Explain better how to run the AlphaFold-Multimer system.

* Remove a confusing example that folds multiple complexes at once.
* Add examples on how to create the multimer input FASTA files.
* Add a note about the `model_preset` flag to the API changes.

PiperOrigin-RevId: 407774039
Change-Id: I80277c47febc977ba3956d0615944e62b0d5c3fc

README.md

@@ -196,6 +196,10 @@ change the following:
     happens inside the Multimer model.
 *   The `preset` flag in `run_alphafold.py` and `run_docker.py` was split into
     `db_preset` and `model_preset`.
+*   The models to use are not specified using `model_names` but rather using the
+    `model_preset` flag. If you want to customize which models are used for each
+    preset, you will have to modify the the `MODEL_PRESETS` dictionary in
+    `alphafold/model/config.py`.
 *   Setting the `data_dir` flag is now needed when using `run_docker.py`.
 
 
@@ -299,18 +303,124 @@ All steps are the same as when running the monomer system, but you will have to
     whether all input sequences in the given fasta file are prokaryotic. If that
     is not the case or the origin is unknown, set to `false` for that fasta.
 
-An example that folds two protein complexes `multimer1` and `multimer2` where
-the first is prokaryotic and the second isn't:
+An example that folds a protein complex `multimer.fasta` that is prokaryotic:
 
 ```bash
 python3 docker/run_docker.py \
-  --fasta_paths=multimer1.fasta,multimer2.fasta \
-  --is_prokaryote_list=true,false \
+  --fasta_paths=multimer.fasta \
+  --is_prokaryote_list=true \
   --max_template_date=2020-05-14 \
   --model_preset=multimer \
   --data_dir=$DOWNLOAD_DIR
 ```
 
+### Examples
+
+Below are examples on how to use AlphaFold in different scenarios.
+
+#### Folding a monomer
+
+Say we have a monomer with the sequence `<SEQUENCE>`. The input fasta should be:
+
+```fasta
+>sequence_name
+<SEQUENCE>
+```
+
+Then run the following command:
+
+```bash
+python3 docker/run_docker.py \
+  --fasta_paths=monomer.fasta \
+  --max_template_date=2021-11-01 \
+  --model_preset=monomer \
+  --data_dir=$DOWNLOAD_DIR
+```
+
+#### Folding a homomer
+
+Say we have a homomer from a prokaryote with 3 copies of the same sequence
+`<SEQUENCE>`. The input fasta should be:
+
+```fasta
+>sequence_1
+<SEQUENCE>
+>sequence_2
+<SEQUENCE>
+>sequence_3
+<SEQUENCE>
+```
+
+Then run the following command:
+
+```bash
+python3 docker/run_docker.py \
+  --fasta_paths=homomer.fasta \
+  --is_prokaryote_list=true \
+  --max_template_date=2021-11-01 \
+  --model_preset=multimer \
+  --data_dir=$DOWNLOAD_DIR
+```
+
+#### Folding a heteromer
+
+Say we have a heteromer A2B3 of unknown origin, i.e. with 2 copies of
+`<SEQUENCE A>` and 3 copies of `<SEQUENCE B>`. The input fasta should be:
+
+```fasta
+>sequence_1
+<SEQUENCE A>
+>sequence_2
+<SEQUENCE A>
+>sequence_3
+<SEQUENCE B>
+>sequence_4
+<SEQUENCE B>
+>sequence_5
+<SEQUENCE B>
+```
+
+Then run the following command:
+
+```bash
+python3 docker/run_docker.py \
+  --fasta_paths=heteromer.fasta \
+  --is_prokaryote_list=false \
+  --max_template_date=2021-11-01 \
+  --model_preset=multimer \
+  --data_dir=$DOWNLOAD_DIR
+```
+
+#### Folding multiple monomers one after another
+
+Say we have a two monomers, `monomer1.fasta` and `monomer2.fasta`.
+
+We can fold both sequentially by using the following command:
+
+```bash
+python3 docker/run_docker.py \
+  --fasta_paths=monomer1.fasta,monomer2.fasta \
+  --max_template_date=2021-11-01 \
+  --model_preset=monomer \
+  --data_dir=$DOWNLOAD_DIR
+```
+
+#### Folding multiple multimers one after another
+
+Say we have a two multimers, `multimer1.fasta` and `multimer2.fasta`. Both are
+from a prokaryotic organism.
+
+We can fold both sequentially by using the following command:
+
+```bash
+python3 docker/run_docker.py \
+  --fasta_paths=multimer1.fasta,multimer2.fasta \
+  --is_prokaryote_list=true,true \
+  --max_template_date=2021-11-01 \
+  --model_preset=multimer \
+  --data_dir=$DOWNLOAD_DIR
+```
+
 ### AlphaFold output
 
 The outputs will be saved in a subdirectory of the directory provided via the

docker/run_docker.py

@@ -32,17 +32,17 @@ flags.DEFINE_string(
     'gpu_devices', 'all',
     'Comma separated list of devices to pass to NVIDIA_VISIBLE_DEVICES.')
 flags.DEFINE_list(
-    'fasta_paths', None,
-    'Paths to FASTA files, each containing one sequence. Paths should be '
+    'fasta_paths', None, 'Paths to FASTA files, each containing a prediction '
+    'target that will be folded one after another. If a FASTA file contains '
+    'multiple sequences, then it will be folded as a multimer. Paths should be '
     'separated by commas. All FASTA paths must have a unique basename as the '
     'basename is used to name the output directories for each prediction.')
-flags.DEFINE_list('is_prokaryote_list', None, 'Optional for multimer system, '
-                  'not used by the single chain system. '
-                  'This list should contain a boolean for each fasta '
-                  'specifying true where the target complex is from a '
-                  'prokaryote, and false where it is not, or where the '
-                  'origin is unknown. These values determine the pairing '
-                  'method for the MSA.')
+flags.DEFINE_list(
+    'is_prokaryote_list', None, 'Optional for multimer system, not used by the '
+    'single chain system. This list should contain a boolean for each fasta '
+    'specifying true where the target complex is from a prokaryote, and false '
+    'where it is not, or where the origin is unknown. These values determine '
+    'the pairing method for the MSA.')
 flags.DEFINE_string(
     'output_dir', '/tmp/alphafold',
     'Path to a directory that will store the results.')

run_alphafold.py

@@ -43,18 +43,18 @@ from alphafold.model import data
 
 logging.set_verbosity(logging.INFO)
 
-flags.DEFINE_list('fasta_paths', None, 'Paths to FASTA files, each containing '
-                  'a prediction target. Paths should be separated by commas. '
-                  'All FASTA paths must have a unique basename as the '
-                  'basename is used to name the output directories for '
-                  'each prediction.')
-flags.DEFINE_list('is_prokaryote_list', None, 'Optional for multimer system, '
-                  'not used by the single chain system. '
-                  'This list should contain a boolean for each fasta '
-                  'specifying true where the target complex is from a '
-                  'prokaryote, and false where it is not, or where the '
-                  'origin is unknown. These values determine the pairing '
-                  'method for the MSA.')
+flags.DEFINE_list(
+    'fasta_paths', None, 'Paths to FASTA files, each containing a prediction '
+    'target that will be folded one after another. If a FASTA file contains '
+    'multiple sequences, then it will be folded as a multimer. Paths should be '
+    'separated by commas. All FASTA paths must have a unique basename as the '
+    'basename is used to name the output directories for each prediction.')
+flags.DEFINE_list(
+    'is_prokaryote_list', None, 'Optional for multimer system, not used by the '
+    'single chain system. This list should contain a boolean for each fasta '
+    'specifying true where the target complex is from a prokaryote, and false '
+    'where it is not, or where the origin is unknown. These values determine '
+    'the pairing method for the MSA.')
 
 flags.DEFINE_string('data_dir', None, 'Path to directory of supporting data.')
 flags.DEFINE_string('output_dir', None, 'Path to a directory that will '