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Add checkpoint and CASP13 dataset file sizes to the README and make the requirements more strict.

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PiperOrigin-RevId: 289091312
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Augustin Zidek
2020-01-10 15:46:55 +00:00
committed by Diego de Las Casas
parent 2160fc7f17
commit 3c6b08d3ca
1 changed files with 8 additions and 7 deletions
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alphafold_casp13/README.md
+8 -7
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@@ -15,10 +15,11 @@ Pushmeet Kohli, David T. Jones, David Silver, Koray Kavukcuoglu, Demis Hassabis.
### Dependencies ### Dependencies
* Python 3.6+. * Python 3.6+.
* [Abseil 0.8.0+](https://github.com/abseil/abseil-py) * [Abseil 0.8.0](https://github.com/abseil/abseil-py)
* [Numpy 1.16+](https://numpy.org) * [Numpy 1.16](https://numpy.org)
* [Six 1.12+](https://pypi.org/project/six/) * [Six 1.12](https://pypi.org/project/six/)
* [Sonnet 1.35+](https://github.com/deepmind/sonnet) * [Setuptools 41.0.0](https://setuptools.readthedocs.io/en/latest/)
* [Sonnet 1.35](https://github.com/deepmind/sonnet)
* [TensorFlow 1.14](https://tensorflow.org). Not compatible with TensorFlow * [TensorFlow 1.14](https://tensorflow.org). Not compatible with TensorFlow
2.0+. 2.0+.
* [TensorFlow Probability 0.7.0](https://www.tensorflow.org/probability) * [TensorFlow Probability 0.7.0](https://www.tensorflow.org/probability)
@@ -34,10 +35,10 @@ pip install -r alphafold_casp13/requirements.txt
### Input data ### Input data
The dataset can be downloaded from The dataset to reproduce AlphaFold's CASP13 results can be downloaded from
[Google Cloud Storage](https://console.cloud.google.com/storage/browser/alphafold_casp13_data). [Google Cloud Storage](https://console.cloud.google.com/storage/browser/alphafold_casp13_data).
Download it e.g. using `wget`: Download it e.g. using `wget` (the file is about 43.5 GB):
```shell ```shell
wget https://storage.googleapis.com/alphafold_casp13_data/casp13_data.zip wget https://storage.googleapis.com/alphafold_casp13_data/casp13_data.zip
@@ -69,7 +70,7 @@ targets to get the contact map.
The model checkpoints can be downloaded from The model checkpoints can be downloaded from
[Google Cloud Storage](https://console.cloud.google.com/storage/browser/alphafold_casp13_data). [Google Cloud Storage](https://console.cloud.google.com/storage/browser/alphafold_casp13_data).
Download them e.g. using `wget`: Download them e.g. using `wget` (the file is about 210 MB):
```shell ```shell
wget https://storage.googleapis.com/alphafold_casp13_data/alphafold_casp13_weights.zip wget https://storage.googleapis.com/alphafold_casp13_data/alphafold_casp13_weights.zip