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tsoc
openmm
Commits
cb0b20f5
"serialization/tests/TestSerializeCustomBondForce.cpp" did not exist on "85da5e0f9018719e95350c76b483a2160c84d9d3"
Commit
cb0b20f5
authored
Apr 23, 2012
by
Peter Eastman
Browse files
Set units correctly on Numpy arrays
parent
c9d7d1e9
Changes
1
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1 changed file
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7 additions
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7 deletions
+7
-7
wrappers/python/simtk/openmm/app/amberinpcrdfile.py
wrappers/python/simtk/openmm/app/amberinpcrdfile.py
+7
-7
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wrappers/python/simtk/openmm/app/amberinpcrdfile.py
View file @
cb0b20f5
...
@@ -32,7 +32,7 @@ __author__ = "Peter Eastman"
...
@@ -32,7 +32,7 @@ __author__ = "Peter Eastman"
__version__
=
"1.0"
__version__
=
"1.0"
from
simtk.openmm.app.internal
import
amber_file_parser
from
simtk.openmm.app.internal
import
amber_file_parser
from
simtk.unit
import
nanometers
,
picoseconds
from
simtk.unit
import
Quantity
,
nanometers
,
picoseconds
try
:
try
:
import
numpy
import
numpy
except
:
except
:
...
@@ -84,7 +84,7 @@ class AmberInpcrdFile(object):
...
@@ -84,7 +84,7 @@ class AmberInpcrdFile(object):
"""
"""
if
asNumpy
:
if
asNumpy
:
if
self
.
_numpyPositions
is
None
:
if
self
.
_numpyPositions
is
None
:
self
.
_numpyPositions
=
numpy
.
array
(
self
.
positions
.
value_in_unit
(
nanometers
))
*
nanometers
self
.
_numpyPositions
=
Quantity
(
numpy
.
array
(
self
.
positions
.
value_in_unit
(
nanometers
))
,
nanometers
)
return
self
.
_numpyPositions
return
self
.
_numpyPositions
return
self
.
positions
return
self
.
positions
...
@@ -96,7 +96,7 @@ class AmberInpcrdFile(object):
...
@@ -96,7 +96,7 @@ class AmberInpcrdFile(object):
"""
"""
if
asNumpy
:
if
asNumpy
:
if
self
.
_numpyVelocities
is
None
:
if
self
.
_numpyVelocities
is
None
:
self
.
_numpyVelocities
=
numpy
.
array
(
self
.
velocities
.
value_in_unit
(
nanometers
/
picoseconds
))
*
nanometers
/
picoseconds
self
.
_numpyVelocities
=
Quantity
(
numpy
.
array
(
self
.
velocities
.
value_in_unit
(
nanometers
/
picoseconds
))
,
nanometers
/
picoseconds
)
return
self
.
_numpyVelocities
return
self
.
_numpyVelocities
return
self
.
velocities
return
self
.
velocities
...
@@ -109,9 +109,9 @@ class AmberInpcrdFile(object):
...
@@ -109,9 +109,9 @@ class AmberInpcrdFile(object):
if
asNumpy
:
if
asNumpy
:
if
self
.
_numpyBoxVectors
is
None
:
if
self
.
_numpyBoxVectors
is
None
:
self
.
_numpyBoxVectors
=
[]
self
.
_numpyBoxVectors
=
[]
self
.
_numpyBoxVectors
.
append
(
numpy
.
array
(
self
.
boxVectors
[
0
].
value_in_unit
(
nanometers
))
*
nanometers
)
self
.
_numpyBoxVectors
.
append
(
Quantity
(
numpy
.
array
(
self
.
boxVectors
[
0
].
value_in_unit
(
nanometers
))
,
nanometers
)
)
self
.
_numpyBoxVectors
.
append
(
numpy
.
array
(
self
.
boxVectors
[
1
].
value_in_unit
(
nanometers
))
*
nanometers
)
self
.
_numpyBoxVectors
.
append
(
Quantity
(
numpy
.
array
(
self
.
boxVectors
[
1
].
value_in_unit
(
nanometers
))
,
nanometers
)
)
self
.
_numpyBoxVectors
.
append
(
numpy
.
array
(
self
.
boxVectors
[
2
].
value_in_unit
(
nanometers
))
*
nanometers
)
self
.
_numpyBoxVectors
.
append
(
Quantity
(
numpy
.
array
(
self
.
boxVectors
[
2
].
value_in_unit
(
nanometers
))
,
nanometers
)
)
return
self
.
_numpyBoxVectors
return
self
.
_numpyBoxVectors
return
self
.
boxVectors
return
self
.
boxVectors
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