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OpenDAS
OpenFold
Commits
0d348792
Commit
0d348792
authored
Jul 16, 2023
by
Geoffrey Yu
Browse files
fixed the error when loading a monomeric training object
parent
caac73c0
Changes
1
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1 changed file
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2 additions
and
4 deletions
+2
-4
openfold/data/data_modules.py
openfold/data/data_modules.py
+2
-4
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openfold/data/data_modules.py
View file @
0d348792
...
...
@@ -434,7 +434,6 @@ class OpenFoldSingleMultimerDataset(torch.utils.data.Dataset):
self
.
multimer_data_pipeline
=
data_pipeline
.
DataPipelineMultimer
(
monomer_data_pipeline
=
self
.
data_pipeline
)
self
.
feature_pipeline
=
feature_pipeline
.
FeaturePipeline
(
config
)
def
_parse_mmcif
(
self
,
path
,
file_id
,
chain_id
,
alignment_dir
,
alignment_index
):
...
...
@@ -470,18 +469,17 @@ class OpenFoldSingleMultimerDataset(torch.utils.data.Dataset):
def
__getitem__
(
self
,
idx
):
mmcif_id
=
self
.
idx_to_mmcif_id
(
idx
)
chains
=
self
.
mmcif_data_cache
[
mmcif_id
][
'chain_ids'
]
is_multimer
=
(
len
(
chains
)
>
1
)
seqs
=
self
.
mmcif_data_cache
[
mmcif_id
][
'seqs'
]
fasta_str
=
""
for
c
,
s
in
zip
(
chains
,
seqs
):
fasta_str
+=
f
">
{
mmcif_id
}
_
{
c
}
\n
{
s
}
\n
"
with
temp_fasta_file
(
fasta_str
)
as
fasta_file
:
all_chain_features
=
self
.
multimer_data_pipeline
.
process_fasta
(
fasta_file
,
self
.
alignment_dir
)
# process all_chain_features
all_chain_features
=
self
.
feature_pipeline
.
process_features
(
all_chain_features
,
mode
=
self
.
mode
,
is_multimer
=
is_multimer
)
is_multimer
=
True
)
alignment_index
=
None
ground_truth
=
[]
...
...
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