Change boltz references

README.md

@@ -4,7 +4,7 @@
 ![Coverage](https://raw.githubusercontent.com/rigdenlab/ABCFold/refs/heads/main/.blob/coverage.svg)
 
 
-Scripts to run AlphaFold3, Boltz-1 and Chai-1 with MMseqs2 Multiple sequence alignments (MSAs) and custom templates.
+Scripts to run AlphaFold3, Boltz and Chai-1 with MMseqs2 Multiple sequence alignments (MSAs) and custom templates.
 
 ## Table of Contents
 - [Installation](#installation)
@@ -57,7 +57,7 @@ python -m pre_commit install
 
 ### Running ABCfold
 
-ABCFold will run Alphafold3, Boltz-1 and Chai-1 consecutively. The program takes an input of a JSON in the Alphafold3 format (For full instruction on how to format this, click [here](https://github.com/google-deepmind/alphafold3/blob/main/docs/input.md)). An example JSON is shown below:
+ABCFold will run Alphafold3, Boltz and Chai-1 consecutively. The program takes an input of a JSON in the Alphafold3 format (For full instruction on how to format this, click [here](https://github.com/google-deepmind/alphafold3/blob/main/docs/input.md)). An example JSON is shown below:
 
 ```json
 {
@@ -76,7 +76,7 @@ ABCFold will run Alphafold3, Boltz-1 and Chai-1 consecutively. The program takes
 }
 ```
 
-Please make sure you have AlphaFold3 installed on your system (Instructions [here](https://github.com/google-deepmind/alphafold3/blob/main/docs/installation.md)) and have procured the model parameters. Boltz-1 and Chai-1 are installed upon runtime.
+Please make sure you have AlphaFold3 installed on your system (Instructions [here](https://github.com/google-deepmind/alphafold3/blob/main/docs/installation.md)) and have procured the model parameters. Boltz and Chai-1 are installed upon runtime.
 
 For the majority of jobs, ABCFold can be run as follows:
 ```bash
@@ -100,7 +100,7 @@ However, there you may wish to use the following flags to add run time options s
 #### Main arguments
 - `<input_json>`: Path to the input AlphaFold3 JSON file.
 - `<output_dir>`: Path to the output directory.
-- `-a`, `-b`, `-c` (`--alphafold3`, `--boltz1`,`--chai1`): Flags to run Alphafold3, Boltz-1 and Chai-1 respectively. If none of these flags are provided, Alphafold3 will be run by default.
+- `-a`, `-b`, `-c` (`--alphafold3`, `--boltz`,`--chai1`): Flags to run Alphafold3, Boltz and Chai-1 respectively. If none of these flags are provided, Alphafold3 will be run by default.
 - `--mmseqs2`: [optional] Flag to use MMseqs2 MSAs and templates (if specified).
 - `--mmseqs_database`: [optional] The path to the database used by a local copy of MMSeqs2, provided mmseqs is installed, the inclusion of this flag allows MMseqs2 to be run locally.
 - `--override`: [optional] Flag to override the existing output directory.
@@ -168,7 +168,7 @@ you will find `open_output.py` in your `<output_dir>`. This needs to be run from
 Below are scripts for adding MMseqs2 MSAs and custom templates to AlphaFold3 input JSON files.
 
 > [!WARNING]
-> These scripts will only modify the input JSON files, I.E. they will NOT run AlphaFold3, Boltz-1 and Chai-1.
+> These scripts will only modify the input JSON files, I.E. they will NOT run AlphaFold3, Boltz and Chai-1.
 
 ### Adding MMseqs2 MSAs and templates
 
@@ -275,9 +275,9 @@ Below is an example of a hetero-3-mer. When modelling a homo-oligomer, id is giv
 
 If you want to add a custom template to the first sequence, you can use `--target_id A`. If you wish to add a custom template to the second sequence, use `--target_id B` or `--target_id C`.
 
-#### Boltz-1 limitations
+#### Boltz limitations
 
-If modelling multiple copies of the same sequence in Boltz-1, the input JSON must be set up as follows:
+If modelling multiple copies of the same sequence in Boltz, the input JSON must be set up as follows:
 
 ```json
 {
@@ -320,7 +320,7 @@ If the identical sequences are given as seperate entities (as shown below) you w
 }
 ```
 
-Additionally, Boltz-1 currently lacks the ability to create linked-ligands and therefore covalent bonds between the chain/ligand will be missing.
+Additionally, Boltz currently lacks the ability to create linked-ligands and therefore covalent bonds between the chain/ligand will be missing.
 
 ## Contributing
 

abcfold/abcfold.py

@@ -95,10 +95,10 @@ def run(args, config, defaults, config_file):
 
         check_af3_install(interactive=False, sif_path=args.sif_path)
 
-    if args.boltz1:
-        from abcfold.boltz1.check_install import check_boltz1
+    if args.boltz:
+        from abcfold.boltz.check_install import check_boltz
 
-        check_boltz1()
+        check_boltz()
 
     if args.chai1:
         from abcfold.chai1.check_install import check_chai1
@@ -141,7 +141,8 @@ def run(args, config, defaults, config_file):
                     seq.get("protein", {}).get("unpairedMsa")
                     or seq.get("protein", {}).get("unpairedMsaPath")
                     for seq in input_params["sequences"]
-                    )):
+                )
+            ):
                 af3_database = make_dummy_af3_db(temp_dir)
 
             af3_success = run_alphafold3(
@@ -167,8 +168,8 @@ def run(args, config, defaults, config_file):
                 run_json = ao.input_json
             successful_runs.append(af3_success)
 
-        if args.boltz1:
-            from abcfold.boltz1.run_boltz import run_boltz
+        if args.boltz:
+            from abcfold.boltz.run_boltz import run_boltz
 
             boltz_success = run_boltz(
                 input_json=run_json,
@@ -241,34 +242,33 @@ def run(args, config, defaults, config_file):
                         plddt = model.residue_plddts
                         if len(indicies) > 0:
                             plddt = insert_none_by_minus_one(
-                                indicies[index_counter],
-                                plddt
-                                )
+                                indicies[index_counter], plddt
+                            )
                         index_counter += 1
                         model_data = get_model_data(
-                            model, plot_dict, "AlphaFold3",
-                            plddt, score_file, args.output_dir
+                            model,
+                            plot_dict,
+                            "AlphaFold3",
+                            plddt,
+                            score_file,
+                            args.output_dir,
                         )
                         alphafold_models["models"].append(model_data)
 
         boltz_models = {"models": []}
-        if args.boltz1:
+        if args.boltz:
             if boltz_success:
-                programs_run.append("Boltz-1")
+                programs_run.append("Boltz")
                 for idx in bo.output.keys():
                     model = bo.output[idx]["cif"]
                     model.check_clashes()
                     score_file = bo.output[idx]["json"]
                     plddt = model.residue_plddts
                     if len(indicies) > 0:
-                        plddt = insert_none_by_minus_one(
-                            indicies[index_counter],
-                            plddt
-                            )
+                        plddt = insert_none_by_minus_one(indicies[index_counter], plddt)
                     index_counter += 1
                     model_data = get_model_data(
-                        model, plot_dict, "Boltz-1",
-                        plddt, score_file, args.output_dir
+                        model, plot_dict, "Boltz", plddt, score_file, args.output_dir
                     )
                     boltz_models["models"].append(model_data)
 
@@ -284,13 +284,16 @@ def run(args, config, defaults, config_file):
                         plddt = model.residue_plddts
                         if len(indicies) > 0:
                             plddt = insert_none_by_minus_one(
-                                indicies[index_counter],
-                                plddt
-                                )
+                                indicies[index_counter], plddt
+                            )
                         index_counter += 1
                         model_data = get_model_data(
-                            model, plot_dict, "Chai-1",
-                            plddt, score_file, args.output_dir
+                            model,
+                            plot_dict,
+                            "Chai-1",
+                            plddt,
+                            score_file,
+                            args.output_dir,
                         )
                         chai_models["models"].append(model_data)
 
@@ -305,7 +308,7 @@ def run(args, config, defaults, config_file):
             cif_file = args.output_dir.joinpath(model["model_path"])
             if model["model_source"] == "AlphaFold3":
                 output_name = "af3_model_" + model["model_id"][-1] + ".cif"
-            elif model["model_source"] == "Boltz-1":
+            elif model["model_source"] == "Boltz":
                 output_name = "boltz_model_" + model["model_id"][-1] + ".cif"
             elif model["model_source"] == "Chai-1":
                 output_name = "chai_model_" + model["model_id"][-1] + ".cif"
@@ -399,11 +402,11 @@ def run(args, config, defaults, config_file):
 
 def main():
     """
-    Run AlphaFold3 / Boltz1 / Chai-1
+    Run AlphaFold3 / Boltz / Chai-1
     """
     import argparse
 
-    parser = argparse.ArgumentParser(description="Run AlphaFold3 / Boltz1 / Chai-1")
+    parser = argparse.ArgumentParser(description="Run AlphaFold3 / Boltz / Chai-1")
 
     defaults = {}
     config_file = Path(__file__).parent.joinpath("data", "config.ini")

abcfold/argparse_utils.py

@@ -23,12 +23,9 @@ def main_argpase_util(parser):
     parser.add_argument(
         "input_json",
         type=validate_json_file,
-        help="Path to the input JSON in AlphaFold3 format"
-    )
-    parser.add_argument(
-        "output_dir",
-        help="Path to the output directory"
+        help="Path to the input JSON in AlphaFold3 format",
     )
+    parser.add_argument("output_dir", help="Path to the output directory")
     parser.add_argument(
         "--override",
         help="[optional] Override the existing output directory, if it exists",
@@ -53,12 +50,10 @@ def mmseqs2_argparse_util(parser):
     parser.add_argument(
         "--mmseqs_database",
         help="[optional] The database directory for the generation of the MSA. This \
-is only required if using a local installation of MMseqs2"
+is only required if using a local installation of MMseqs2",
     )
     parser.add_argument(
-        "--templates",
-        action="store_true",
-        help="[optional] Enable template search"
+        "--templates", action="store_true", help="[optional] Enable template search"
     )
     parser.add_argument(
         "--num_templates",
@@ -118,9 +113,9 @@ def prediction_argparse_util(parser):
 def boltz_argparse_util(parser):
     parser.add_argument(
         "-b",
-        "--boltz1",
+        "--boltz",
         action="store_true",
-        help="Run Boltz1",
+        help="Run Boltz",
     )
     if "--save_input" not in parser._option_string_actions:
         parser.add_argument(
@@ -200,9 +195,9 @@ def visuals_argparse_util(parser):
 
 
 def raise_argument_errors(args):
-    if not args.alphafold3 and not args.boltz1 and not args.chai1:
+    if not args.alphafold3 and not args.boltz and not args.chai1:
         logger.info(
-            "Neither AlphaFold3, Boltz-1, or Chai-1 selected. Running AlphaFold3 \
+            "Neither AlphaFold3, Boltz, or Chai-1 selected. Running AlphaFold3 \
 by default"
         )
         args.alphafold3 = True
@@ -216,9 +211,7 @@ def raise_argument_errors(args):
         sys.exit(1)
 
     if args.templates and not args.mmseqs2 and not args.alphafold3:
-        logger.error(
-            "Cannot use --templates flag without using MMseqs2 or Alphafold3"
-        )
+        logger.error("Cannot use --templates flag without using MMseqs2 or Alphafold3")
         sys.exit(1)
 
     if (

abcfold/boltz1/check_install.py → abcfold/boltz/check_install.py

@@ -4,10 +4,10 @@
 
 logger = logging.getLogger("logger")
 
-BOLTZ_VERSION = "1.0.0"
+BOLTZ_VERSION = "2.1.1"
 
 
-def check_boltz1():
+def check_boltz():
     try:
         import boltz as _  # noqa F401
 
@@ -55,3 +55,5 @@ def check_boltz1():
                 if proc.stderr:
                     logger.error(proc.stderr.read().decode())
                 raise subprocess.CalledProcessError(proc.returncode, proc.args)
+
+    logger.info(f"Running Boltz version: {BOLTZ_VERSION}")

abcfold/boltz1/run_boltz.py → abcfold/boltz/run_boltz.py

@@ -5,8 +5,8 @@
 from pathlib import Path
 from typing import Union
 
-from abcfold.boltz1.af3_to_boltz1 import BoltzYaml
-from abcfold.boltz1.check_install import check_boltz1
+from abcfold.boltz.af3_to_boltz import BoltzYaml
+from abcfold.boltz.check_install import check_boltz
 
 logger = logging.getLogger("logger")
 
@@ -20,7 +20,7 @@ def run_boltz(
     num_recycles: int = 10,
 ) -> bool:
     """
-    Run Boltz1 using the input JSON file
+    Run Boltz using the input JSON file
 
     Args:
         input_json (Union[str, Path]): Path to the input JSON file
@@ -31,18 +31,18 @@ def run_boltz(
         number_of_models (int): Number of models to generate
 
     Returns:
-        Bool: True if the Boltz1 run was successful, False otherwise
+        Bool: True if the Boltz run was successful, False otherwise
 
     Raises:
-        subprocess.CalledProcessError: If the Boltz1 command returns an error
+        subprocess.CalledProcessError: If the Boltz command returns an error
 
 
     """
     input_json = Path(input_json)
     output_dir = Path(output_dir)
 
-    logger.debug("Checking if boltz1 is installed")
-    check_boltz1()
+    logger.debug("Checking if boltz is installed")
+    check_boltz()
 
     with tempfile.TemporaryDirectory() as temp_dir:
         working_dir = Path(temp_dir)
@@ -55,7 +55,7 @@ def run_boltz(
         out_file = working_dir.joinpath(f"{input_json.stem}.yaml")
 
         boltz_yaml.write_yaml(out_file)
-        logger.info("Running Boltz1")
+        logger.info("Running Boltz")
         cmd = (
             generate_boltz_command(out_file, output_dir, number_of_models, num_recycles)
             if not test
@@ -81,16 +81,16 @@ def run_boltz(
                     with open(output_err_file, "w") as f:
                         f.write(stderr.decode())
                     logger.error(
-                        "Boltz1 run failed. Error log is in %s", output_err_file
+                        "Boltz run failed. Error log is in %s", output_err_file
                     )
                 else:
-                    logger.error("Boltz1 run failed")
+                    logger.error("Boltz run failed")
                 return False
             elif "WARNING: ran out of memory" in stdout:
-                logger.error("Boltz1 ran out of memory")
+                logger.error("Boltz ran out of memory")
                 return False
 
-        logger.info("Boltz1 run complete")
+        logger.info("Boltz run complete")
         logger.info("Output files are in %s", output_dir)
         return True
 
@@ -102,15 +102,15 @@ def generate_boltz_command(
     num_recycles: int = 10,
 ) -> list:
     """
-    Generate the Boltz1 command
+    Generate the Boltz command
 
     Args:
         input_yaml (Union[str, Path]): Path to the input YAML file
         output_dir (Union[str, Path]): Path to the output directory
         number_of_models (int): Number of models to generate
 
     Returns:
-        list: The Boltz1 command
+        list: The Boltz command
     """
     return [
         "boltz",
@@ -130,13 +130,13 @@ def generate_boltz_command(
 
 def generate_boltz_test_command() -> list:
     """
-    Generate the test command for Boltz1
+    Generate the test command for Boltz
 
     Args:
         None
 
     Returns:
-        list: The Boltz1 test command
+        list: The Boltz test command
     """
 
     return [