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tsoc
openmm
Commits
ee1323b9
"plugins/cpupme/vscode:/vscode.git/clone" did not exist on "f6aae604f4ca808e98fe7aa4e3772dfee6742fc8"
Commit
ee1323b9
authored
Oct 01, 2013
by
Robert McGibbon
Browse files
Bugfix: dms.positions should be a Quantity(list(Vec3)), not a list(Quantity(Vec3))
parent
552544ab
Changes
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wrappers/python/simtk/openmm/app/desmonddmsfile.py
wrappers/python/simtk/openmm/app/desmonddmsfile.py
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wrappers/python/simtk/openmm/app/desmonddmsfile.py
View file @
ee1323b9
...
...
@@ -146,11 +146,12 @@ class DesmondDMSFile(object):
atomName
=
atomReplacements
[
atomName
]
atoms
[
atomId
]
=
top
.
addAtom
(
atomName
,
elem
,
r
)
positions
.
append
(
mm
.
Vec3
(
x
,
y
,
z
)
*
angstrom
)
positions
.
append
(
mm
.
Vec3
(
x
,
y
,
z
))
for
p0
,
p1
in
self
.
_conn
.
execute
(
'SELECT p0, p1 FROM bond'
):
top
.
addBond
(
atoms
[
p0
],
atoms
[
p1
])
positions
=
positions
*
angstroms
return
top
,
positions
def
createSystem
(
self
,
nonbondedMethod
=
ff
.
NoCutoff
,
nonbondedCutoff
=
1.0
*
nanometer
,
...
...
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