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tsoc
openmm
Commits
7762d9fc
Commit
7762d9fc
authored
Feb 20, 2016
by
Rafal P. Wiewiora
Browse files
no multiple generators
parent
004db14a
Changes
1
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1 changed file
with
30 additions
and
10 deletions
+30
-10
wrappers/python/simtk/openmm/app/forcefield.py
wrappers/python/simtk/openmm/app/forcefield.py
+30
-10
No files found.
wrappers/python/simtk/openmm/app/forcefield.py
View file @
7762d9fc
...
...
@@ -1194,8 +1194,12 @@ class HarmonicBondGenerator(object):
@
staticmethod
def
parseElement
(
element
,
ff
):
generator
=
HarmonicBondGenerator
(
ff
)
ff
.
registerGenerator
(
generator
)
existing
=
[
f
for
f
in
ff
.
_forces
if
isinstance
(
f
,
HarmonicBondGenerator
)]
if
len
(
existing
)
==
0
:
generator
=
HarmonicBondGenerator
(
ff
)
ff
.
registerGenerator
(
generator
)
else
:
generator
=
existing
[
0
]
for
bond
in
element
.
findall
(
'Bond'
):
generator
.
registerBond
(
bond
.
attrib
)
...
...
@@ -1247,8 +1251,12 @@ class HarmonicAngleGenerator(object):
@
staticmethod
def
parseElement
(
element
,
ff
):
generator
=
HarmonicAngleGenerator
(
ff
)
ff
.
registerGenerator
(
generator
)
existing
=
[
f
for
f
in
ff
.
_forces
if
isinstance
(
f
,
HarmonicAngleGenerator
)]
if
len
(
existing
)
==
0
:
generator
=
HarmonicAngleGenerator
(
ff
)
ff
.
registerGenerator
(
generator
)
else
:
generator
=
existing
[
0
]
for
angle
in
element
.
findall
(
'Angle'
):
generator
.
registerAngle
(
angle
.
attrib
)
...
...
@@ -1331,8 +1339,12 @@ class PeriodicTorsionGenerator(object):
@
staticmethod
def
parseElement
(
element
,
ff
):
generator
=
PeriodicTorsionGenerator
(
ff
)
ff
.
registerGenerator
(
generator
)
existing
=
[
f
for
f
in
ff
.
_forces
if
isinstance
(
f
,
PeriodicTorsionGenerator
)]
if
len
(
existing
)
==
0
:
generator
=
PeriodicTorsionGenerator
(
ff
)
ff
.
registerGenerator
(
generator
)
else
:
generator
=
existing
[
0
]
for
torsion
in
element
.
findall
(
'Proper'
):
generator
.
registerProperTorsion
(
torsion
.
attrib
)
for
torsion
in
element
.
findall
(
'Improper'
):
...
...
@@ -1430,8 +1442,12 @@ class RBTorsionGenerator(object):
@
staticmethod
def
parseElement
(
element
,
ff
):
generator
=
RBTorsionGenerator
(
ff
)
ff
.
registerGenerator
(
generator
)
existing
=
[
f
for
f
in
ff
.
_forces
if
isinstance
(
f
,
RBTorsionGenerator
)]
if
len
(
existing
)
==
0
:
generator
=
RBTorsionGenerator
(
ff
)
ff
.
registerGenerator
(
generator
)
else
:
generator
=
existing
[
0
]
for
torsion
in
element
.
findall
(
'Proper'
):
types
=
ff
.
_findAtomTypes
(
torsion
.
attrib
,
4
)
if
None
not
in
types
:
...
...
@@ -1534,8 +1550,12 @@ class CMAPTorsionGenerator(object):
@
staticmethod
def
parseElement
(
element
,
ff
):
generator
=
CMAPTorsionGenerator
(
ff
)
ff
.
registerGenerator
(
generator
)
existing
=
[
f
for
f
in
ff
.
_forces
if
isinstance
(
f
,
CMAPTorsionGenerator
)]
if
len
(
existing
)
==
0
:
generator
=
CMAPTorsionGenerator
(
ff
)
ff
.
registerGenerator
(
generator
)
else
:
generator
=
existing
[
0
]
for
map
in
element
.
findall
(
'Map'
):
values
=
[
float
(
x
)
for
x
in
map
.
text
.
split
()]
size
=
sqrt
(
len
(
values
))
...
...
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