Move patch_mmcif README

tools/alphafold/scripts/db/patch_mmcif/README.md

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+# Patching the MMCIF database
+
+Due to the PDB MMCIF databases being out-of-sync with other AlphaFold
+reference databases, the following error has been seen in AlphaFold2:
+
+```
+FileNotFoundError: [Errno 2] No such file or directory: '/alphafold_dbs/pdb_mmcif/mmcif_files/XXXX.cif'
+```
+
+`patch_mmcif.py` is a standalone script that cross-references your AlphaFold2 databases and attempts to patch missing .cif files from the RCSB database.
+
+## Usage
+
+- Copy this script to your server
+- Ensure that `python >= 3.8` is available
+- `pip install requests`
+- Run patch_mmcif.py from any directory
+
+You must specify the path to your databases when you run the script.
+
+```
+$ python patch_mmcif.py --help
+usage: patch_mmcif.py [-h] [-i ID] [--write-db] [--log] db_path
+
+Patch missing MMCIF files in your AlphaFold DB. This script will sniff your databases for missing .cif files and download them from the RCSB PDB. If the --write-db flag is set, the files will be copied directly to the AlphaFold database mmcif_files directory.
+
+Example usage:
+
+  # Write mmcif files locally (don't write to AF databases)
+  python patch_mmcif.py /my/alphafold/db/
+
+  # Patch all missing files in the database and log changes
+  python patch_mmcif.py /my/alphafold/db/ --write-db --log
+
+  # Patch a single missing file
+  python patch_mmcif.py /my/alphafold/db/ -i 4ri6 --write-db
+
+positional arguments:
+  db_path         Path to your AlphaFold database root
+
+options:
+  -h, --help      show this help message and exit
+  -i ID, --id ID  4-char PDB ID for a .cif file to patch (non-case-sensitive) (if
+                  excluded, will attempt to sniff the database and patch all missing
+                  files)
+  --write-db      Copy the files directly to the AlphaFold database mmcif_files directory.
+                  If this option is omitted, files will be written locally to
+                  ./mmcif_files/*.cif and must then be manually copied to the database
+                  pdb_mmcif/mmcif_files directory. Omit this option to prevent the script
+                  from writing to your database.
+  --log           Write patched PDB files/IDs to ./logs/. This is useful for keeping track
+                  of which files were patched. The following files will be written:
+                  [required_ids.log, existing_ids.log, missing_ids.log]. Patched MMCIF
+                  files will be copied to ./logs/mmcif_patches/.
+
+```
+
+## How does it work
+
+The script enumerates unique PDB identifiers in the database file `pdb70/pdb70_clu.tsv`, which looks like this:
+
+```
+3TC3_B  3TC3_B
+3TC3_B  4GLE_A
+3TC3_B  3TC3_A
+4RI6_A  4RI6_A
+4RI6_A  4RI6_B
+4RI6_A  4RI7_A
+4RI7_A  4RI7_B
+```
+
+The identifiers here are what is expected to be in the `mmcif_files` directory at runtime.
+The script extracts a unique list of identifiers from this file, then subtracts those that are already present in the `pdb_mmcif/mmcif_files/` directory to get a list of missing files. It then downloads these from https://files.rcsb.org/download/ and writes them to the appropriate location.
+
+## Tests
+
+Run unit tests for `patch_mmcif.py` from this directory:
+
+```sh
+python -m unittest tests/test_patch_all.py
+```