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tsoc
openmm
Commits
6e89e067
Commit
6e89e067
authored
Aug 19, 2013
by
Robert McGibbon
Browse files
force integer division
parent
260b9598
Changes
1
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1 changed file
with
11 additions
and
11 deletions
+11
-11
wrappers/python/simtk/openmm/app/internal/amber_file_parser.py
...ers/python/simtk/openmm/app/internal/amber_file_parser.py
+11
-11
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wrappers/python/simtk/openmm/app/internal/amber_file_parser.py
View file @
6e89e067
...
...
@@ -335,8 +335,8 @@ class PrmtopLoader(object):
%
((
bondPointers
[
ii
],
bondPointers
[
ii
+
1
]),))
iType
=
int
(
bondPointers
[
ii
+
2
])
-
1
returnList
.
append
((
int
(
bondPointers
[
ii
])
/
3
,
int
(
bondPointers
[
ii
+
1
])
/
3
,
returnList
.
append
((
int
(
bondPointers
[
ii
])
/
/
3
,
int
(
bondPointers
[
ii
+
1
])
/
/
3
,
float
(
forceConstant
[
iType
])
*
forceConstConversionFactor
,
float
(
bondEquil
[
iType
])
*
lengthConversionFactor
))
return
returnList
...
...
@@ -383,9 +383,9 @@ class PrmtopLoader(object):
anglePointers
[
ii
+
1
],
anglePointers
[
ii
+
2
]),))
iType
=
int
(
anglePointers
[
ii
+
3
])
-
1
self
.
_angleList
.
append
((
int
(
anglePointers
[
ii
])
/
3
,
int
(
anglePointers
[
ii
+
1
])
/
3
,
int
(
anglePointers
[
ii
+
2
])
/
3
,
self
.
_angleList
.
append
((
int
(
anglePointers
[
ii
])
/
/
3
,
int
(
anglePointers
[
ii
+
1
])
/
/
3
,
int
(
anglePointers
[
ii
+
2
])
/
/
3
,
float
(
forceConstant
[
iType
])
*
forceConstConversionFactor
,
float
(
angleEquil
[
iType
])))
return
self
.
_angleList
...
...
@@ -411,10 +411,10 @@ class PrmtopLoader(object):
dihedralPointers
[
ii
+
2
],
dihedralPointers
[
ii
+
3
]),))
iType
=
int
(
dihedralPointers
[
ii
+
4
])
-
1
self
.
_dihedralList
.
append
((
int
(
dihedralPointers
[
ii
])
/
3
,
int
(
dihedralPointers
[
ii
+
1
])
/
3
,
abs
(
int
(
dihedralPointers
[
ii
+
2
]))
/
3
,
abs
(
int
(
dihedralPointers
[
ii
+
3
]))
/
3
,
self
.
_dihedralList
.
append
((
int
(
dihedralPointers
[
ii
])
/
/
3
,
int
(
dihedralPointers
[
ii
+
1
])
/
/
3
,
abs
(
int
(
dihedralPointers
[
ii
+
2
]))
/
/
3
,
abs
(
int
(
dihedralPointers
[
ii
+
3
]))
/
/
3
,
float
(
forceConstant
[
iType
])
*
forceConstConversionFactor
,
float
(
phase
[
iType
]),
int
(
0.5
+
float
(
periodicity
[
iType
]))))
...
...
@@ -429,8 +429,8 @@ class PrmtopLoader(object):
nonbondTerms
=
self
.
getNonbondTerms
()
for
ii
in
range
(
0
,
len
(
dihedralPointers
),
5
):
if
int
(
dihedralPointers
[
ii
+
2
])
>
0
and
int
(
dihedralPointers
[
ii
+
3
])
>
0
:
iAtom
=
int
(
dihedralPointers
[
ii
])
/
3
lAtom
=
int
(
dihedralPointers
[
ii
+
3
])
/
3
iAtom
=
int
(
dihedralPointers
[
ii
])
/
/
3
lAtom
=
int
(
dihedralPointers
[
ii
+
3
])
/
/
3
chargeProd
=
charges
[
iAtom
]
*
charges
[
lAtom
]
(
rVdwI
,
epsilonI
)
=
nonbondTerms
[
iAtom
]
(
rVdwL
,
epsilonL
)
=
nonbondTerms
[
lAtom
]
...
...
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