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mrdna
Commits
e93e6468
Commit
e93e6468
authored
Oct 21, 2021
by
cmaffeo2
Browse files
Enable group site restraints
parent
455420b8
Changes
1
Hide whitespace changes
Inline
Side-by-side
mrdna/arbdmodel/__init__.py
View file @
e93e6468
...
...
@@ -74,7 +74,8 @@ class Parent():
self
.
exclusions
=
[]
self
.
bond_angles
=
[]
self
.
product_potentials
=
[]
self
.
group_sites
=
[]
self
.
rigid
=
False
## TODO: self.cacheInvalid = True # What will be in the cache?
...
...
@@ -172,7 +173,7 @@ class Parent():
def
get_restraints
(
self
):
ret
=
[]
for
c
in
self
.
children
:
for
c
in
self
.
children
+
self
.
group_sites
:
ret
.
extend
(
c
.
get_restraints
()
)
return
ret
...
...
@@ -761,7 +762,8 @@ class ArbdModel(PdbModel):
raise
NotImplementedError
self
.
particles
=
particles
self
.
idx
=
None
self
.
restraints
=
[]
def
get_center
(
self
):
c
=
np
.
array
((
0
,
0
,
0
))
for
p
in
self
.
particles
:
...
...
@@ -769,6 +771,12 @@ class ArbdModel(PdbModel):
c
=
c
/
len
(
self
.
particles
)
return
c
def
add_restraint
(
self
,
restraint
):
self
.
restraints
.
append
(
restraint
)
def
get_restraints
(
self
):
return
[(
self
,
r
)
for
r
in
self
.
restraints
]
def
__init__
(
self
,
children
,
origin
=
None
,
dimensions
=
(
1000
,
1000
,
1000
),
temperature
=
291
,
timestep
=
50e-6
,
particle_integrator
=
'Brown'
,
cutoff
=
50
,
decomp_period
=
1000
,
pairlist_distance
=
None
,
nonbonded_resolution
=
0.1
,
...
...
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