From 243b2e1a57a96f347c26e77ef60c4ba110eb1a42 Mon Sep 17 00:00:00 2001
From: Fatboy <87150253+gefei-qian-nih@users.noreply.github.com>
Date: Sat, 23 Dec 2023 20:14:51 -0500
Subject: [PATCH] Move the scripts folder into esm package

The latest einops version is not compatible with python 3.7. 0.6.1 is the latest version that works with python 3.7.
---
 environment.yml                                                 | 2 +-
 {scripts => esm/scripts}/__init__.py                            | 0
 {scripts => esm/scripts}/atlas/README.md                        | 0
 {scripts => esm/scripts}/atlas/v0/full/bins.txt                 | 0
 {scripts => esm/scripts}/atlas/v0/full/esm2_embeddings.txt      | 0
 .../esm2_embeddings/backfill_v0_tm_.40_.50_plddt_.40_.50.txt    | 0
 .../esm2_embeddings/backfill_v0_tm_.40_.50_plddt_.50_.60.txt    | 0
 .../esm2_embeddings/backfill_v0_tm_.40_.50_plddt_.60_.70.txt    | 0
 .../full/esm2_embeddings/backfill_v0_tm_.40_.50_plddt_0_.40.txt | 0
 .../esm2_embeddings/backfill_v0_tm_.50_.60_plddt_.40_.50.txt    | 0
 .../esm2_embeddings/backfill_v0_tm_.50_.60_plddt_.50_.60.txt    | 0
 .../esm2_embeddings/backfill_v0_tm_.50_.60_plddt_.60_.70.txt    | 0
 .../esm2_embeddings/backfill_v0_tm_.50_.60_plddt_.70_.80.txt    | 0
 .../full/esm2_embeddings/backfill_v0_tm_.50_.60_plddt_0_.40.txt | 0
 .../esm2_embeddings/backfill_v0_tm_.60_.70_plddt_.40_.50.txt    | 0
 .../esm2_embeddings/backfill_v0_tm_.60_.70_plddt_.50_.60.txt    | 0
 .../esm2_embeddings/backfill_v0_tm_.60_.70_plddt_.60_.70.txt    | 0
 .../esm2_embeddings/backfill_v0_tm_.60_.70_plddt_.70_.80.txt    | 0
 .../esm2_embeddings/backfill_v0_tm_.60_.70_plddt_.80_.90.txt    | 0
 .../esm2_embeddings/backfill_v0_tm_.70_.80_plddt_.50_.60.txt    | 0
 .../esm2_embeddings/backfill_v0_tm_.70_.80_plddt_.60_.70.txt    | 0
 .../esm2_embeddings/backfill_v0_tm_.70_.80_plddt_.70_.80.txt    | 0
 .../esm2_embeddings/backfill_v0_tm_.70_.80_plddt_.80_.90.txt    | 0
 .../full/esm2_embeddings/backfill_v0_tm_.70_.80_plddt_.90_1.txt | 0
 .../esm2_embeddings/backfill_v0_tm_.80_.90_plddt_.60_.70.txt    | 0
 .../esm2_embeddings/backfill_v0_tm_.80_.90_plddt_.70_.80.txt    | 0
 .../esm2_embeddings/backfill_v0_tm_.80_.90_plddt_.80_.90.txt    | 0
 .../full/esm2_embeddings/backfill_v0_tm_.80_.90_plddt_.90_1.txt | 0
 .../full/esm2_embeddings/backfill_v0_tm_.90_1_plddt_.70_.80.txt | 0
 .../full/esm2_embeddings/backfill_v0_tm_.90_1_plddt_.80_.90.txt | 0
 .../full/esm2_embeddings/backfill_v0_tm_.90_1_plddt_.90_1.txt   | 0
 .../full/esm2_embeddings/backfill_v0_tm_0_.40_plddt_.40_.50.txt | 0
 .../full/esm2_embeddings/backfill_v0_tm_0_.40_plddt_.50_.60.txt | 0
 .../full/esm2_embeddings/backfill_v0_tm_0_.40_plddt_0_.40.txt   | 0
 .../atlas/v0/full/esm2_embeddings/tm_.40_.50_plddt_.40_.50.txt  | 0
 .../atlas/v0/full/esm2_embeddings/tm_.40_.50_plddt_.50_.60.txt  | 0
 .../atlas/v0/full/esm2_embeddings/tm_.40_.50_plddt_.60_.70.txt  | 0
 .../atlas/v0/full/esm2_embeddings/tm_.40_.50_plddt_.70_.80.txt  | 0
 .../atlas/v0/full/esm2_embeddings/tm_.40_.50_plddt_.80_.90.txt  | 0
 .../atlas/v0/full/esm2_embeddings/tm_.40_.50_plddt_.90_1.txt    | 0
 .../atlas/v0/full/esm2_embeddings/tm_.40_.50_plddt_0_.40.txt    | 0
 .../atlas/v0/full/esm2_embeddings/tm_.50_.60_plddt_.40_.50.txt  | 0
 .../atlas/v0/full/esm2_embeddings/tm_.50_.60_plddt_.50_.60.txt  | 0
 .../atlas/v0/full/esm2_embeddings/tm_.50_.60_plddt_.60_.70.txt  | 0
 .../atlas/v0/full/esm2_embeddings/tm_.50_.60_plddt_.70_.80.txt  | 0
 .../atlas/v0/full/esm2_embeddings/tm_.50_.60_plddt_.80_.90.txt  | 0
 .../atlas/v0/full/esm2_embeddings/tm_.50_.60_plddt_.90_1.txt    | 0
 .../atlas/v0/full/esm2_embeddings/tm_.50_.60_plddt_0_.40.txt    | 0
 .../atlas/v0/full/esm2_embeddings/tm_.60_.70_plddt_.40_.50.txt  | 0
 .../atlas/v0/full/esm2_embeddings/tm_.60_.70_plddt_.50_.60.txt  | 0
 .../atlas/v0/full/esm2_embeddings/tm_.60_.70_plddt_.60_.70.txt  | 0
 .../atlas/v0/full/esm2_embeddings/tm_.60_.70_plddt_.70_.80.txt  | 0
 .../atlas/v0/full/esm2_embeddings/tm_.60_.70_plddt_.80_.90.txt  | 0
 .../atlas/v0/full/esm2_embeddings/tm_.60_.70_plddt_.90_1.txt    | 0
 .../atlas/v0/full/esm2_embeddings/tm_.60_.70_plddt_0_.40.txt    | 0
 .../atlas/v0/full/esm2_embeddings/tm_.70_.80_plddt_.40_.50.txt  | 0
 .../atlas/v0/full/esm2_embeddings/tm_.70_.80_plddt_.50_.60.txt  | 0
 .../atlas/v0/full/esm2_embeddings/tm_.70_.80_plddt_.60_.70.txt  | 0
 .../atlas/v0/full/esm2_embeddings/tm_.70_.80_plddt_.70_.80.txt  | 0
 .../atlas/v0/full/esm2_embeddings/tm_.70_.80_plddt_.80_.90.txt  | 0
 .../atlas/v0/full/esm2_embeddings/tm_.70_.80_plddt_.90_1.txt    | 0
 .../atlas/v0/full/esm2_embeddings/tm_.70_.80_plddt_0_.40.txt    | 0
 .../atlas/v0/full/esm2_embeddings/tm_.80_.90_plddt_.50_.60.txt  | 0
 .../atlas/v0/full/esm2_embeddings/tm_.80_.90_plddt_.60_.70.txt  | 0
 .../atlas/v0/full/esm2_embeddings/tm_.80_.90_plddt_.70_.80.txt  | 0
 .../atlas/v0/full/esm2_embeddings/tm_.80_.90_plddt_.80_.90.txt  | 0
 .../atlas/v0/full/esm2_embeddings/tm_.80_.90_plddt_.90_1.txt    | 0
 .../atlas/v0/full/esm2_embeddings/tm_.90_1_plddt_.70_.80.txt    | 0
 .../atlas/v0/full/esm2_embeddings/tm_.90_1_plddt_.80_.90.txt    | 0
 .../atlas/v0/full/esm2_embeddings/tm_.90_1_plddt_.90_1.txt      | 0
 .../atlas/v0/full/esm2_embeddings/tm_0_.40_plddt_.40_.50.txt    | 0
 .../atlas/v0/full/esm2_embeddings/tm_0_.40_plddt_.50_.60.txt    | 0
 .../atlas/v0/full/esm2_embeddings/tm_0_.40_plddt_.60_.70.txt    | 0
 .../atlas/v0/full/esm2_embeddings/tm_0_.40_plddt_.70_.80.txt    | 0
 .../atlas/v0/full/esm2_embeddings/tm_0_.40_plddt_.80_.90.txt    | 0
 .../atlas/v0/full/esm2_embeddings/tm_0_.40_plddt_.90_1.txt      | 0
 .../atlas/v0/full/esm2_embeddings/tm_0_.40_plddt_0_.40.txt      | 0
 {scripts => esm/scripts}/atlas/v0/full/foldseekdb.txt           | 0
 .../v0/full/foldseekdb/backfill_v0_tm_.40_.50_plddt_.40_.50.txt | 0
 .../v0/full/foldseekdb/backfill_v0_tm_.40_.50_plddt_.50_.60.txt | 0
 .../v0/full/foldseekdb/backfill_v0_tm_.40_.50_plddt_.60_.70.txt | 0
 .../v0/full/foldseekdb/backfill_v0_tm_.40_.50_plddt_0_.40.txt   | 0
 .../v0/full/foldseekdb/backfill_v0_tm_.50_.60_plddt_.40_.50.txt | 0
 .../v0/full/foldseekdb/backfill_v0_tm_.50_.60_plddt_.50_.60.txt | 0
 .../v0/full/foldseekdb/backfill_v0_tm_.50_.60_plddt_.60_.70.txt | 0
 .../v0/full/foldseekdb/backfill_v0_tm_.50_.60_plddt_.70_.80.txt | 0
 .../v0/full/foldseekdb/backfill_v0_tm_.50_.60_plddt_0_.40.txt   | 0
 .../v0/full/foldseekdb/backfill_v0_tm_.60_.70_plddt_.40_.50.txt | 0
 .../v0/full/foldseekdb/backfill_v0_tm_.60_.70_plddt_.50_.60.txt | 0
 .../v0/full/foldseekdb/backfill_v0_tm_.60_.70_plddt_.60_.70.txt | 0
 .../v0/full/foldseekdb/backfill_v0_tm_.60_.70_plddt_.70_.80.txt | 0
 .../v0/full/foldseekdb/backfill_v0_tm_.60_.70_plddt_.80_.90.txt | 0
 .../v0/full/foldseekdb/backfill_v0_tm_.70_.80_plddt_.50_.60.txt | 0
 .../v0/full/foldseekdb/backfill_v0_tm_.70_.80_plddt_.60_.70.txt | 0
 .../v0/full/foldseekdb/backfill_v0_tm_.70_.80_plddt_.70_.80.txt | 0
 .../v0/full/foldseekdb/backfill_v0_tm_.70_.80_plddt_.80_.90.txt | 0
 .../v0/full/foldseekdb/backfill_v0_tm_.70_.80_plddt_.90_1.txt   | 0
 .../v0/full/foldseekdb/backfill_v0_tm_.80_.90_plddt_.60_.70.txt | 0
 .../v0/full/foldseekdb/backfill_v0_tm_.80_.90_plddt_.70_.80.txt | 0
 .../v0/full/foldseekdb/backfill_v0_tm_.80_.90_plddt_.80_.90.txt | 0
 .../v0/full/foldseekdb/backfill_v0_tm_.80_.90_plddt_.90_1.txt   | 0
 .../v0/full/foldseekdb/backfill_v0_tm_.90_1_plddt_.70_.80.txt   | 0
 .../v0/full/foldseekdb/backfill_v0_tm_.90_1_plddt_.80_.90.txt   | 0
 .../v0/full/foldseekdb/backfill_v0_tm_.90_1_plddt_.90_1.txt     | 0
 .../v0/full/foldseekdb/backfill_v0_tm_0_.40_plddt_.40_.50.txt   | 0
 .../v0/full/foldseekdb/backfill_v0_tm_0_.40_plddt_.50_.60.txt   | 0
 .../v0/full/foldseekdb/backfill_v0_tm_0_.40_plddt_0_.40.txt     | 0
 .../atlas/v0/full/foldseekdb/tm_.40_.50_plddt_.40_.50.txt       | 0
 .../atlas/v0/full/foldseekdb/tm_.40_.50_plddt_.50_.60.txt       | 0
 .../atlas/v0/full/foldseekdb/tm_.40_.50_plddt_.60_.70.txt       | 0
 .../atlas/v0/full/foldseekdb/tm_.40_.50_plddt_.70_.80.txt       | 0
 .../atlas/v0/full/foldseekdb/tm_.40_.50_plddt_.80_.90.txt       | 0
 .../atlas/v0/full/foldseekdb/tm_.40_.50_plddt_.90_1.txt         | 0
 .../atlas/v0/full/foldseekdb/tm_.40_.50_plddt_0_.40.txt         | 0
 .../atlas/v0/full/foldseekdb/tm_.50_.60_plddt_.40_.50.txt       | 0
 .../atlas/v0/full/foldseekdb/tm_.50_.60_plddt_.50_.60.txt       | 0
 .../atlas/v0/full/foldseekdb/tm_.50_.60_plddt_.60_.70.txt       | 0
 .../atlas/v0/full/foldseekdb/tm_.50_.60_plddt_.70_.80.txt       | 0
 .../atlas/v0/full/foldseekdb/tm_.50_.60_plddt_.80_.90.txt       | 0
 .../atlas/v0/full/foldseekdb/tm_.50_.60_plddt_.90_1.txt         | 0
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 .../atlas/v0/full/foldseekdb/tm_.80_.90_plddt_.70_.80.txt       | 0
 .../atlas/v0/full/foldseekdb/tm_.80_.90_plddt_.80_.90.txt       | 0
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 .../atlas/v0/full/foldseekdb/tm_.90_1_plddt_.70_.80.txt         | 0
 .../atlas/v0/full/foldseekdb/tm_.90_1_plddt_.80_.90.txt         | 0
 .../scripts}/atlas/v0/full/foldseekdb/tm_.90_1_plddt_.90_1.txt  | 0
 .../atlas/v0/full/foldseekdb/tm_0_.40_plddt_.40_.50.txt         | 0
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 .../atlas/v0/full/foldseekdb/tm_0_.40_plddt_.70_.80.txt         | 0
 .../atlas/v0/full/foldseekdb/tm_0_.40_plddt_.80_.90.txt         | 0
 .../scripts}/atlas/v0/full/foldseekdb/tm_0_.40_plddt_.90_1.txt  | 0
 .../scripts}/atlas/v0/full/foldseekdb/tm_0_.40_plddt_0_.40.txt  | 0
 {scripts => esm/scripts}/atlas/v0/full/tarballs.txt             | 0
 .../v0/full/tarballs/backfill_v0_tm_.40_.50_plddt_.40_.50.txt   | 0
 .../v0/full/tarballs/backfill_v0_tm_.40_.50_plddt_.50_.60.txt   | 0
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 .../atlas/v0/full/tarballs/backfill_v0_tm_.90_1_plddt_.90_1.txt | 0
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 .../atlas/v0/full/tarballs/backfill_v0_tm_0_.40_plddt_0_.40.txt | 0
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 .../scripts}/atlas/v0/highquality_clust30/foldseekdb.txt        | 0
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 {scripts => esm/scripts}/atlas/v2023_02/full/bins.txt           | 0
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diff --git a/environment.yml b/environment.yml
index 2d1b70d1..78bffc05 100644
--- a/environment.yml
+++ b/environment.yml
@@ -10,7 +10,7 @@ dependencies:
   - conda-forge::openmm=7.5.1
   - conda-forge::pdbfixer
   - conda-forge::cudatoolkit==11.3.*
-  - conda-forge::einops
+  - conda-forge::einops=0.6.1
   - conda-forge::fairscale
   - conda-forge::omegaconf
   - conda-forge::hydra-core
diff --git a/scripts/__init__.py b/esm/scripts/__init__.py
similarity index 100%
rename from scripts/__init__.py
rename to esm/scripts/__init__.py
diff --git a/scripts/atlas/README.md b/esm/scripts/atlas/README.md
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rename from scripts/atlas/README.md
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diff --git a/scripts/atlas/v0/full/bins.txt b/esm/scripts/atlas/v0/full/bins.txt
similarity index 100%
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rename to esm/scripts/atlas/v0/full/bins.txt
diff --git a/scripts/atlas/v0/full/esm2_embeddings.txt b/esm/scripts/atlas/v0/full/esm2_embeddings.txt
similarity index 100%
rename from scripts/atlas/v0/full/esm2_embeddings.txt
rename to esm/scripts/atlas/v0/full/esm2_embeddings.txt
diff --git a/scripts/atlas/v0/full/esm2_embeddings/backfill_v0_tm_.40_.50_plddt_.40_.50.txt b/esm/scripts/atlas/v0/full/esm2_embeddings/backfill_v0_tm_.40_.50_plddt_.40_.50.txt
similarity index 100%
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diff --git a/scripts/atlas/v0/full/esm2_embeddings/backfill_v0_tm_.40_.50_plddt_.50_.60.txt b/esm/scripts/atlas/v0/full/esm2_embeddings/backfill_v0_tm_.40_.50_plddt_.50_.60.txt
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diff --git a/scripts/atlas/v0/full/esm2_embeddings/backfill_v0_tm_.40_.50_plddt_.60_.70.txt b/esm/scripts/atlas/v0/full/esm2_embeddings/backfill_v0_tm_.40_.50_plddt_.60_.70.txt
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diff --git a/scripts/atlas/v0/full/esm2_embeddings/backfill_v0_tm_.40_.50_plddt_0_.40.txt b/esm/scripts/atlas/v0/full/esm2_embeddings/backfill_v0_tm_.40_.50_plddt_0_.40.txt
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diff --git a/scripts/atlas/v0/full/esm2_embeddings/backfill_v0_tm_.50_.60_plddt_.40_.50.txt b/esm/scripts/atlas/v0/full/esm2_embeddings/backfill_v0_tm_.50_.60_plddt_.40_.50.txt
similarity index 100%
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diff --git a/scripts/atlas/v0/full/esm2_embeddings/backfill_v0_tm_.50_.60_plddt_.50_.60.txt b/esm/scripts/atlas/v0/full/esm2_embeddings/backfill_v0_tm_.50_.60_plddt_.50_.60.txt
similarity index 100%
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diff --git a/scripts/atlas/v0/full/esm2_embeddings/backfill_v0_tm_.50_.60_plddt_.60_.70.txt b/esm/scripts/atlas/v0/full/esm2_embeddings/backfill_v0_tm_.50_.60_plddt_.60_.70.txt
similarity index 100%
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diff --git a/scripts/atlas/v0/full/esm2_embeddings/backfill_v0_tm_.50_.60_plddt_.70_.80.txt b/esm/scripts/atlas/v0/full/esm2_embeddings/backfill_v0_tm_.50_.60_plddt_.70_.80.txt
similarity index 100%
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diff --git a/scripts/atlas/v0/full/esm2_embeddings/backfill_v0_tm_.50_.60_plddt_0_.40.txt b/esm/scripts/atlas/v0/full/esm2_embeddings/backfill_v0_tm_.50_.60_plddt_0_.40.txt
similarity index 100%
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diff --git a/scripts/atlas/v0/full/esm2_embeddings/backfill_v0_tm_.60_.70_plddt_.40_.50.txt b/esm/scripts/atlas/v0/full/esm2_embeddings/backfill_v0_tm_.60_.70_plddt_.40_.50.txt
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diff --git a/scripts/atlas/v0/full/esm2_embeddings/backfill_v0_tm_.60_.70_plddt_.50_.60.txt b/esm/scripts/atlas/v0/full/esm2_embeddings/backfill_v0_tm_.60_.70_plddt_.50_.60.txt
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diff --git a/scripts/atlas/v0/full/esm2_embeddings/backfill_v0_tm_.60_.70_plddt_.60_.70.txt b/esm/scripts/atlas/v0/full/esm2_embeddings/backfill_v0_tm_.60_.70_plddt_.60_.70.txt
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diff --git a/scripts/atlas/v0/full/esm2_embeddings/backfill_v0_tm_.60_.70_plddt_.70_.80.txt b/esm/scripts/atlas/v0/full/esm2_embeddings/backfill_v0_tm_.60_.70_plddt_.70_.80.txt
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rename to esm/scripts/atlas/v0/full/esm2_embeddings/backfill_v0_tm_.60_.70_plddt_.70_.80.txt
diff --git a/scripts/atlas/v0/full/esm2_embeddings/backfill_v0_tm_.60_.70_plddt_.80_.90.txt b/esm/scripts/atlas/v0/full/esm2_embeddings/backfill_v0_tm_.60_.70_plddt_.80_.90.txt
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rename to esm/scripts/atlas/v0/full/esm2_embeddings/backfill_v0_tm_.60_.70_plddt_.80_.90.txt
diff --git a/scripts/atlas/v0/full/esm2_embeddings/backfill_v0_tm_.70_.80_plddt_.50_.60.txt b/esm/scripts/atlas/v0/full/esm2_embeddings/backfill_v0_tm_.70_.80_plddt_.50_.60.txt
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diff --git a/scripts/atlas/v0/full/esm2_embeddings/backfill_v0_tm_.70_.80_plddt_.60_.70.txt b/esm/scripts/atlas/v0/full/esm2_embeddings/backfill_v0_tm_.70_.80_plddt_.60_.70.txt
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diff --git a/scripts/atlas/v0/full/esm2_embeddings/backfill_v0_tm_.70_.80_plddt_.80_.90.txt b/esm/scripts/atlas/v0/full/esm2_embeddings/backfill_v0_tm_.70_.80_plddt_.80_.90.txt
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diff --git a/scripts/atlas/v0/full/esm2_embeddings/backfill_v0_tm_.70_.80_plddt_.90_1.txt b/esm/scripts/atlas/v0/full/esm2_embeddings/backfill_v0_tm_.70_.80_plddt_.90_1.txt
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diff --git a/scripts/atlas/v2023_02/full/esm2_embeddings/tm_.60_.70_plddt_0_.40.txt b/esm/scripts/atlas/v2023_02/full/esm2_embeddings/tm_.60_.70_plddt_0_.40.txt
similarity index 100%
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similarity index 100%
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similarity index 100%
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similarity index 100%
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similarity index 100%
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similarity index 100%
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similarity index 100%
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diff --git a/scripts/atlas/v2023_02/full/esm2_embeddings/tm_.70_.80_plddt_0_.40.txt b/esm/scripts/atlas/v2023_02/full/esm2_embeddings/tm_.70_.80_plddt_0_.40.txt
similarity index 100%
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similarity index 100%
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similarity index 100%
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similarity index 100%
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similarity index 100%
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similarity index 100%
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similarity index 100%
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similarity index 100%
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diff --git a/scripts/atlas/v2023_02/full/esm2_embeddings/tm_0_.40_plddt_.40_.50.txt b/esm/scripts/atlas/v2023_02/full/esm2_embeddings/tm_0_.40_plddt_.40_.50.txt
similarity index 100%
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similarity index 100%
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similarity index 100%
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similarity index 100%
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similarity index 100%
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diff --git a/scripts/atlas/v2023_02/full/foldseekdb.txt b/esm/scripts/atlas/v2023_02/full/foldseekdb.txt
similarity index 100%
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similarity index 100%
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similarity index 100%
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similarity index 100%
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similarity index 100%
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similarity index 100%
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similarity index 100%
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similarity index 100%
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similarity index 100%
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