Skip to content
GitLab
Explore
Sign in
Primary navigation
Search or go to…
Project
P
ProMod3
Manage
Activity
Members
Plan
Jira
Code
Repository
Branches
Commits
Tags
Repository graph
Compare revisions
Deploy
Releases
Container registry
Model registry
Analyze
Contributor analytics
Repository analytics
Model experiments
Help
Help
Support
GitLab documentation
Compare GitLab plans
Community forum
Contribute to GitLab
Provide feedback
Keyboard shortcuts
?
Snippets
Groups
Projects
Show more breadcrumbs
schwede
ProMod3
Commits
7f593778
Commit
7f593778
authored
10 years ago
by
Bienchen
Committed by
BIOPZ-Johner Niklaus
10 years ago
Browse files
Options
Downloads
Patches
Plain Diff
Renamed meld to rawmodel
parent
c1478f9e
No related branches found
No related tags found
No related merge requests found
Changes
61
Hide whitespace changes
Inline
Side-by-side
Showing
1 changed file
rawmodel/tests/test_raw_modeling.py
+9
-9
9 additions, 9 deletions
rawmodel/tests/test_raw_modeling.py
with
9 additions
and
9 deletions
rawmodel/tests/test_raw_modeling.py
+
9
−
9
View file @
7f593778
"""
"""
Unit tests for
m
el
d
.
Unit tests for
rawmod
el.
"""
"""
import
unittest
import
unittest
from
promod3
import
m
el
d
from
promod3
import
rawmod
el
from
ost
import
conop
,
seq
,
io
,
mol
from
ost
import
conop
,
seq
,
io
,
mol
class
RawModelingTests
(
unittest
.
TestCase
):
class
RawModelingTests
(
unittest
.
TestCase
):
...
@@ -17,14 +17,14 @@ class RawModelingTests(unittest.TestCase):
...
@@ -17,14 +17,14 @@ class RawModelingTests(unittest.TestCase):
# test that BuildRawModel throws exception when no view is attached
# test that BuildRawModel throws exception when no view is attached
aln
=
seq
.
CreateAlignment
(
seq
.
CreateSequence
(
'
A
'
,
'
acdef
'
),
aln
=
seq
.
CreateAlignment
(
seq
.
CreateSequence
(
'
A
'
,
'
acdef
'
),
seq
.
CreateSequence
(
'
B
'
,
'
ac-ef
'
))
seq
.
CreateSequence
(
'
B
'
,
'
ac-ef
'
))
self
.
assertRaises
(
RuntimeError
,
m
el
d
.
BuildRawModel
,
aln
)
self
.
assertRaises
(
RuntimeError
,
rawmod
el
.
BuildRawModel
,
aln
)
def
testModeledSequence
(
self
):
def
testModeledSequence
(
self
):
# test if the model has the sequence we want.
# test if the model has the sequence we want.
tpl
=
io
.
LoadPDB
(
'
data/raw-modeling/gly.pdb
'
)
tpl
=
io
.
LoadPDB
(
'
data/raw-modeling/gly.pdb
'
)
aln
=
io
.
LoadAlignment
(
'
data/raw-modeling/seq.fasta
'
)
aln
=
io
.
LoadAlignment
(
'
data/raw-modeling/seq.fasta
'
)
aln
.
AttachView
(
1
,
tpl
.
CreateFullView
())
aln
.
AttachView
(
1
,
tpl
.
CreateFullView
())
result
=
m
el
d
.
BuildRawModel
(
aln
)
result
=
rawmod
el
.
BuildRawModel
(
aln
)
seq1
=
seq
.
SequenceFromChain
(
'
MODEL
'
,
result
.
model
.
chains
[
0
])
seq1
=
seq
.
SequenceFromChain
(
'
MODEL
'
,
result
.
model
.
chains
[
0
])
self
.
assertEqual
(
seq1
.
string
,
aln
.
sequences
[
0
].
string
)
self
.
assertEqual
(
seq1
.
string
,
aln
.
sequences
[
0
].
string
)
...
@@ -33,7 +33,7 @@ class RawModelingTests(unittest.TestCase):
...
@@ -33,7 +33,7 @@ class RawModelingTests(unittest.TestCase):
tpl
=
io
.
LoadPDB
(
'
data/raw-modeling/gly.pdb
'
)
tpl
=
io
.
LoadPDB
(
'
data/raw-modeling/gly.pdb
'
)
aln
=
io
.
LoadAlignment
(
'
data/raw-modeling/del.fasta
'
)
aln
=
io
.
LoadAlignment
(
'
data/raw-modeling/del.fasta
'
)
aln
.
AttachView
(
1
,
tpl
.
CreateFullView
())
aln
.
AttachView
(
1
,
tpl
.
CreateFullView
())
result
=
m
el
d
.
BuildRawModel
(
aln
)
result
=
rawmod
el
.
BuildRawModel
(
aln
)
residues
=
result
.
model
.
residues
residues
=
result
.
model
.
residues
self
.
assertEqual
(
len
(
result
.
gaps
),
1
)
self
.
assertEqual
(
len
(
result
.
gaps
),
1
)
self
.
assertEqual
(
result
.
gaps
[
0
].
before
,
residues
[
2
])
self
.
assertEqual
(
result
.
gaps
[
0
].
before
,
residues
[
2
])
...
@@ -45,7 +45,7 @@ class RawModelingTests(unittest.TestCase):
...
@@ -45,7 +45,7 @@ class RawModelingTests(unittest.TestCase):
tpl
=
io
.
LoadPDB
(
'
data/raw-modeling/gly.pdb
'
)
tpl
=
io
.
LoadPDB
(
'
data/raw-modeling/gly.pdb
'
)
aln
=
io
.
LoadAlignment
(
'
data/raw-modeling/ins.fasta
'
)
aln
=
io
.
LoadAlignment
(
'
data/raw-modeling/ins.fasta
'
)
aln
.
AttachView
(
1
,
tpl
.
CreateFullView
())
aln
.
AttachView
(
1
,
tpl
.
CreateFullView
())
result
=
m
el
d
.
BuildRawModel
(
aln
)
result
=
rawmod
el
.
BuildRawModel
(
aln
)
residues
=
result
.
model
.
residues
residues
=
result
.
model
.
residues
self
.
assertEqual
(
len
(
result
.
gaps
),
1
)
self
.
assertEqual
(
len
(
result
.
gaps
),
1
)
self
.
assertEqual
(
result
.
gaps
[
0
].
before
,
residues
[
1
])
self
.
assertEqual
(
result
.
gaps
[
0
].
before
,
residues
[
1
])
...
@@ -58,7 +58,7 @@ class RawModelingTests(unittest.TestCase):
...
@@ -58,7 +58,7 @@ class RawModelingTests(unittest.TestCase):
tpl
=
io
.
LoadPDB
(
'
data/raw-modeling/gly.pdb
'
)
tpl
=
io
.
LoadPDB
(
'
data/raw-modeling/gly.pdb
'
)
aln
=
io
.
LoadAlignment
(
'
data/raw-modeling/ter.fasta
'
)
aln
=
io
.
LoadAlignment
(
'
data/raw-modeling/ter.fasta
'
)
aln
.
AttachView
(
1
,
tpl
.
CreateFullView
())
aln
.
AttachView
(
1
,
tpl
.
CreateFullView
())
result
=
m
el
d
.
BuildRawModel
(
aln
)
result
=
rawmod
el
.
BuildRawModel
(
aln
)
residues
=
result
.
model
.
residues
residues
=
result
.
model
.
residues
self
.
assertEqual
(
len
(
result
.
gaps
),
2
)
self
.
assertEqual
(
len
(
result
.
gaps
),
2
)
self
.
assertEqual
(
result
.
gaps
[
0
].
before
,
mol
.
ResidueHandle
())
self
.
assertEqual
(
result
.
gaps
[
0
].
before
,
mol
.
ResidueHandle
())
...
@@ -73,7 +73,7 @@ class RawModelingTests(unittest.TestCase):
...
@@ -73,7 +73,7 @@ class RawModelingTests(unittest.TestCase):
tpl
=
io
.
LoadPDB
(
'
data/raw-modeling/sep.pdb
'
)
tpl
=
io
.
LoadPDB
(
'
data/raw-modeling/sep.pdb
'
)
aln
=
io
.
LoadAlignment
(
'
data/raw-modeling/sep.fasta
'
)
aln
=
io
.
LoadAlignment
(
'
data/raw-modeling/sep.fasta
'
)
aln
.
AttachView
(
1
,
tpl
.
CreateFullView
())
aln
.
AttachView
(
1
,
tpl
.
CreateFullView
())
result
=
m
el
d
.
BuildRawModel
(
aln
)
result
=
rawmod
el
.
BuildRawModel
(
aln
)
residues
=
result
.
model
.
residues
residues
=
result
.
model
.
residues
self
.
assertEqual
(
len
(
residues
),
1
)
self
.
assertEqual
(
len
(
residues
),
1
)
self
.
assertEqual
(
len
(
residues
[
0
].
atoms
),
6
)
self
.
assertEqual
(
len
(
residues
[
0
].
atoms
),
6
)
...
@@ -89,7 +89,7 @@ class RawModelingTests(unittest.TestCase):
...
@@ -89,7 +89,7 @@ class RawModelingTests(unittest.TestCase):
tpl
=
io
.
LoadPDB
(
'
data/raw-modeling/cbeta.pdb
'
)
tpl
=
io
.
LoadPDB
(
'
data/raw-modeling/cbeta.pdb
'
)
aln
=
io
.
LoadAlignment
(
'
data/raw-modeling/cbeta.fasta
'
)
aln
=
io
.
LoadAlignment
(
'
data/raw-modeling/cbeta.fasta
'
)
aln
.
AttachView
(
1
,
tpl
.
CreateFullView
())
aln
.
AttachView
(
1
,
tpl
.
CreateFullView
())
result
=
m
el
d
.
BuildRawModel
(
aln
)
result
=
rawmod
el
.
BuildRawModel
(
aln
)
residues
=
result
.
model
.
residues
residues
=
result
.
model
.
residues
self
.
assertFalse
(
residues
[
0
].
FindAtom
(
"
CB
"
).
IsValid
())
self
.
assertFalse
(
residues
[
0
].
FindAtom
(
"
CB
"
).
IsValid
())
self
.
assertFalse
(
residues
[
1
].
FindAtom
(
"
CB
"
).
IsValid
())
self
.
assertFalse
(
residues
[
1
].
FindAtom
(
"
CB
"
).
IsValid
())
...
...
This diff is collapsed.
Click to expand it.
Prev
1
2
3
4
Next
Preview
0%
Loading
Try again
or
attach a new file
.
Cancel
You are about to add
0
people
to the discussion. Proceed with caution.
Finish editing this message first!
Save comment
Cancel
Please
register
or
sign in
to comment