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calc_chaperone_table.py
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Created
Tue, Sep 10, 02:27
Size
2 KB
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text/x-python
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Thu, Sep 12, 02:27 (2 d)
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blob
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20633761
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rLAMMPS lammps
calc_chaperone_table.py
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#!/usr/bin/env python
# Calculate a table of pairwise energies and forces between atoms in the
# protein and a chaperone provided in the supplemental materials section of:
# AI Jewett, A Baumketner and J-E Shea, PNAS, 101 (36), 13192-13197, (2004)
# This is stored in a tabulated force field with a singularity at a distance R.
#
# To calculate the table for interaction between
# ...the chaperone and a hydrophobic bead (2004 PNAS paper), use this table:
# ./calc_chaperone_table.py 1.0 1.0 6.0 0.475 0.0 5.9 1181
# ...the chaperone and a hydrophilic bead (2004 PNAS paper), use this table:
# ./calc_chaperone_table.py 1.0 1.0 6.0 0.0 0.0 5.9 1181
# ...the chaperone and a hydrophobic bead (2006 JMB paper), use this table:
# ./calc_chaperone_table.py 1.0 1.0 3.0 0.60 3.1 8.0 981 True
# ...the chaperone and a hydrophilic bead (2006 JMB paper), use this table:
# ./calc_chaperone_table.py 1.0 1.0 3.0 0.0 3.1 8.0 981 True
from
math
import
*
import
sys
def
U
(
r
,
eps
,
sigma
,
R
,
h
):
#print('r='+str(r)+' eps='+str(eps)+' s='+str(sigma)+' R='+str(R)+' h='+str(h))
# Formula is undefined at r=0, but you can take the limit:
if
r
<=
0
:
return
4.0
*
pi
*
R
*
R
*
4.0
*
eps
*
(
pow
((
sigma
/
R
),
12.0
)
-
h
*
pow
((
sigma
/
R
),
6.0
))
xp
=
sigma
/
(
r
+
R
)
xm
=
sigma
/
(
r
-
R
)
term10
=
pow
(
xm
,
10.0
)
-
pow
(
xp
,
10.0
)
term4
=
pow
(
xm
,
4.0
)
-
pow
(
xp
,
4.0
)
return
4.0
*
pi
*
eps
*
(
R
/
r
)
*
(
0.2
*
term10
-
0.5
*
h
*
term4
)
def
F
(
r
,
eps
,
sigma
,
R
,
h
):
# Formula is undefined at r=0, but you can take the limit:
if
r
<=
0
:
return
0.0
product_term_a
=
U
(
r
,
eps
,
sigma
,
R
,
h
)
/
r
ixp
=
(
r
+
R
)
/
sigma
ixm
=
(
r
-
R
)
/
sigma
dix_dr
=
1.0
/
sigma
term10
=
(
10.0
/
sigma
)
*
(
pow
(
ixm
,
-
11.0
)
-
pow
(
ixp
,
-
11.0
))
term4
=
(
4.0
/
sigma
)
*
(
pow
(
ixm
,
-
5.0
)
-
pow
(
ixp
,
-
5.0
))
product_term_b
=
4.0
*
eps
*
pi
*
(
R
/
r
)
*
(
0.2
*
term10
-
0.5
*
h
*
term4
)
return
product_term_a
+
product_term_b
class
InputError
(
Exception
):
""" A generic exception object containing a string for error reporting.
"""
def
__init__
(
self
,
err_msg
):
self
.
err_msg
=
err_msg
def
__str__
(
self
):
return
self
.
err_msg
def
__repr__
(
self
):
return
str
(
self
)
if
len
(
sys
.
argv
)
<
8
:
sys
.
stderr
.
write
(
"Error: expected 7 arguments:
\n
"
"
\n
"
"Usage: "
+
sys
.
argv
[
0
]
+
" epsilon sigma R h rmin rmax N
\n\n
"
)
sys
.
exit
(
-
1
)
epsilon
=
float
(
sys
.
argv
[
1
])
sigma
=
float
(
sys
.
argv
[
2
])
R
=
float
(
sys
.
argv
[
3
])
h
=
float
(
sys
.
argv
[
4
])
rmin
=
float
(
sys
.
argv
[
5
])
rmax
=
float
(
sys
.
argv
[
6
])
N
=
int
(
sys
.
argv
[
7
])
subtract_Urcut
=
False
if
len
(
sys
.
argv
)
==
9
:
subtract_Urcut
=
True
rcut
=
rmax
for
i
in
range
(
0
,
N
):
r
=
rmin
+
i
*
(
rmax
-
rmin
)
/
(
N
-
1
)
U_r
=
U
(
r
,
epsilon
,
sigma
,
R
,
h
)
F_r
=
F
(
r
,
epsilon
,
sigma
,
R
,
h
)
if
subtract_Urcut
:
U_r
-=
U
(
rcut
,
epsilon
,
sigma
,
R
,
h
)
if
(
r
>=
rcut
)
or
(
i
==
N
-
1
):
U_r
=
0.0
F_r
=
0.0
print
(
str
(
i
+
1
)
+
' '
+
str
(
r
)
+
' '
+
str
(
U_r
)
+
' '
+
str
(
F_r
))
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