Add training data necessary for overfitting experiments (#182)

* Update README.md

* Create 209d-assembly1.cif

* Create 721p-assembly1.cif

* Create 209d-assembly1C_protein_pdball_230102_db.m8

* Create 209d-assembly1C_protein.a3m

* Add files via upload

* Add files via upload

* Create 7a4d-assembly1.cif

Author: amorehead

README.md

@@ -307,7 +307,7 @@ python scripts/cluster_pdb_test_mmcifs.py --mmcif_dir <mmcif_dir> --reference_1_
 
 **Note**: The `--clustering_filtered_pdb_dataset` flag is recommended when clustering the filtered PDB dataset as curated using the scripts above, as this flag will enable faster runtimes in this context (since filtering leaves each chain's residue IDs 1-based). However, this flag must **not** be provided when clustering other (i.e., non-PDB) datasets of mmCIF files. Otherwise, interface clustering may be performed incorrectly, as these datasets' mmCIF files may not use strict 1-based residue indexing for each chain.
 
-**Note**: One can instead download preprocessed (i.e., filtered) mmCIF (`train`/`val`/`test`) files (~25GB, comprising 148k complexes) and chain/interface clustering (`train`/`val`/`test`) files (~3GB) for the PDB's `20240101` AWS snapshot via a [shared OneDrive folder](https://mailmissouri-my.sharepoint.com/:f:/g/personal/acmwhb_umsystem_edu/EqU8tjUmmKxJr-FAlq4tzaIBi2TIBtmw5Vl3k_kmgNlepA?e=mzlyv6). Each of these `tar` archives should be uncompressed within the `data/pdb_data/` directory.
+**Note**: One can instead download preprocessed (i.e., filtered) mmCIF (`train`/`val`/`test`) files (~25GB, comprising 148k complexes) and chain/interface clustering (`train`/`val`/`test`) files (~3GB) for the PDB's `20240101` AWS snapshot via a [shared OneDrive folder](https://mailmissouri-my.sharepoint.com/:f:/g/personal/acmwhb_umsystem_edu/EqU8tjUmmKxJr-FAlq4tzaIBi2TIBtmw5Vl3k_kmgNlepA?e=mzlyv6). Each of these `tar.gz` archives should be decompressed within the `data/pdb_data/` directory e.g., via `tar -xzf data_caches.tar.gz -C data/pdb_data/`.
 
 ## Contributing
 

data/pdb_data/data_caches/msa/train_msas/209d-assembly1C_protein.a3m

@@ -0,0 +1,4 @@
+>101
+TXPGVTXPGV
+>101
+TXPGVTXPGV

data/pdb_data/data_caches/msa/train_msas/721p-assembly1A_protein.a3m

@@ -0,0 +1,4 @@
+>101
+LEEELKQLEEELQAIEEQLAQLQWKAQARKEKLAQLKEKL
+>101
+LEEELKQLEEELQAIEEQLAQLQWKAQARKEKLAQLKEKL

data/pdb_data/data_caches/msa/train_msas/721p-assembly1B_protein.a3m

@@ -0,0 +1,4 @@
+>101
+LEEELKQLEEELQAIEEQLAQLQWKAQARKEKLAQLKEKL
+>101
+LEEELKQLEEELQAIEEQLAQLQWKAQARKEKLAQLKEKL