update readme std

9c213d7a · zhuwenwen · 898a3706 · 9c213d7a
Commit 9c213d7a authored Sep 07, 2023 by zhuwenwen
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README.md README.md +32 -20

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@@ -42,33 +42,44 @@ docker run -it --name alphafold --shm-size=32G  --device=/dev/kfd --device=/dev/
 ## 数据集
 推荐使用AlphaFold2中的开源数据集，包括BFD、MGnify、PDB70、Uniclust、Uniref90等,数据集大小约2.2TB。数据集格式如下：
 ```
-$DOWNLOAD_DIR/                             # Total: ~ 2.2 TB (download: 438 GB)
+$DOWNLOAD_DIR/                             
-    bfd/                                   # ~ 1.7 TB (download: 271.6 GB)
+    bfd/  
-        # 6 files.
+        bfd_metaclust_clu_complete_id30_c90_final_seq.sorted_opt_hhm.ffindex
-    mgnify/                                # ~ 64 GB (download: 32.9 GB)
+        bfd_metaclust_clu_complete_id30_c90_final_seq.sorted_opt_hhm.ffdata 
+        bfd_metaclust_clu_complete_id30_c90_final_seq.sorted_opt_cs219.ffindex                           
+        ...
+    mgnify/                                
        mgy_clusters_2018_12.fa
-    params/                                # ~ 3.5 GB (download: 3.5 GB)
+    params/                                
-        # 5 CASP14 models,
+        params_model_1.npz
-        # 5 pTM models,
+        params_model_2.npz
-        # 5 AlphaFold-Multimer models,
+        params_model_3.npz
-        # LICENSE,
+        ...
-        # = 16 files.
+    pdb70/                                
-    pdb70/                                 # ~ 56 GB (download: 19.5 GB)
+        pdb_filter.dat
-        # 9 files.
+        pdb70_hhm.ffindex
-    pdb_mmcif/                             # ~ 206 GB (download: 46 GB)
+        pdb70_hhm.ffdata
+        ...
+    pdb_mmcif/                            
        mmcif_files/
-            # About 180,000 .cif files.
+            100d.cif
+            101d.cif
+            101m.cif
+            ...
        obsolete.dat
-    pdb_seqres/                            # ~ 0.2 GB (download: 0.2 GB)
+    pdb_seqres/                            
        pdb_seqres.txt
-    small_bfd/                             # ~ 17 GB (download: 9.6 GB)
+    small_bfd/                           
        bfd-first_non_consensus_sequences.fasta
-    uniclust30/                            # ~ 86 GB (download: 24.9 GB)
+    uniclust30/                            
        uniclust30_2018_08/
-            # 13 files.
+            uniclust30_2018_08_md5sum
-    uniprot/                               # ~ 98.3 GB (download: 49 GB)
+            uniclust30_2018_08_hhm_db.index
+            uniclust30_2018_08_hhm_db
+            ...
+    uniprot/                               
        uniprot.fasta
-    uniref90/                              # ~ 58 GB (download: 29.7 GB)
+    uniref90/                             
        uniref90.fasta
 ```
@@ -137,6 +148,7 @@ multimer.fasta为推理的多体序列，data为数据集下载路径，其他
        ...
 ```
+查看蛋白质3D结构：[https://www.pdbus.org/3d-view](https://www.pdbus.org/3d-view)
 ![img](./docs/result_pdb.png)
 ## 精度