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tsoc
openmm
Commits
25c22045
Commit
25c22045
authored
Jul 12, 2013
by
Lee-Ping Wang
Browse files
Removed an if statement that was causing addHydrogens() to fail for systems containing OH groups.
parent
604a8538
Changes
1
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1 changed file
with
3 additions
and
4 deletions
+3
-4
wrappers/python/simtk/openmm/app/modeller.py
wrappers/python/simtk/openmm/app/modeller.py
+3
-4
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wrappers/python/simtk/openmm/app/modeller.py
View file @
25c22045
...
...
@@ -734,9 +734,8 @@ class Modeller(object):
else
:
delta
=
Vec3
(
random
.
random
(),
random
.
random
(),
random
.
random
())
*
nanometer
delta
*=
0.1
*
nanometer
/
norm
(
delta
)
if
len
(
expected
)
>
1
:
delta
+=
0.05
*
Vec3
(
random
.
random
(),
random
.
random
(),
random
.
random
())
*
nanometer
delta
*=
0.1
*
nanometer
/
norm
(
delta
)
delta
+=
0.05
*
Vec3
(
random
.
random
(),
random
.
random
(),
random
.
random
())
*
nanometer
delta
*=
0.1
*
nanometer
/
norm
(
delta
)
newPositions
.
append
(
self
.
positions
[
parent
.
index
]
+
delta
)
newTopology
.
addBond
(
newAtom
,
newH
)
else
:
...
...
@@ -922,4 +921,4 @@ class Modeller(object):
if
bond
[
0
]
in
newAtoms
and
bond
[
1
]
in
newAtoms
:
newTopology
.
addBond
(
newAtoms
[
bond
[
0
]],
newAtoms
[
bond
[
1
]])
self
.
topology
=
newTopology
self
.
positions
=
newPositions
\ No newline at end of file
self
.
positions
=
newPositions
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