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James Graham
pycgtool
Commits
fc57e818
Commit
fc57e818
authored
8 years ago
by
James Graham
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Refactor tests for Frame class - no more xfail
parent
81ed384d
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Changes
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3 changed files
pycgtool/frame.py
+8
-1
8 additions, 1 deletion
pycgtool/frame.py
test/data/water.pdb
+669
-0
669 additions, 0 deletions
test/data/water.pdb
test/test_frame.py
+45
-36
45 additions, 36 deletions
test/test_frame.py
with
722 additions
and
37 deletions
pycgtool/frame.py
+
8
−
1
View file @
fc57e818
...
...
@@ -346,7 +346,8 @@ class Frame:
if
gro
is
not
None
:
open_xtc
=
{
"
simpletraj
"
:
FrameReaderSimpleTraj
,
"
mdtraj
"
:
FrameReaderMDTraj
}
"
mdtraj
"
:
FrameReaderMDTraj
,
"
mdanalysis
"
:
FrameReaderMDAnalysis
}
try
:
self
.
_trajreader
=
open_xtc
[
xtc_reader
](
gro
,
xtc
,
frame_start
=
frame_start
)
except
KeyError
as
e
:
...
...
@@ -364,6 +365,12 @@ class Frame:
@classmethod
def
instance_from_reader
(
cls
,
reader
):
"""
Return Frame instance initialised from existing FrameReader object
:param FrameReader reader: FrameReader object
:return: Frame instance
"""
obj
=
cls
()
obj
.
_trajreader
=
reader
obj
.
_trajreader
.
initialise_frame
(
obj
)
...
...
This diff is collapsed.
Click to expand it.
test/data/water.pdb
0 → 100644
+
669
−
0
View file @
fc57e818
This diff is collapsed.
Click to expand it.
test/test_frame.py
+
45
−
36
View file @
fc57e818
...
...
@@ -6,7 +6,7 @@ import logging
import
numpy
as
np
from
pycgtool.frame
import
Atom
,
Residue
,
Frame
from
pycgtool.frame
import
FrameReaderSimpleTraj
,
FrameReaderMDAnalysis
,
FrameReader
from
pycgtool.frame
import
FrameReaderSimpleTraj
,
FrameReaderMDAnalysis
,
FrameReader
MDTraj
,
FrameReader
try
:
import
mdtraj
...
...
@@ -54,6 +54,31 @@ class ResidueTest(unittest.TestCase):
class
FrameTest
(
unittest
.
TestCase
):
def
helper_read_xtc
(
self
,
frame
,
first_only
=
False
,
skip_names
=
False
):
self
.
assertEqual
(
663
,
frame
.
natoms
)
self
.
assertEqual
(
221
,
len
(
frame
.
residues
))
self
.
assertEqual
(
3
,
len
(
frame
.
residues
[
0
].
atoms
))
if
not
skip_names
:
# MDTraj renames water
self
.
assertEqual
(
"
SOL
"
,
frame
.
residues
[
0
].
name
)
self
.
assertEqual
(
"
OW
"
,
frame
.
residues
[
0
].
atoms
[
0
].
name
)
atom0_coords
=
np
.
array
([
[
0.696
,
1.330
,
1.211
],
[
1.176
,
1.152
,
1.586
],
[
1.122
,
1.130
,
1.534
]
])
box_vectors
=
np
.
array
([
[
1.89868
,
1.89868
,
1.89868
],
[
1.9052
,
1.9052
,
1.9052
],
[
1.90325272
,
1.90325272
,
1.90325272
]
])
for
i
in
range
(
1
if
first_only
else
len
(
atom0_coords
)):
np
.
testing
.
assert_allclose
(
atom0_coords
[
i
],
frame
.
residues
[
0
].
atoms
[
0
].
coords
)
np
.
testing
.
assert_allclose
(
box_vectors
[
i
],
frame
.
box
,
rtol
=
1e-4
)
# PDB files are f9.3
frame
.
next_frame
()
def
test_frame_create
(
self
):
Frame
()
...
...
@@ -64,35 +89,39 @@ class FrameTest(unittest.TestCase):
self
.
assertEqual
(
residue
,
frame
.
residues
[
0
])
self
.
assertTrue
(
residue
is
frame
.
residues
[
0
])
def
helper_read_gro
(
self
,
frame
):
self
.
assertEqual
(
221
,
len
(
frame
.
residues
))
self
.
assertEqual
(
"
SOL
"
,
frame
.
residues
[
0
].
name
)
self
.
assertEqual
(
3
,
len
(
frame
.
residues
[
0
].
atoms
))
self
.
assertEqual
(
"
OW
"
,
frame
.
residues
[
0
].
atoms
[
0
].
name
)
np
.
testing
.
assert_allclose
(
np
.
array
([
0.696
,
1.33
,
1.211
]),
frame
.
residues
[
0
].
atoms
[
0
].
coords
)
def
test_frame_simpletraj_read_gro
(
self
):
frame
=
Frame
(
"
test/data/water.gro
"
,
xtc_reader
=
"
simpletraj
"
)
self
.
helper_read_
gro
(
frame
)
self
.
helper_read_
xtc
(
frame
,
first_only
=
True
)
# MDTRAJ changes water name to HOH
@unittest.expectedFailure
@unittest.skipIf
(
not
mdtraj_present
,
"
MDTRAJ or Scipy not present
"
)
def
test_frame_mdtraj_read_gro
(
self
):
logging
.
disable
(
logging
.
WARNING
)
frame
=
Frame
(
"
test/data/water.gro
"
,
xtc_reader
=
"
mdtraj
"
)
logging
.
disable
(
logging
.
NOTSET
)
self
.
helper_read_
gro
(
frame
)
self
.
helper_read_
xtc
(
frame
,
first_only
=
True
,
skip_names
=
True
)
@unittest.skipIf
(
not
mdanalysis_present
,
"
MDAnalysis not present
"
)
def
test_frame_mdanalysis_read_gro
(
self
):
reader
=
FrameReaderMDAnalysis
(
"
test/data/water.gro
"
)
frame
=
Frame
.
instance_from_reader
(
reader
)
self
.
helper_read_gro
(
frame
)
self
.
helper_read_xtc
(
frame
,
first_only
=
True
)
@unittest.skipIf
(
not
mdtraj_present
,
"
MDTRAJ or Scipy not present
"
)
def
test_frame_mdtraj_read_pdb
(
self
):
reader
=
FrameReaderMDTraj
(
"
test/data/water.pdb
"
)
frame
=
Frame
.
instance_from_reader
(
reader
)
self
.
helper_read_xtc
(
frame
,
first_only
=
True
,
skip_names
=
True
)
@unittest.skipIf
(
not
mdanalysis_present
,
"
MDAnalysis not present
"
)
def
test_frame_mdanalysis_read_pdb
(
self
):
reader
=
FrameReaderMDAnalysis
(
"
test/data/water.pdb
"
)
frame
=
Frame
.
instance_from_reader
(
reader
)
self
.
helper_read_xtc
(
frame
,
first_only
=
True
)
def
test_frame_output_gro
(
self
):
frame
=
Frame
(
"
test/data/water.gro
"
)
...
...
@@ -113,26 +142,6 @@ class FrameTest(unittest.TestCase):
logging
.
disable
(
logging
.
NOTSET
)
self
.
assertEqual
(
11
,
frame
.
numframes
)
def
helper_read_xtc
(
self
,
frame
):
self
.
assertEqual
(
663
,
frame
.
natoms
)
# These are the coordinates from the gro file
np
.
testing
.
assert_allclose
(
np
.
array
([
0.696
,
1.33
,
1.211
]),
frame
.
residues
[
0
].
atoms
[
0
].
coords
)
np
.
testing
.
assert_allclose
(
np
.
array
([
1.89868
,
1.89868
,
1.89868
]),
frame
.
box
)
frame
.
next_frame
()
# These coordinates are from the xtc file
np
.
testing
.
assert_allclose
(
np
.
array
([
1.176
,
1.152
,
1.586
]),
frame
.
residues
[
0
].
atoms
[
0
].
coords
)
np
.
testing
.
assert_allclose
(
np
.
array
([
1.9052
,
1.9052
,
1.9052
]),
frame
.
box
)
frame
.
next_frame
()
np
.
testing
.
assert_allclose
(
np
.
array
([
1.122
,
1.130
,
1.534
]),
frame
.
residues
[
0
].
atoms
[
0
].
coords
)
np
.
testing
.
assert_allclose
(
np
.
array
([
1.90325272
,
1.90325272
,
1.90325272
]),
frame
.
box
)
def
test_frame_simpletraj_read_xtc
(
self
):
frame
=
Frame
(
gro
=
"
test/data/water.gro
"
,
xtc
=
"
test/data/water.xtc
"
,
xtc_reader
=
"
simpletraj
"
)
...
...
@@ -145,7 +154,7 @@ class FrameTest(unittest.TestCase):
xtc_reader
=
"
mdtraj
"
)
logging
.
disable
(
logging
.
NOTSET
)
self
.
helper_read_xtc
(
frame
)
self
.
helper_read_xtc
(
frame
,
skip_names
=
True
)
@unittest.skipIf
(
not
mdanalysis_present
,
"
MDAnalysis not present
"
)
def
test_frame_mdanalysis_read_xtc
(
self
):
...
...
@@ -173,7 +182,7 @@ class FrameTest(unittest.TestCase):
reader
=
FrameReaderSimpleTraj
(
"
test/data/water.gro
"
)
frame
=
Frame
.
instance_from_reader
(
reader
)
self
.
helper_read_
gro
(
frame
)
self
.
helper_read_
xtc
(
frame
,
first_only
=
True
)
def
test_frame_instance_from_reader_dummy
(
self
):
class
DummyReader
(
FrameReader
):
...
...
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