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tsoc
openmm
Commits
4f48402f
Commit
4f48402f
authored
Jan 04, 2020
by
John Chodera
Browse files
Fix typo, and add documentation for 'ordering'
parent
bf57b12e
Changes
2
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2 changed files
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17 additions
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1 deletion
+17
-1
docs-source/usersguide/application.rst
docs-source/usersguide/application.rst
+16
-0
wrappers/python/tests/TestForceField.py
wrappers/python/tests/TestForceField.py
+1
-1
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docs-source/usersguide/application.rst
View file @
4f48402f
...
@@ -2331,6 +2331,22 @@ second atom has class OS and the third has class P:
...
@@ -2331,6 +2331,22 @@ second atom has class OS and the third has class P:
<
Proper
class1
=
""
class2
=
"OS"
class3
=
"P"
class4
=
""
periodicity1
=
"3"
phase1
=
"0.0"
k1
=
"1.046"
/>
<
Proper
class1
=
""
class2
=
"OS"
class3
=
"P"
class4
=
""
periodicity1
=
"3"
phase1
=
"0.0"
k1
=
"1.046"
/>
The
:
code
:`<
PeriodicTorsionForce
>`
tag
also
supports
an
optional
:
code
:`
ordering
`
attribute
to
provide
better
compatibility
with
the
way
impropers
are
assigned
in
different
simulation
packages
:
*
:
code
:`
ordering
=
"default"
`
specifies
the
default
behavior
if
the
attribute
is
omitted
.
*
:
code
:`
ordering
=
"amber"
`
produces
behavior
that
replicates
the
behavior
of
AmberTools
LEaP
*
:
code
:`
ordering
=
"charmm"
`
produces
behavior
more
consistent
with
CHARMM
*
:
code
:`
ordering
=
"smirnoff"
`
allows
multiple
impropers
to
be
added
using
exact
matching
to
replicate
the
beheavior
of
`
SMIRNOFF
<
https
://
open
-
forcefield
-
toolkit
.
readthedocs
.
io
/
en
/
latest
/
smirnoff
.
html
>`
_
impropers
Different
:
code
:`<
PeriodicTorsionForce
>`
tags
can
specify
different
:
code
:`
ordering
`
values
to
be
used
for
the
sub
-
elements
appearing
within
their
tags
.
<
RBTorsionForce
>
<
RBTorsionForce
>
================
================
...
...
wrappers/python/tests/TestForceField.py
View file @
4f48402f
...
@@ -970,7 +970,7 @@ class TestForceField(unittest.TestCase):
...
@@ -970,7 +970,7 @@ class TestForceField(unittest.TestCase):
for
index
in
range
(
force
.
getNumTorsions
()):
for
index
in
range
(
force
.
getNumTorsions
()):
i
,
j
,
k
,
l
,
_
,
_
,
_
=
force
.
getTorsionParameters
(
index
)
i
,
j
,
k
,
l
,
_
,
_
,
_
=
force
.
getTorsionParameters
(
index
)
created_torsions
.
add
((
i
,
j
,
k
,
l
))
created_torsions
.
add
((
i
,
j
,
k
,
l
))
expected_torsions
=
set
((
0
,
3
,
1
,
2
),
(
0
,
1
,
2
,
3
),
(
0
,
2
,
3
,
1
))
expected_torsions
=
set
(
[
(
0
,
3
,
1
,
2
),
(
0
,
1
,
2
,
3
),
(
0
,
2
,
3
,
1
)
]
)
self
.
assertEqual
(
expected_torsions
,
created_torsions
)
self
.
assertEqual
(
expected_torsions
,
created_torsions
)
def
test_Disulfides
(
self
):
def
test_Disulfides
(
self
):
...
...
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