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)

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

)

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	,
		:
	)

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)

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

num_res_env

num_res_env = zeros(20,2)

P

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

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