad3__
end end end sum symm	aasurf_surf_da1 =zeros(NAA,30,16)
	aacore_surf_da1 =squeeze(sum(core_surf_th1,2))
	aasurf_core_da1 =squeeze(sum(surf_core_th1,2))
	aacore_core_da1 =squeeze(sum(core_core_th1,2))
	aasurf_surf_da2 =squeeze(sum(surf_surf_th1))
	aacore_surf_da2 =squeeze(sum(surf_core_th1))
	aasurf_core_da2 =squeeze(sum(core_surf_th1))
	aacore_core_da2 =squeeze(sum(core_core_th1))
	Na1_r_surf_surf = squeeze(sum(aasurf_surf_da1))
	Na1_r_surf_core = squeeze(sum(aasurf_core_da1))
	Na1_r_core_surf = squeeze(sum(aacore_surf_da1))
	Na1_r_core_core = squeeze(sum(aacore_core_da1))
	Na2_r_surf_surf = squeeze(sum(aasurf_surf_da2))
	Na2_r_surf_core = squeeze(sum(aasurf_core_da2))
	Na2_r_core_surf = squeeze(sum(aacore_surf_da2))
	Na2_r_core_core = squeeze(sum(aacore_core_da2))
	aa_aa_th1 = (surf_surf_th1 + surf_core_th1 + core_surf_th1 + core_core_th1)
NAAaa to NAAaa cal	ntype = NAA
	dat_a_a_r_ang = aa_aa_th1
old way	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)
for	kk
end shift	shift = zeros(30,16)
end debug if debug	f = figure()
	wj = num_res_env(jjj,1)/sum(num_res_env(jjj,:))
	p_ii_jj = squeeze(p_a_a_r_ang( iii, jjj, :, : ))
	p_ii = p_a_r_ang1(iii, :, :)
	p_ii_w = calc_Pi_ang_sc(aasurf_surf_da1(iii,:,:), aasurf_core_da1(iii,:,:), aacore_surf_da1(iii,:,:), aacore_core_da1(iii,:,:), wi, wj)
	p_jj = p_a_r_ang2(jjj, :, :)
	p_jj_w = calc_Pi_ang_sc(aasurf_surf_da2(jjj,:,:), aasurf_core_da2(jjj,:,:), aacore_surf_da2(jjj,:,:), aacore_core_da2(jjj,:,:), wj, wi)
	p_ii_p_jj = squeeze(p_ii .* p_jj)
	p_ii_p_jj_w = squeeze(p_ii_w .* p_jj_w)
	p = (p_ii_jj .* p_r_ang) ./ (p_ii_p_jj)
	p_r_ang_w = calc_Pi_ang_sc(Na1_r_surf_surf, Na1_r_surf_core, Na1_r_core_surf, Na1_r_core_core, wi, wj)
	p_w = (p_ii_jj .* p_r_ang_w + shift) ./ (p_ii_p_jj_w + shift)
	score = -log(p)
	score_w = -log(p_w)
	fname = [ "score_", int2str(iii), "_", int2str(jjj), ".png" ]
ANGLE1	__pad4__
for	yy
for	xx

Function Documentation

aacore_core_da1()

aacore_core_da1	(	i	,
		:	,
		:
	)

aacore_core_da2()

aacore_core_da2	(	i	,
		:	,
		:
	)

aacore_surf_da1()

aacore_surf_da1	(	i	,
		:	,
		:
	)

aacore_surf_da2()

aacore_surf_da2	(	i	,
		:	,
		:
	)

aasurf_core_da1()

aasurf_core_da1	(	i	,
		:	,
		:
	)

aasurf_core_da2()

aasurf_core_da2	(	i	,
		:	,
		:
	)

aasurf_surf_da2()

aasurf_surf_da2	(	i	,
		:	,
		:
	)

beta()

id beta ( )

virtual

contourf() [1/9]

plot (1:16,score(24,:),"r",1:16,score_w(24,:),"b") %axis([1 16 -0.2 0.2]) %plot(1 contourf	(	xx	,
		yy	,
		Na1_r_core_core
	)

contourf() [2/9]

plot (1:16,score(24,:),"r",1:16,score_w(24,:),"b") %axis([1 16 -0.2 0.2]) %plot(1 contourf	(	xx	,
		yy	,
		Na1_r_core_surf
	)

contourf() [3/9]

plot (1:16,score(24,:),"r",1:16,score_w(24,:),"b") %axis([1 16 -0.2 0.2]) %plot(1 contourf	(	xx	,
		yy	,
		Na1_r_surf_core
	)

contourf() [4/9]

plot (1:16,score(24,:),"r",1:16,score_w(24,:),"b") %axis([1 16 -0.2 0.2]) %plot(1 contourf	(	xx	,
		yy	,
		Na1_r_surf_surf
	)

contourf() [5/9]

plot (1:16,score(24,:),"r",1:16,score_w(24,:),"b") %axis([1 16 -0.2 0.2]) %plot(1 contourf	(	xx	,
		yy	,
		Na2_r_core_surf
	)

contourf() [6/9]

plot (1:16,score(24,:),"r",1:16,score_w(24,:),"b") %axis([1 16 -0.2 0.2]) %plot(1 contourf	(	xx	,
		yy	,
		Na2_r_surf_core
	)

contourf() [7/9]

plot (1:16,score(24,:),"r",1:16,score_w(24,:),"b") %axis([1 16 -0.2 0.2]) %plot(1 contourf	(	xx	,
		yy	,
		Na2_r_surf_surf
	)

contourf() [8/9]

contourf	(	xx	,
		yy	,
		score
	)

contourf() [9/9]

contourf	(	xx	,
		yy	,
		score_w
	)

core_core_th1() [1/3]

core_core_th1	(	ai	,
		aj	,
		:	,
		:
	)

core_core_th1() [2/3]

core_core_th1	(	i	,
		j	,
		:	,
		:
	)

core_core_th1() [3/3]

core_core_th1	(	j	,
		i	,
		:	,
		:
	)

core_surf_th1() [1/3]

end else core_surf_th1	(	ai	,
		aj	,
		:	,
		:
	)

core_surf_th1() [2/3]

core_surf_th1	(	i	,
		j	,
		:	,
		:
	)

core_surf_th1() [3/3]

core_surf_th1	(	j	,
		i	,
		:	,
		:
	)

env_index()

end end get env env_index

(

i

)

exist()

end if exist	(	"iii"	,
		"var"
	)

fprintf() [1/2]

end fprintf	(	fp_ang	,
		"%.6f "	,
		score(xx, 16)
	)

fprintf() [2/2]

end fprintf	(	fp_ang	,
		"\n"
	)

i:()

id i: ( aasurf_surf_da1(i,:,:)  calc_NtoP )

virtual

if() [1/4]

if	(	ai	,
		NAA
	)

if() [2/4]

if	(	aj	,
		NAA
	)

if() [3/4]

end else if

(

env_index(j)

= =1

)

if() [4/4]

if

(

i!

= j

)

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	,
		:
	)

plot()

plot	(	1:16	,
		p_ii_w(30,:)	,
		1:16	,
		squeeze(p_ii(1, 30,:))	,
		1:16	,
		squeeze(aa_surf_da1(4, 30,:))/sum(squeeze(aa_surf_da1(4, 30,:)))	,
		1:16	,
		squeeze(aa_core_da1(4, 30,:))/sum(squeeze(aa_core_da1(4, 30,:)))
	)

pre_fill_dfire_2D()

core_core_th1 NAA pre_fill_dfire_2D ( )

staticvirtual

print()

print	(	fname	,
		"-dpng"
	)

printf() [1/2]

end end end if debug printf

(

"Done!\n"

)

printf() [2/2]

debug if debug printf

(

"score_w(%d,%d):

max = %f

)

reslist() [1/2]

ANGLE1 reslist	(	iii	,
		:
	)

reslist() [2/2]

ANGLE1 reslist	(	jjj	,
		:
	)

set() [1/2]

set	(	f	,
		"visible"	,
		"off"
	)

set() [2/2]

set	(	f	,
		"visible"	,
		"on"
	)

squeeze()

sum(surf_surf_th1,2 squeeze ( )

virtual

subplot()

end debug subplot	(	2	,
		1	,
		1
	)

surf_core_th1() [1/3]

surf_core_th1	(	ai	,
		aj	,
		:	,
		:
	)

surf_core_th1() [2/3]

surf_core_th1	(	i	,
		j	,
		:	,
		:
	)

surf_core_th1() [3/3]

surf_core_th1	(	j	,
		i	,
		:	,
		:
	)

surf_surf_th1() [1/2]

surf_surf_th1	(	ai	,
		aj	,
		:	,
		:
	)

surf_surf_th1() [2/2]

surf_surf_th1	(	i	,
		j	,
		:	,
		:
	)

th1_table()

i, j, :, : th1_table ( )

virtual

zeros()

NAA,30,16 zeros ( )

virtual

Variable Documentation

__pad0__

__pad0__

__pad1__

__pad1__

__pad2__

__pad2__

__pad3__

__pad3__

__pad4__

ANGLE1 __pad4__

aa_aa_th1

aa_aa_th1 = (surf_surf_th1 + surf_core_th1 + core_surf_th1 + core_core_th1)

aacore_core_da1

aacore_core_da1 =squeeze(sum(core_core_th1,2))

aacore_core_da2

aacore_core_da2 =squeeze(sum(core_core_th1))

aacore_surf_da1

aacore_surf_da1 =squeeze(sum(core_surf_th1,2))

aacore_surf_da2

aacore_surf_da2 =squeeze(sum(surf_core_th1))

aasurf_core_da1

aasurf_core_da1 =squeeze(sum(surf_core_th1,2))

aasurf_core_da2

aasurf_core_da2 =squeeze(sum(core_surf_th1))

aasurf_surf_da1

end end end sum symm aasurf_surf_da1 =zeros(NAA,30,16)

aasurf_surf_da2

aasurf_surf_da2 =squeeze(sum(surf_surf_th1))

aj

end else aj

ALA

ALA

ARG

ARG

ASN

ASN

ASP

ASP

Bcut

Bcut = 24

break

break

core_core_th1

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

core_surf_th1

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

CYS

CYS

dat_a_a_r_ang

dat_a_a_r_ang = aa_aa_th1

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_r_ang

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

debug

debug = 0

env_index

env_index = zeros(40,1)

f

end debug if debug f = figure()

fname

fname = [ "score_", int2str(iii), "_", int2str(jjj), ".png" ]

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

j

kk

for kk

Initial value:

= 1:30
  for ii = 1:ntype
    for jj = 1:ntype
      p_a_a_r_ang(ii,jj,kk,:) = dat_a_a_r_ang(ii,jj,kk,:) / sum_a_a_r(ii,jj,kk)

LEU

LEU

LYS

LYS

MET

MET

Na1_r_core_core

Na1_r_core_core = squeeze(sum(aacore_core_da1))

Na1_r_core_surf

Na1_r_core_surf = squeeze(sum(aacore_surf_da1))

Na1_r_surf_core

Na1_r_surf_core = squeeze(sum(aasurf_core_da1))

Na1_r_surf_surf

end Na1_r_surf_surf = squeeze(sum(aasurf_surf_da1))

Na2_r_core_core

Na2_r_core_core = squeeze(sum(aacore_core_da2))

Na2_r_core_surf

Na2_r_core_surf = squeeze(sum(aacore_surf_da2))

Na2_r_surf_core

Na2_r_surf_core = squeeze(sum(aasurf_core_da2))

Na2_r_surf_surf

Na2_r_surf_surf = squeeze(sum(aasurf_surf_da2))

NAA

should not contain ALA GLY PRO NAA = 17

ntype

NAAaa to NAAaa cal ntype = NAA

num_res_env

num_res_env = zeros(NAA,2)

p

p = (p_ii_jj .* p_r_ang) ./ (p_ii_p_jj)

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_ii

p_ii = p_a_r_ang1(iii, :, :)

p_ii_jj

p_ii_jj = squeeze(p_a_a_r_ang( iii, jjj, :, : ))

p_ii_p_jj

p_ii_p_jj = squeeze(p_ii .* p_jj)

p_ii_p_jj_w

p_ii_p_jj_w = squeeze(p_ii_w .* p_jj_w)

p_ii_w

p_ii_w = calc_Pi_ang_sc(aasurf_surf_da1(iii,:,:), aasurf_core_da1(iii,:,:), aacore_surf_da1(iii,:,:), aacore_core_da1(iii,:,:), wi, wj)

p_jj

p_jj = p_a_r_ang2(jjj, :, :)

p_jj_w

p_jj_w = calc_Pi_ang_sc(aasurf_surf_da2(jjj,:,:), aasurf_core_da2(jjj,:,:), aacore_surf_da2(jjj,:,:), aacore_core_da2(jjj,:,:), wj, wi)

p_r_ang

p_r_ang = zeros(30, 16)

p_r_ang_w

p_r_ang_w = calc_Pi_ang_sc(Na1_r_surf_surf, Na1_r_surf_core, Na1_r_core_surf, Na1_r_core_core, wi, wj)

p_w

p_w = (p_ii_jj .* p_r_ang_w + shift) ./ (p_ii_p_jj_w + shift)

PHE

PHE

PRO

PRO

Rcut

Rcut = 12

res_index

buildlist res_index = zeros(40,1)

reslist

reslist

Initial value:

= 

score

score = -log(p)

score_w

score_w = -log(p_w)

SER

SER

shift

end shift shift = zeros(30,16)

smoothed

smoothed = smooth_2D(surf_core_th1(i,j,:,:), [15, 0.1, 2], [360, 40, 2])

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

old way 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_th1

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

surf_surf_th1

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

THR

THR

TRP

TRP

VAL

VAL

wj

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

xx

for xx

Initial value:

=1:Bcut
    fprintf(fp_ang, "%.6f ", score(xx,1))

yy

end debug yy

Initial value:

=1:18
    fprintf(fp_ang, "%.6f ", 0)