gen_vdw_radius.m File Reference

Functions
clean the clash	nonidcen_counts (:,:, 1:6)=0
	Nint (ndx)
end if	Prm (ndx) > pcut rvdw2

Variables
	cutoff = 0.003
	pcut
	dic = [ "Nbb"
	CAbb
	CB
	CObb
	OCbb
	ALA
	CYS
	ASP
	GLU
	PHE
	GLY
	HIS
	ILE
	LYS
	LEU
	MET
	ASN
	PRO
	GLN
	ARG
	SER
	THR
	VAL
	TRP
	TYR
	rvdw1 = 0
	rvdw2 = 0
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
	Nall = 0
for	ndx
end	Nc = Nall*cutoff
	rm = 0:0.01:10
	Nrm = interp1( r, Nint, rm, 'linear')
	Prm = interp1( r, Pr, rm, 'linear')
	oldp = 0
	P1 =-1
	P2 =-1
	break
end end	rvdw = rvdw1

Function Documentation

Nint()

Nint

(

ndx

)

nonidcen_counts()

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

pure virtual

Prm()

end if Prm

(

ndx

)

Variable Documentation

aandx

for aandx

Initial value:

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

ALA

ALA

ARG

ARG

ASN

ASN

ASP

ASP

break

break

CAbb

CAbb

CB

CB

Referenced by add_constraints(), vancomycin::add_constraints(), design(), design_1comp(), dock(), lactamize::find_lactams(), ik_his_clamp(), intersecting_bpy_axes(), intersecting_disulfide_axes(), main(), run(), set_disulf(), and CrystFFTDock::setup_maps().

CObb

CObb

cutoff

cutoff = 0.003

CYS

CYS

dic

dic = [ "Nbb"

GLN

GLN

GLU

GLU

GLY

GLY

HIS

HIS

ii

for ii

Initial value:

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

ILE

ILE

LEU

LEU

LYS

LYS

MET

MET

Nall

Nall = 0

Nc

end Nc = Nall*cutoff

ndx

for ndx

Initial value:

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

Referenced by SetOfClusters::consolidate(), get_best_rotamer_index(), get_numeric_deriv(), my_main(), and set_up_engine().

Nint

Nint = Nr

Nr

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

Nrm

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

OCbb

OCbb

oldp

oldp = 0

P1

P1 =-1

Referenced by run().

P2

P2 =-1

Referenced by run().

pcut

pcut

Initial value:

= 0.1
 
aaa = 16

PHE

PHE

Pr

Pr = Nr ./ shell

Prm

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

PRO

PRO

r

r = 0.25:0.5:15

rm

rm = 0:0.01:10

rvdw

end end rvdw = rvdw1

rvdw1

rvdw1 = 0

rvdw2

rvdw2 = 0

SER

SER

shell

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

THR

THR

TRP

TRP

TYR

TYR

VAL

VAL