gen_env_dep_orient.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, :, :)+
20, 30, 16	zeros ()
	aa_surf_da1 (i,:,:)+
	aa_core_da1 (i,:,:)+ = reshape(squeeze(core_core_th2(j,i,:,:)+core_surf_th2(j,i,:,:)),1,30,16)
	aa_surf_da2 (i,:,:)+ = reshape(squeeze(core_surf_th2(i,j,:,:)+surf_surf_th2(i,j,:,:)),1,30,16)
	aa_core_da2 (i,:,:)+ = reshape(squeeze(core_core_th2(i,j,:,:)+surf_core_th2(i,j,:,:)),1,30,16)
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,:)
end if	exist ("iii", "var") iii else iii
	score (score >1)
	score_w (score_w >1)
	printf ("score(%d,%d): max=%f, min=%f\n", ii, jj, max(max(score)), min(min(score)))
	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_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	aa_surf_da1 =zeros(20,30,16)
end end 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))
	aa_surf_sum_r = sum(aa_surf_dat_r_ang, 2)
	aa_core_sum_r = sum(aa_core_dat_r_ang, 2)
	aa_surf_p_r_ang = zeros(30,16)
	aa_core_p_r_ang = zeros(30,16)
	p_ii = p_a_r_ang1(iii, :, :)
	p_ii_w = calc_Pi_ang(aa_surf_da1, aa_core_da1, iii, num_res_env(jjj,1)/sum(num_res_env(jjj,:)))
	p_jj_w = calc_Pi_ang(aa_surf_da2, aa_core_da2, jjj, num_res_env(iii,1)/sum(num_res_env(iii,:)))
	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_w = (p_ii_jj .* p_r_ang) ./ (p_ii_p_jj_w)
	score = -log(p)
	score_w = -log(p_w)

Function Documentation

aa_core_da1()

aa_core_da1	(	i	,
		:	,
		:
	)		= reshape(squeeze(core_core_th2(j,i,:,:)+core_surf_th2(j,i,:,:)),1,30,16)

aa_core_da2()

aa_core_da2	(	i	,
		:	,
		:
	)		= reshape(squeeze(core_core_th2(i,j,:,:)+surf_core_th2(i,j,:,:)),1,30,16)

aa_core_p_r_ang()

aa_core_p_r_ang	(	kk	,
		:
	)

aa_surf_da1()

aa_surf_da1	(	i	,
		:	,
		:
	)

aa_surf_da2()

aa_surf_da2	(	i	,
		:	,
		:
	)		= reshape(squeeze(core_surf_th2(i,j,:,:)+surf_surf_th2(i,j,:,:)),1,30,16)

aa_surf_p_r_ang()

aa_surf_p_r_ang	(	kk	,
		:
	)

contourf()

contourf	(	xx	,
		yy	,
		score
	)

core_core_th2()

core_core_th2	(	ai	,
		aj	,
		:	,
		:
	)

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

)

exist()

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

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	,
		:
	)

printf()

printf

(

"score(%d,%d):

max = %f

)

score()

score	(	score	,
		1
	)

score_w()

score_w	(	score_w	,
		1
	)

surf_core_th2()

surf_core_th2	(	ai	,
		aj	,
		:	,
		:
	)

surf_surf_th2()

surf_surf_th2	(	ai	,
		aj	,
		:	,
		:
	)

th1_table()

i, j, :, : th1_table ( )

virtual

zeros()

20,30,16 zeros ( )

virtual

Variable Documentation

aa

for aa

Initial value:

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

Referenced by aa2index(), myspace::aa_to_id(), adjust_ref_weights(), Sasa::apply(), blosum_score_alignment(), calc_scores(), numeric::ccd_angle(), check_hydrophobic(), check_option_conflicts(), correct_dunbrack(), correct_rama(), design_test(), dump_insert_pdb_and_remodel_blueprint(), fetch_atom_names(), ga_main(), gen_pep_bb_rama(), get_helixCAInContact(), get_rotamer_type_index(), get_vallfrags(), is_semi_rot(), main(), VallReader::make_fragment_lines(), VallReader::make_nmer_profile(), molten_get_vallfrags(), my_main(), new_pose_generator(), parse_sequence(), place_sf4(), place_zns(), pose_from_scratch(), MPInterfaceStatistics::print_aa_statistics(), Bola::random_close_phipsi_from_rama(), read_rama_map_file(), myspace::DataClass::report_by_aa(), EnvToolMover::representative_atom_name(), CapriTwoBodyEnergy::residue_pair_energy(), RunPepSpec(), scan_Evalue(), ScoreFragInfo::ScoreFragInfo(), sequence_tolerance_main(), sequence_tolerance_mf_main(), set_basic_dock_options(), set_secstruct_from_psipred_ss2(), numeric::kinematic_closure::sincos(), and numeric::kinematic_closure::radians::sincos().

aa_aa_th1

end end end end smooth sum 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_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_da1

to aa_surf_da1 =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

core_core_th1

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

core_core_th2

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

core_surf_th1

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

core_surf_th2

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

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))

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

end end cal ntype = 20

num_res_env

num_res_env = zeros(20,2)

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_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(aa_surf_da1, aa_core_da1, iii, num_res_env(jjj,1)/sum(num_res_env(jjj,:)))

p_jj_w

p_jj_w = calc_Pi_ang(aa_surf_da2, aa_core_da2, jjj, num_res_env(iii,1)/sum(num_res_env(iii,:)))

p_r_ang

p_r_ang = zeros(30, 16)

p_w

p_w = (p_ii_jj .* p_r_ang) ./ (p_ii_p_jj_w)

PHE

PHE

PRO

PRO

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

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_th1

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

surf_core_th2

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

surf_surf_th1

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

surf_surf_th2

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

THR

THR

TRP

TRP

TYR

TYR

VAL

VAL