gen_env_dep_pair_decompose.m File Reference

Functions
20, 2	zeros ()
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
id	beta ()
surf_surf	pre_fill_dfire ()
	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,:)
	N (ai, r)
	N (r)
	P (r)
	N (aa)
id	i: (i Sum_r_surf_surf)
	sr_surf_core (i,:)/
	sr_core_surf (i,:)/
	sr_core_core (i,:)/
cal i j if	exist ("ii", "var") % ii %else % ii
	score (1:cutoff)=0
	score_w (1:cutoff)=0
	score_w2 (1:cutoff)=0
	score_w3 (1:cutoff)=0
end	score_w2 (25:30)=0
draw	subplot (4, 5, jj)
	axis ([0 25 -1.5 1]) %set(h(2)
	set (h(3), "linewidth", 2) %t
	text (2, score(10), t)
	fprintf (fp_pair, "PAIR: %s %s ", reslist(ii,:), reslist(jj,:))
	fprintf (fp_pair, "%.2f %.2f ", 0.25, 0.25+(range *2-1) *0.5)
	fprintf (fp_pair, "%d ", length(y2))
end	fprintf (fp_pair, "\n")
end end	fprintf (fp_pair, "# END\n")
	fclose (fp_pair)

Variables
	cutoff =2
	range =12
	reslist
	CYS
	ASP
	GLU
	PHE
	GLY
	HIS
	ILE
	LYS
	LEU
	MET
	ASN
	PRO
	GLN
	ARG
	SER
	THR
	VAL
	TRP
	TYR
mark each table column row	res_index = zeros(40,1)
residue index	env_index = zeros(40,1)
env	__pad0__
residue number for surf &core for	i
	break
end split x4	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
smooth data	L =5
	CONV1 = gausswin(2*L+1, 4)
	smoothed = conv(squeeze(surf_core(i,j,:)), CONV1)
	__pad1__
	__pad2__
end end end sum	aa_aa = (surf_surf+surf_core+core_surf+core_core)
to	pair_counts_symm = aa_aa
init	pair_sums_aan = squeeze(sum(pair_counts_symm))
	N
	sr_surf_core = squeeze(sum(surf_core, 2))
	sr_core_surf = squeeze(sum(core_surf, 2))
	sr_core_core = squeeze(sum(core_core, 2))
	Sum_r_surf_surf = squeeze(sum(sr_surf_surf,2))
	Sum_r_surf_core = squeeze(sum(sr_surf_core,2))
	Sum_r_core_surf = squeeze(sum(sr_core_surf,2))
	Sum_r_core_core = squeeze(sum(sr_core_core,2))
	Nr_surf_surf = sum(sr_surf_surf)
	Nr_core_surf = sum(sr_core_surf)
	Nr_surf_core = sum(sr_surf_core)
	Nr_core_core = sum(sr_core_core)
for	ii
	P_ii_jj = squeeze(pair_counts_symm(ii,jj,:)) ./ sum_ij
	P_ii = pair_sums_aan(ii, :) / sum_r_aa(ii)
	P_jj = pair_sums_aan(jj, :) / sum_r_aa(jj)
be careful	! wi = num_res_env(ii,1)/sum(num_res_env(ii,:))
	wj = num_res_env(jj,1)/sum(num_res_env(jj,:))
	P_ii_w = calc_Pi_sc(sr_surf_surf(ii,:), sr_surf_core(ii,:), sr_core_surf(ii,:), sr_core_core(ii,:), wi, wj)
	P_jj_w = calc_Pi_sc(sr_surf_surf(jj,:), sr_surf_core(jj,:), sr_core_surf(jj,:), sr_core_core(jj,:), wj, wi)
	P = P_ii_jj' .* P_r ./ (P_ii .* P_jj)
	Pr_w = calc_Pi_sc(Nr_surf_surf, Nr_surf_core, Nr_core_surf, Nr_core_core, num_res_env(ii,1)/sum(num_res_env(ii,:)), num_res_env(jj,1)/sum(num_res_env(jj,:)))
	P_w = P_ii_jj' .* P_r ./ (P_ii_w .* P_jj_w)
	P_w2 = P_ii_jj' .* Pr_w ./ (P_ii_w .* P_jj_w)
	P_w3 = P_ii_jj' ./ (P_ii_w .* P_jj_w) .* Pr_w .* Pr_w ./ P_r
score	score = -log(P)
	score_w = -log(P_w)
	score_w2 = -log(P_w2)
	score_w3 = -log(P_w3)
shift the tail for	kk
	h =plot(1:30, score, 'r', 1:30, score_w, 'b', 1:30, score_w2, 'g', 1:30, score_w3)
	linewidth
output	y2 = score_w2(1:range*2)
for	k

Function Documentation

axis()

axis

(

)

beta()

id beta ( )

virtual

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"
	)

fclose()

fclose

(

fp_pair

)

fprintf() [1/5]

end end fprintf	(	fp_pair	,
		"# END\n"
	)

fprintf() [2/5]

fprintf	(	fp_pair	,
		"%.2f %.2f "	,
		0.	25,
		0.25+(range *2-1) *0.	5
	)

fprintf() [3/5]

fprintf	(	fp_pair	,
		"%d "	,
		length(y2)
	)

fprintf() [4/5]

end fprintf	(	fp_pair	,
		"\n"
	)

fprintf() [5/5]

fprintf	(	fp_pair	,
		"PAIR: %s %s "	,
		reslist(ii,:)	,
		reslist(jj,:)
	)

i:()

id i: ( i  Sum_r_surf_surf )

virtual

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

Referenced by add_histograms_together(), bind_std_functional_hash(), bind_std_stl_multiset(), bind_std_unordered_map(), bind_T42_stl_names_map(), bind_T42_stl_names_multi(), bind_T42_stl_names_multimap(), dist(), doit(), FloppyTailMover::FloppyTailMover(), get_loop_scorefxn(), get_loop_scorefxn_old(), utility::json_spirit::Config_vector< String >::get_name(), utility::json_spirit::Config_map< String >::get_name(), utility::json_spirit::Config_vector< String >::get_value(), utility::json_spirit::Config_map< String >::get_value(), go_main(), gpu_refold_test(), initialize_free_and_fixed(), initialize_from_pdb(), input_coordCstsMapped(), main(), parse_nonstandard_angles(), parse_nonstandard_bondlengths(), perturb(), RBSegmentRelax_test(), core::pack::annealer::FixbbSimAnnealer::run(), simple_centroid_test(), simple_loop_modeling_test(), and simple_opte_test().

pre_fill_dfire()

core_core pre_fill_dfire ( )

staticvirtual

score()

score ( 1:cutoff  )

pure virtual

score_w()

score_w ( 1:cutoff  )

pure virtual

score_w2() [1/2]

score_w2 ( 1:cutoff  )

pure virtual

score_w2() [2/2]

end score_w2 ( 25:30  )

pure virtual

score_w3()

score_w3 ( 1:cutoff  )

pure virtual

set()

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

sr_core_core()

sr_core_core	(	i	,
		:
	)

sr_core_surf()

sr_core_surf	(	i	,
		:
	)

sr_surf_core()

sr_surf_core	(	i	,
		:
	)

subplot()

draw 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	,
		:
	)

text()

text	(	2	,
		score(10)	,
		t
	)

zeros()

20,2 zeros ( )

virtual

Variable Documentation

! wi

be careful ! wi = num_res_env(ii,1)/sum(num_res_env(ii,:))

__pad0__

env __pad0__

__pad1__

__pad1__

__pad2__

__pad2__

aa_aa

end end end sum aa_aa = (surf_surf+surf_core+core_surf+core_core)

aj

end else aj

ARG

ARG

ASN

ASN

ASP

ASP

break

break

CONV1

CONV1 = gausswin(2*L+1, 4)

core_core

core_core =zeros(20,20,30)

core_surf

core_surf =zeros(20,20,30)

cutoff

cutoff =2

CYS

CYS

env_index

residue index env_index = zeros(40,1)

GLN

GLN

GLU

GLU

GLY

GLY

h

h =plot(1:30, score, 'r', 1:30, score_w, 'b', 1:30, score_w2, 'g', 1:30, score_w3)

HIS

HIS

i

i

Initial value:

= 1:40
  %get aa
  for n = 1:20
    if (list(i,1:3)==reslist(n,:))
      res_index(i)=n

ii

for ii

Initial value:

= 1:20
for jj = ii:20
  sum_ij = sum(pair_counts_symm(ii,jj,:))

ILE

ILE

j

j

Initial value:

= 1:40
    aj = res_index(j)

k

for k

Initial value:

=1:length(y2)
    fprintf(fp_pair, "%f ", y2(k))

kk

shift the tail for kk

Initial value:

= 1:4
    score_w2(kk+20) = score_w2(20)*(4-kk)/4

L

smooth data L =5

LEU

LEU

linewidth

linewidth

LYS

LYS

MET

MET

N

N

Initial value:

= sum_r N(r)
P_r = pair_sums_tot / totalsum

Nr_core_core

Nr_core_core = sum(sr_core_core)

Nr_core_surf

Nr_core_surf = sum(sr_core_surf)

Nr_surf_core

Nr_surf_core = sum(sr_surf_core)

Nr_surf_surf

end Nr_surf_surf = sum(sr_surf_surf)

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_jj

P_ii_jj = squeeze(pair_counts_symm(ii,jj,:)) ./ sum_ij

P_ii_w

P_ii_w = calc_Pi_sc(sr_surf_surf(ii,:), sr_surf_core(ii,:), sr_core_surf(ii,:), sr_core_core(ii,:), wi, wj)

P_jj

P_jj = pair_sums_aan(jj, :) / sum_r_aa(jj)

P_jj_w

P_jj_w = calc_Pi_sc(sr_surf_surf(jj,:), sr_surf_core(jj,:), sr_core_surf(jj,:), sr_core_core(jj,:), wj, wi)

P_w

P_w = P_ii_jj' .* P_r ./ (P_ii_w .* P_jj_w)

P_w2

P_w2 = P_ii_jj' .* Pr_w ./ (P_ii_w .* P_jj_w)

P_w3

P_w3 = P_ii_jj' ./ (P_ii_w .* P_jj_w) .* Pr_w .* Pr_w ./ P_r

pair_counts_symm

to pair_counts_symm = aa_aa

pair_sums_aan

init pair_sums_aan = squeeze(sum(pair_counts_symm))

PHE

PHE

Pr_w

Pr_w = calc_Pi_sc(Nr_surf_surf, Nr_surf_core, Nr_core_surf, Nr_core_core, num_res_env(ii,1)/sum(num_res_env(ii,:)), num_res_env(jj,1)/sum(num_res_env(jj,:)))

PRO

PRO

range

range =12

res_index

mark each table column row res_index = zeros(40,1)

reslist

reslist

Initial value:

= 

score

score score = -log(P)

score_w

score_w = -log(P_w)

score_w2

score_w2 = -log(P_w2)

score_w3

score_w3 = -log(P_w3)

SER

SER

smoothed

smoothed = conv(squeeze(surf_core(i,j,:)), CONV1)

sr_core_core

sr_core_core = squeeze(sum(core_core, 2))

sr_core_surf

sr_core_surf = squeeze(sum(core_surf, 2))

sr_surf_core

sr_surf_core = squeeze(sum(surf_core, 2))

Sum_r_core_core

Sum_r_core_core = squeeze(sum(sr_core_core,2))

Sum_r_core_surf

Sum_r_core_surf = squeeze(sum(sr_core_surf,2))

Sum_r_surf_core

Sum_r_surf_core = squeeze(sum(sr_surf_core,2))

Sum_r_surf_surf

Sum_r_surf_surf = squeeze(sum(sr_surf_surf,2))

surf_core

surf_core =zeros(20,20,30)

surf_surf

end split x4 surf_surf =zeros(20,20,30)

THR

THR

TRP

TRP

TYR

TYR

VAL

VAL

wj

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

y2

output y2 = score_w2(1:range*2)