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OpenDAS
OpenFold
Commits
26d555d5
Commit
26d555d5
authored
Jan 29, 2024
by
Jennifer
Browse files
readme and small updates for soloseq support on multimer
parent
30195c4a
Changes
2
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2 changed files
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3 additions
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3 deletions
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-3
README.md
README.md
+1
-1
openfold/data/templates.py
openfold/data/templates.py
+2
-2
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README.md
View file @
26d555d5
...
@@ -351,7 +351,7 @@ python3 run_pretrained_openfold.py \
...
@@ -351,7 +351,7 @@ python3 run_pretrained_openfold.py \
--output_dir
./
\
--output_dir
./
\
--model_device
"cuda:0"
\
--model_device
"cuda:0"
\
--config_preset
"seq_model_esm1b_ptm"
\
--config_preset
"seq_model_esm1b_ptm"
\
--openfold_checkpoint_path
openfold/resources/openfold_params/seq_model_esm1b_ptm.pt
\
--openfold_checkpoint_path
openfold/resources/openfold_
soloseq-
params/seq_model_esm1b_ptm.pt
\
--uniref90_database_path
data/uniref90/uniref90.fasta
\
--uniref90_database_path
data/uniref90/uniref90.fasta
\
--pdb70_database_path
data/pdb70/pdb70
\
--pdb70_database_path
data/pdb70/pdb70
\
--jackhmmer_binary_path
lib/conda/envs/openfold_venv/bin/jackhmmer
\
--jackhmmer_binary_path
lib/conda/envs/openfold_venv/bin/jackhmmer
\
...
...
openfold/data/templates.py
View file @
26d555d5
...
@@ -101,8 +101,8 @@ def empty_template_feats(n_res):
...
@@ -101,8 +101,8 @@ def empty_template_feats(n_res):
"template_all_atom_positions"
:
np
.
zeros
(
"template_all_atom_positions"
:
np
.
zeros
(
(
0
,
n_res
,
residue_constants
.
atom_type_num
,
3
),
np
.
float32
(
0
,
n_res
,
residue_constants
.
atom_type_num
,
3
),
np
.
float32
),
),
"template_domain_names"
:
np
.
array
([
''
.
encode
()],
dtype
=
np
.
object
),
"template_domain_names"
:
np
.
array
([
''
.
encode
()],
dtype
=
object
),
"template_sequence"
:
np
.
array
([
''
.
encode
()],
dtype
=
np
.
object
),
"template_sequence"
:
np
.
array
([
''
.
encode
()],
dtype
=
object
),
"template_sum_probs"
:
np
.
zeros
((
0
,
1
),
dtype
=
np
.
float32
),
"template_sum_probs"
:
np
.
zeros
((
0
,
1
),
dtype
=
np
.
float32
),
}
}
...
...
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