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Scientific Software
mmtk
Commits
c84fe5f3
Commit
c84fe5f3
authored
Dec 11, 2017
by
eric pellegrini
Browse files
completed the oldnumeric removal
parent
a09f317d
Changes
53
Hide whitespace changes
Inline
Side-by-side
Examples/Forcefield/ElectricField/C/setup.py
View file @
c84fe5f3
...
...
@@ -10,15 +10,9 @@ import os, sys
compile_args
=
[]
include_dirs
=
[
'../../../../Include'
]
from
Scientific
import
N
try
:
num_package
=
N
.
package
except
AttributeError
:
num_package
=
"Numeric"
if
num_package
==
"NumPy"
:
compile_args
.
append
(
"-DNUMPY=1"
)
import
numpy.distutils.misc_util
include_dirs
.
extend
(
numpy
.
distutils
.
misc_util
.
get_numpy_include_dirs
())
compile_args
.
append
(
"-DNUMPY=1"
)
import
numpy.distutils.misc_util
include_dirs
.
extend
(
numpy
.
distutils
.
misc_util
.
get_numpy_include_dirs
())
setup
(
name
=
"ElectricField"
,
version
=
"1.0"
,
...
...
Examples/Forcefield/ElectricField/Cython/setup.py
View file @
c84fe5f3
...
...
@@ -11,15 +11,9 @@ import os, sys
compile_args
=
[]
include_dirs
=
[
'../../../../Include'
]
from
Scientific
import
N
try
:
num_package
=
N
.
package
except
AttributeError
:
num_package
=
"Numeric"
if
num_package
==
"NumPy"
:
compile_args
.
append
(
"-DNUMPY=1"
)
import
numpy.distutils.misc_util
include_dirs
.
extend
(
numpy
.
distutils
.
misc_util
.
get_numpy_include_dirs
())
compile_args
.
append
(
"-DNUMPY=1"
)
import
numpy.distutils.misc_util
include_dirs
.
extend
(
numpy
.
distutils
.
misc_util
.
get_numpy_include_dirs
())
setup
(
name
=
"ElectricField"
,
version
=
"1.0"
,
...
...
Examples/Forcefield/HarmonicOscillator/C/setup.py
View file @
c84fe5f3
...
...
@@ -10,15 +10,9 @@ import os, sys
compile_args
=
[]
include_dirs
=
[
'../../../../Include'
]
from
Scientific
import
N
try
:
num_package
=
N
.
package
except
AttributeError
:
num_package
=
"Numeric"
if
num_package
==
"NumPy"
:
compile_args
.
append
(
"-DNUMPY=1"
)
import
numpy.distutils.misc_util
include_dirs
.
extend
(
numpy
.
distutils
.
misc_util
.
get_numpy_include_dirs
())
compile_args
.
append
(
"-DNUMPY=1"
)
import
numpy.distutils.misc_util
include_dirs
.
extend
(
numpy
.
distutils
.
misc_util
.
get_numpy_include_dirs
())
setup
(
name
=
"HarmonicOscillatorForceField"
,
version
=
"1.0"
,
...
...
Examples/Forcefield/HarmonicOscillator/Cython/setup.py
View file @
c84fe5f3
...
...
@@ -11,15 +11,9 @@ import os, sys
compile_args
=
[]
include_dirs
=
[
'../../../../Include'
]
from
Scientific
import
N
try
:
num_package
=
N
.
package
except
AttributeError
:
num_package
=
"Numeric"
if
num_package
==
"NumPy"
:
compile_args
.
append
(
"-DNUMPY=1"
)
import
numpy.distutils.misc_util
include_dirs
.
extend
(
numpy
.
distutils
.
misc_util
.
get_numpy_include_dirs
())
compile_args
.
append
(
"-DNUMPY=1"
)
import
numpy.distutils.misc_util
include_dirs
.
extend
(
numpy
.
distutils
.
misc_util
.
get_numpy_include_dirs
())
setup
(
name
=
"HarmonicOscillatorForceField"
,
version
=
"1.0"
,
...
...
Examples/LangevinDynamics/setup.py
View file @
c84fe5f3
...
...
@@ -6,20 +6,14 @@ import os, sys
compile_args
=
[]
include_dirs
=
[
'.'
]
from
Scientific
import
N
try
:
num_package
=
N
.
package
except
AttributeError
:
num_package
=
"Numeric"
if
num_package
==
"NumPy"
:
compile_args
.
append
(
"-DNUMPY=1"
)
if
sys
.
platform
==
'win32'
:
include_dirs
.
append
(
os
.
path
.
join
(
sys
.
prefix
,
"Lib/site-packages/numpy/core/include"
))
else
:
include_dirs
.
append
(
os
.
path
.
join
(
sys
.
prefix
,
"lib/python%s.%s/site-packages/numpy/core/include"
%
sys
.
version_info
[:
2
]))
compile_args
.
append
(
"-DNUMPY=1"
)
if
sys
.
platform
==
'win32'
:
include_dirs
.
append
(
os
.
path
.
join
(
sys
.
prefix
,
"Lib/site-packages/numpy/core/include"
))
else
:
include_dirs
.
append
(
os
.
path
.
join
(
sys
.
prefix
,
"lib/python%s.%s/site-packages/numpy/core/include"
%
sys
.
version_info
[:
2
]))
setup
(
name
=
"MMTK-LangevinDynamics"
,
version
=
"2.7"
,
...
...
Examples/MDIntegrator/setup.py
View file @
c84fe5f3
...
...
@@ -8,9 +8,6 @@ import os, sys
compile_args
=
[
'-g'
,
'-O0'
]
include_dirs
=
[
'.'
,
'../../Include'
]
from
Scientific
import
N
assert
N
.
package
==
"NumPy"
compile_args
.
append
(
"-DNUMPY=1"
)
include_dirs
.
extend
(
numpy
.
distutils
.
misc_util
.
get_numpy_include_dirs
())
...
...
Examples/Miscellaneous/thermal_fluctuations.py
View file @
c84fe5f3
# Retrieve atomic fluctuation information from a PDBConfiguration object.
#
import
numpy
from
MMTK
import
*
from
MMTK.PDB
import
PDBConfiguration
from
Scientific
import
N
# Read a PDB file containing ANISOU records.
conf
=
PDBConfiguration
(
'1G66.pdb'
)
...
...
@@ -37,4 +38,4 @@ for c in conf.peptide_chains:
u_trace
=
pdb_atom
.
properties
[
'u'
].
trace
()
/
3.
*
Units
.
Ang
**
2
except
KeyError
:
u_trace
=
"[no ANISOU record]"
print
atom
,
b_factor
/
(
8
*
N
.
pi
**
2
),
u_trace
print
atom
,
b_factor
/
(
8
*
numpy
.
pi
**
2
),
u_trace
Examples/NormalModes/constrained_modes.py
View file @
c84fe5f3
# A normal mode calculation in the subspace of residue rigid-body motion.
#
import
numpy
from
MMTK
import
*
from
MMTK.Proteins
import
Protein
from
MMTK.ForceFields
import
Amber94ForceField
...
...
@@ -9,8 +11,6 @@ from MMTK.Subspace import RigidMotionSubspace
from
MMTK.Minimization
import
ConjugateGradientMinimizer
from
MMTK.Trajectory
import
StandardLogOutput
from
Scientific
import
N
# Construct system
universe
=
InfiniteUniverse
(
Amber94ForceField
())
universe
.
protein
=
Protein
(
'bala1'
)
...
...
@@ -38,8 +38,8 @@ for i in range(6, len(modes)):
overlap
=
[]
for
m2
in
full_modes
:
o
=
m1
.
massWeightedDotProduct
(
m2
)
/
\
N
.
sqrt
(
m1
.
massWeightedDotProduct
(
m1
))
/
\
N
.
sqrt
(
m2
.
massWeightedDotProduct
(
m2
))
numpy
.
sqrt
(
m1
.
massWeightedDotProduct
(
m1
))
/
\
numpy
.
sqrt
(
m2
.
massWeightedDotProduct
(
m2
))
overlap
.
append
(
abs
(
o
))
best
=
N
.
argsort
(
overlap
)[
-
1
]
best
=
numpy
.
argsort
(
overlap
)[
-
1
]
print
m1
.
frequency
,
full_modes
[
best
].
frequency
,
overlap
[
best
]
Examples/NormalModes/mode_analysis.py
View file @
c84fe5f3
import
numpy
from
MMTK
import
*
from
MMTK.Subspace
import
Subspace
from
Scientific.Statistics.Histogram
import
WeightedHistogram
,
Histogram
from
Scientific
import
N
#
# You ned to provide a mode file as input for this script; the
...
...
@@ -22,13 +23,13 @@ for chain in protein:
dihedrals_with_index
=
zip
(
range
(
1
,
1
+
len
(
dihedrals
)),
dihedrals
)
helix_indices
=
[
index
for
index
,
(
phi
,
psi
)
in
dihedrals_with_index
if
4.5
<
phi
<
5.8
and
5.
<
psi
<
6.
]
helix_indices
=
N
.
array
(
helix_indices
)
breaks
=
N
.
repeat
(
N
.
arange
(
len
(
helix_indices
)
-
1
),
helix_indices
=
numpy
.
array
(
helix_indices
)
breaks
=
numpy
.
repeat
(
numpy
.
arange
(
len
(
helix_indices
)
-
1
),
(
helix_indices
[
1
:]
-
helix_indices
[:
-
1
])
>
1
)
breaks
=
N
.
concatenate
(([
0
],
breaks
+
1
))
breaks
=
numpy
.
concatenate
(([
0
],
breaks
+
1
))
backbone
=
chain
.
backbone
()
for
i
in
range
(
len
(
breaks
)
-
1
):
residues
=
N
.
take
(
backbone
,
helix_indices
[
breaks
[
i
]:
breaks
[
i
+
1
]])
residues
=
numpy
.
take
(
backbone
,
helix_indices
[
breaks
[
i
]:
breaks
[
i
+
1
]])
helices
.
append
(
Collection
(
list
(
residues
)))
helices
=
[
h
for
h
in
helices
if
len
(
h
)
>
4
]
...
...
@@ -41,7 +42,7 @@ for helix in helices:
cms
,
inertia
=
helix
.
centerAndMomentOfInertia
()
moments
,
axes
=
inertia
.
diagonalization
()
axes
=
[
a
.
asVector
()
for
a
in
axes
]
helix_axis
=
axes
[
N
.
argmax
([
abs
(
end_to_end
*
v
)
for
v
in
axes
])]
helix_axis
=
axes
[
numpy
.
argmax
([
abs
(
end_to_end
*
v
)
for
v
in
axes
])]
hmv
=
ParticleVector
(
universe
)
helix_motion_vectors
.
append
(
hmv
)
for
residue
in
helix
:
...
...
Examples/NormalModes/subset_modes.py
View file @
c84fe5f3
...
...
@@ -9,8 +9,6 @@ from MMTK.Subspace import Subspace
from
MMTK.Minimization
import
ConjugateGradientMinimizer
from
MMTK.Trajectory
import
StandardLogOutput
from
Scientific
import
N
# Construct system
universe
=
InfiniteUniverse
(
Amber94ForceField
())
universe
.
protein1
=
Protein
(
'bala1'
)
...
...
Examples/Proteins/rotamers.py
View file @
c84fe5f3
# Modify sidechain dihedral angles
#
import
numpy
from
MMTK
import
*
from
MMTK.Proteins
import
Protein
from
MMTK.Trajectory
import
Trajectory
,
SnapshotGenerator
,
TrajectoryOutput
from
Scientific
import
N
# Construct system: lysozyme in vaccuum
universe
=
InfiniteUniverse
()
...
...
@@ -27,7 +28,7 @@ snapshot()
for
residue
in
residues
:
print
residue
chi
=
residue
.
chiAngle
()
for
angle
in
N
.
arange
(
-
N
.
pi
,
N
.
pi
,
N
.
pi
/
10.
):
for
angle
in
numpy
.
arange
(
-
numpy
.
pi
,
numpy
.
pi
,
numpy
.
pi
/
10.
):
chi
.
setValue
(
angle
)
print
angle
snapshot
()
...
...
Examples/Trajectories/calpha_trajectory.py
View file @
c84fe5f3
...
...
@@ -9,10 +9,11 @@
# "full_trajectory.nc" below.
#
import
numpy
from
MMTK
import
*
from
MMTK.Trajectory
import
Trajectory
,
TrajectoryOutput
,
SnapshotGenerator
from
MMTK.Proteins
import
Protein
,
PeptideChain
from
Scientific
import
N
# Open the input trajectory.
trajectory
=
Trajectory
(
None
,
'full_trajectory.nc'
)
...
...
@@ -62,7 +63,7 @@ first = 1
for
step
in
trajectory
:
conf
=
universe
.
contiguousObjectConfiguration
(
proteins
,
step
[
'configuration'
])
conf_calpha
=
Configuration
(
universe_calpha
,
N
.
take
(
conf
.
array
,
map
),
conf_calpha
=
Configuration
(
universe_calpha
,
numpy
.
take
(
conf
.
array
,
map
),
None
)
universe_calpha
.
setConfiguration
(
conf_calpha
)
if
first
:
...
...
Examples/Visualization/additional_objects.py
View file @
c84fe5f3
# Generate a protein backbone representation plus an indication
# of the principal axes of inertia by arrows.
#
import
numpy
from
MMTK
import
*
from
MMTK.Proteins
import
Protein
from
Scientific
import
N
,
LA
from
Scientific
import
LA
# Import the graphics module. Substitute any other graphics
# module name to make the example use that module.
...
...
@@ -16,7 +19,7 @@ center, inertia = protein.centerAndMomentOfInertia()
# Diagonalize the inertia tensor and scale the axes to a suitable length.
mass
=
protein
.
mass
()
diagonal
,
directions
=
LA
.
eigenvectors
(
inertia
.
array
)
diagonal
=
N
.
sqrt
(
diagonal
/
mass
)
diagonal
=
numpy
.
sqrt
(
diagonal
/
mass
)
# Generate the backbone graphics objects.
graphics
=
protein
.
graphicsObjects
(
graphics_module
=
module
,
...
...
Include/MMTK/numeric.pxi
View file @
c84fe5f3
...
...
@@ -24,7 +24,7 @@ cdef extern from "MMTK/arrayobject.h":
PyArray_Descr
*
descr
int
flags
ctypedef
class
Scientific
.
N
.
ArrayType
[
object
PyArrayObject
]:
ctypedef
class
numpy
.
ndarray
[
object
PyArrayObject
]:
cdef
char
*
data
cdef
int
nd
cdef
int
*
dimensions
,
*
strides
...
...
MMTK/Database/Atoms/ch
View file @
c84fe5f3
...
...
@@ -7,9 +7,9 @@ color = 'black'
vdW_radius = 0.17
from Scientific
import
N
import
numpy
b_coherent = (6.648 + (-3.741))*fm
b_incoherent =
N
.sqrt(0.285**2 + 25.217**2)*fm
b_incoherent =
numpy
.sqrt(0.285**2 + 25.217**2)*fm
b_coherent_deut = (6.648 + (6.674))*fm
b_incoherent_deut =
N
.sqrt(0.285**2 + 4.022**2)*fm
del
N
b_incoherent_deut =
numpy
.sqrt(0.285**2 + 4.022**2)*fm
del
numpy
MMTK/Database/Atoms/ch2
View file @
c84fe5f3
...
...
@@ -7,9 +7,9 @@ color = 'black'
vdW_radius = 0.17
from Scientific
import
N
import
numpy
b_coherent = (6.648 + 2*(-3.741))*fm
b_incoherent =
N
.sqrt(0.285**2 + 2*25.217**2)*fm
b_incoherent =
numpy
.sqrt(0.285**2 + 2*25.217**2)*fm
b_coherent_deut = (6.648 + 2*6.674)*fm
b_incoherent_deut =
N
.sqrt(0.285**2 + 2*4.022**2)*fm
del
N
b_incoherent_deut =
numpy
.sqrt(0.285**2 + 2*4.022**2)*fm
del
numpy
MMTK/Database/Atoms/ch3
View file @
c84fe5f3
...
...
@@ -7,9 +7,9 @@ color = 'black'
vdW_radius = 0.17
from Scientific
import
N
import
numpy
b_coherent = (6.648 + 3*(-3.741))*fm
b_incoherent =
N
.sqrt(0.285**2 + 3*25.217**2)*fm
b_incoherent =
numpy
.sqrt(0.285**2 + 3*25.217**2)*fm
b_coherent_deut = (6.648 + 3*6.674)*fm
b_incoherent_deut =
N
.sqrt(0.285**2 + 3*4.022**2)*fm
del
N
b_incoherent_deut =
numpy
.sqrt(0.285**2 + 3*4.022**2)*fm
del
numpy
MMTK/Database/Atoms/deut.py
View file @
c84fe5f3
import
numpy
from
MMTK
import
*
from
MMTK.ChemicalObjects
import
Group
from
Scientific.N
import
sqrt
residues
=
[
'alanine'
,
'arginine'
,
'asparagine'
,
'aspartic_acid'
,
'cysteine'
,
'cystine_ss'
,
'glutamic_acid'
,
'glutamine'
,
...
...
@@ -23,7 +24,7 @@ for r in residues:
bcoh_deut_sq
=
bcoh_deut_sq
+
(
a
.
b_coherent_deut
/
Units
.
fm
)
**
2
mass
=
mass
+
a
.
mass
()
print
r
print
"b_coherent = %f*fm"
%
sqrt
(
bcoh_sq
)
print
"b_coherent = %f*fm"
%
numpy
.
sqrt
(
bcoh_sq
)
print
"b_incoherent = %f*fm"
%
binc
print
"b_coherent_deut = %f*fm"
%
sqrt
(
bcoh_deut_sq
)
print
"b_coherent_deut = %f*fm"
%
numpy
.
sqrt
(
bcoh_deut_sq
)
print
"b_incoherent_deut = %f*fm"
%
binc_deut
MMTK/Database/Atoms/nh
View file @
c84fe5f3
...
...
@@ -4,9 +4,9 @@ mass = 15.014699
color = 'blue'
vdW_radius = 0.155000
from Scientific
import
N
import
numpy
b_coherent = (9.300 + 1*(-3.741))*fm
b_incoherent =
N
.sqrt(2.241**2 + 1*25.217**2)*fm
b_incoherent =
numpy
.sqrt(2.241**2 + 1*25.217**2)*fm
b_coherent_deut = (9.300 + 1*6.674)*fm
b_incoherent_deut =
N
.sqrt(2.241**2 + 1*4.022**2)*fm
del
N
b_incoherent_deut =
numpy
.sqrt(2.241**2 + 1*4.022**2)*fm
del
numpy
MMTK/Database/Atoms/nh2
View file @
c84fe5f3
...
...
@@ -4,9 +4,9 @@ mass = 16.022675
color = 'blue'
vdW_radius = 0.155000
from Scientific
import
N
import
numpy
b_coherent = (9.300 + 2*(-3.741))*fm
b_incoherent =
N
.sqrt(2.241**2 + 2*25.217**2)*fm
b_incoherent =
numpy
.sqrt(2.241**2 + 2*25.217**2)*fm
b_coherent_deut = (9.300 + 2*6.674)*fm
b_incoherent_deut =
N
.sqrt(2.241**2 + 2*4.022**2)*fm
del
N
b_incoherent_deut =
numpy
.sqrt(2.241**2 + 2*4.022**2)*fm
del
numpy
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