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tools
mrdna
Commits
0d46571b
Commit
0d46571b
authored
Aug 06, 2020
by
cmaffeo2
Browse files
Added support to arbdmodel for product potentials
parent
5d01a8a5
Changes
1
Hide whitespace changes
Inline
Side-by-side
mrdna/arbdmodel/__init__.py
View file @
0d46571b
...
...
@@ -72,6 +72,7 @@ class Parent():
self
.
impropers
=
[]
self
.
exclusions
=
[]
self
.
bond_angles
=
[]
self
.
product_potentials
=
[]
self
.
rigid
=
False
...
...
@@ -156,6 +157,18 @@ class Parent():
# for b in (i,j): assert(b in beads)
self
.
bond_angles
.
append
(
(
i
,
j
,
k
,
l
,
bond_angle
)
)
def
add_product_potential_angle
(
self
,
potential_list
):
""" potential_list: list of tuples of form (particle_i, particle_j,..., TabulatedPotential) """
if
len
(
terms
)
<
2
:
raise
ValueError
(
"Too few potentials"
)
for
elem
in
potential_list
:
beads
=
elem
[:
-
1
]
pot
=
elem
[
-
1
]
if
len
(
beads
)
<
2
:
raise
ValueError
(
"Too few particles specified in product_potential"
)
if
len
(
beads
)
>
4
:
raise
ValueError
(
"Too many particles specified in product_potential"
)
self
.
product_potentials
.
append
(
potential_list
)
## TODO: how to handle duplicating and cloning bonds
def
get_restraints
(
self
):
ret
=
[]
for
c
in
self
.
children
:
...
...
@@ -217,6 +230,15 @@ class Parent():
else
:
return
ret
def
get_product_potentials
(
self
):
ret
=
self
.
product_potentials
for
c
in
self
.
children
:
if
isinstance
(
c
,
Parent
):
ret
.
extend
(
c
.
get_product_potentials
()
)
if
self
.
remove_duplicate_bonded_terms
:
return
list
(
set
(
ret
))
else
:
return
ret
def
_get_bond_potentials
(
self
):
bonds
=
[
b
for
i
,
j
,
b
,
ex
in
self
.
get_bonds
()]
bondangles1
=
[
b
[
1
]
for
i
,
j
,
k
,
l
,
b
in
self
.
get_bond_angles
()]
...
...
@@ -893,6 +915,7 @@ class ArbdModel(PdbModel):
self
.
_dihedral_filename
=
"%s/%s.dihedrals.txt"
%
(
d
,
prefix
)
self
.
_exclusion_filename
=
"%s/%s.exculsions.txt"
%
(
d
,
prefix
)
self
.
_bond_angle_filename
=
"%s/%s.bondangles.txt"
%
(
d
,
prefix
)
self
.
_product_potential_filename
=
"%s/%s.prodpot.txt"
%
(
d
,
prefix
)
# self._writeArbdCoordFile( prefix + ".coord.txt" )
self
.
_writeArbdParticleFile
(
prefix
+
".particles.txt"
)
...
...
@@ -902,6 +925,7 @@ class ArbdModel(PdbModel):
self
.
_writeArbdDihedralFile
()
self
.
_writeArbdExclusionFile
()
self
.
_writeArbdBondAngleFile
()
self
.
_writeArbdProductPotentialFile
()
self
.
_writeArbdPotentialFiles
(
prefix
,
directory
=
d
)
self
.
_writeArbdConf
(
prefix
,
numSteps
=
numSteps
,
outputPeriod
=
outputPeriod
,
restart_file
=
restart_file
)
...
...
@@ -1098,6 +1122,7 @@ tabulatedPotential 1
dihedrals
=
self
.
get_dihedrals
()
exclusions
=
self
.
get_exclusions
()
bond_angles
=
self
.
get_bond_angles
()
prod_pots
=
self
.
get_product_potentials
()
if
len
(
bonds
)
>
0
:
for
b
in
self
.
_get_bond_potentials
():
fh
.
write
(
"tabulatedBondFile %s
\n
"
%
b
)
...
...
@@ -1122,6 +1147,8 @@ tabulatedPotential 1
fh
.
write
(
"inputExcludes %s
\n
"
%
self
.
_exclusion_filename
)
if
len
(
bond_angles
)
>
0
:
fh
.
write
(
"inputBondAngles %s
\n
"
%
self
.
_bond_angle_filename
)
if
len
(
prod_pots
)
>
0
:
fh
.
write
(
"inputProductPotentials %s
\n
"
%
self
.
_product_potential_filename
)
write_null_dx
=
False
for
pt
,
num
in
self
.
getParticleTypesAndCounts
():
...
...
@@ -1242,6 +1269,25 @@ component "data" value 3
item
=
tuple
([
p
.
idx
for
p
in
b
[:
-
1
]]
+
[
str
(
p
)
for
p
in
b
[
-
1
]])
fh
.
write
(
"BONDANGLE %d %d %d %d %s %s %s
\n
"
%
item
)
def
_writeArbdProductPotentialFile
(
self
):
if
len
(
self
.
product_potentials
)
>
0
:
with
open
(
self
.
_product_potential_filename
,
'w'
)
as
fh
:
for
ijk_tb
in
self
.
get_product_potentials
():
ijk
=
ijk_b
[:
-
1
]
tb
=
ijk_tb
[
-
1
]
if
not
(
type
(
tb
)
is
tuple
or
type
(
tb
)
is
list
):
if
len
(
tb
)
!=
2
:
raise
ValueError
(
"Invalid product potential"
)
type_
,
b
=
tb
if
type
(
type_
)
is
not
str
:
raise
ValueError
(
"Invalid product potential: unrecognized specification of potential type"
)
else
:
type_
=
""
b
=
tb
if
type
(
b
)
is
not
str
and
not
isinstance
(
b
,
Path
):
b
.
write_file
()
fh
.
write
(
"PRODUCTPOTENTIAL "
+
" "
.
join
([
str
(
x
)
for
x
in
ijk
+
[
type_
,
b
]
if
x
!=
""
]))
def
dimensions_from_structure
(
self
,
padding_factor
=
1.5
,
isotropic
=
False
):
## TODO: cache coordinates using numpy arrays for quick min/max
raise
(
NotImplementedError
)
...
...
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