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OpenDAS
OpenFold
Commits
621b3645
Commit
621b3645
authored
Oct 21, 2021
by
Gustaf Ahdritz
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Reformat README
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bd0c4d48
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@@ -17,7 +17,7 @@ Try it out with our [Colab notebook](https://colab.research.google.com/github/aq
...
@@ -17,7 +17,7 @@ Try it out with our [Colab notebook](https://colab.research.google.com/github/aq
Unlike DeepMind's public code, OpenFold is also trainable. It can be trained
Unlike DeepMind's public code, OpenFold is also trainable. It can be trained
with or without
[
DeepSpeed
](
https://github.com/microsoft/deepspeed
)
and with
with or without
[
DeepSpeed
](
https://github.com/microsoft/deepspeed
)
and with
mixed precision. bfloat16 training is not currently supported, but will be
mixed precision.
`
bfloat16
`
training is not currently supported, but will be
in the future.
in the future.
## Installation (Linux)
## Installation (Linux)
...
@@ -96,10 +96,13 @@ python3 scripts/precompute_alignments.py mmcif_dir/ alignment_dir/ \
...
@@ -96,10 +96,13 @@ python3 scripts/precompute_alignments.py mmcif_dir/ alignment_dir/ \
Expect this step to take a very long time, even for small numbers of proteins.
Expect this step to take a very long time, even for small numbers of proteins.
Next, generate a cache of certain datapoints in the mmCIF files
as follows
:
Next, generate a cache of certain datapoints in the mmCIF files:
```
bash
```
bash
python3 scripts/generate_mmcif_cache.py mmcif_dir/ mmcif_cache.json
--no_workers
16
python3 scripts/generate_mmcif_cache.py
\
mmcif_dir/
\
mmcif_cache.json
\
--no_workers
16
```
```
This cache is used to minimize the number of mmCIF parses performed during
This cache is used to minimize the number of mmCIF parses performed during
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