Skip to content
GitLab
Menu
Projects
Groups
Snippets
Loading...
Help
Help
Support
Community forum
Keyboard shortcuts
?
Submit feedback
Contribute to GitLab
Sign in / Register
Toggle navigation
Menu
Open sidebar
OpenDAS
OpenFold
Commits
0a0a741f
Commit
0a0a741f
authored
Oct 07, 2021
by
Gustaf Ahdritz
Browse files
Fix circular import
parent
1a341511
Changes
1
Hide whitespace changes
Inline
Side-by-side
Showing
1 changed file
with
3 additions
and
10 deletions
+3
-10
openfold/np/relax/amber_minimize.py
openfold/np/relax/amber_minimize.py
+3
-10
No files found.
openfold/np/relax/amber_minimize.py
View file @
0a0a741f
...
...
@@ -24,14 +24,7 @@ from openfold.np import (
protein
,
residue_constants
,
)
from
openfold.utils.loss
import
(
find_structural_violations_np
,
compute_violation_metrics_np
,
)
find_structural_violations
=
find_structural_violations_np
compute_violation_metrics
=
compute_violation_metrics_np
import
openfold.utils.loss
as
loss
from
openfold.np.relax
import
cleanup
,
utils
import
ml_collections
import
numpy
as
np
...
...
@@ -343,14 +336,14 @@ def find_violations(prot_np: protein.Protein):
batch
[
"seq_mask"
]
=
np
.
ones_like
(
batch
[
"aatype"
],
np
.
float32
)
batch
=
make_atom14_positions
(
batch
)
violations
=
find_structural_violations
(
violations
=
loss
.
find_structural_violations
_np
(
batch
=
batch
,
atom14_pred_positions
=
batch
[
"atom14_gt_positions"
],
config
=
ml_collections
.
ConfigDict
(
{
"violation_tolerance_factor"
:
12
,
# Taken from model config.
"clash_overlap_tolerance"
:
1.5
,
# Taken from model config.
}))
violation_metrics
=
compute_violation_metrics
(
violation_metrics
=
loss
.
compute_violation_metrics
_np
(
batch
=
batch
,
atom14_pred_positions
=
batch
[
"atom14_gt_positions"
],
violations
=
violations
,
...
...
Write
Preview
Markdown
is supported
0%
Try again
or
attach a new file
.
Attach a file
Cancel
You are about to add
0
people
to the discussion. Proceed with caution.
Finish editing this message first!
Cancel
Please
register
or
sign in
to comment