Rosettafold addition

README.md

@@ -4,7 +4,7 @@
 ![Coverage](https://raw.githubusercontent.com/rigdenlab/ABCFold/refs/heads/main/.blob/coverage.svg)
 
 
-Scripts to run AlphaFold3, Boltz, Chai-1, OpenFold3 and Protenix with MMseqs2 Multiple sequence alignments (MSAs) and custom templates.
+Scripts to run AlphaFold3, Boltz, Chai-1, OpenFold3, Protenix and RosettaFold3 with MMseqs2 Multiple sequence alignments (MSAs) and custom templates.
 
 ## Table of Contents
 - [Installation](#installation)
@@ -26,7 +26,7 @@ micromamba activate abcfold
 > **Environment note**
 >
 > - Your main Python environment can be Conda, micromamba, or virtualenv.
-> - `abcfold` will automatically create **internal micromamba environments** to run Boltz, Chai-1, OpenFold3 and Protenix safely, therefore a micromamba installation is required.
+> - `abcfold` will automatically create **internal micromamba environments** to run Boltz, Chai-1, OpenFold3, Protenix and RosettaFold3 safely, therefore a micromamba installation is required.
 > - This prevents package conflicts with your main environment and ensures reproducible results.
 
 
@@ -57,7 +57,7 @@ python -m pre_commit install
 
 ### Running ABCfold
 
-ABCFold will run Alphafold3, Boltz, Chai-1, OpenFold3 and Protenix 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, Chai-1, OpenFold3, Protenix and RosettaFold3 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, Chai-1, OpenFold3 and Protenix consecutively
 }
 ```
 
-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, Chai-1, OpenFold3 and Protenix 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, Chai-1, OpenFold3, Protenix and RosettaFold3 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`, `-o`, `-p` (`--alphafold3`, `--boltz`,`--chai1`, `--openfold3`, `--protenix`): Flags to run Alphafold3, Boltz, Chai-1, OpenFold3 and Protenix respectively. If none of these flags are provided, Alphafold3 will be run by default.
+- `-a`, `-b`, `-c`, `-o`, `-p`, `-r` (`--alphafold3`, `--boltz`,`--chai1`, `--openfold3`, `--protenix`, `--rosettafold3`): Flags to run Alphafold3, Boltz, Chai-1, OpenFold3, Protenix and RosettaFold3 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.
@@ -118,7 +118,6 @@ However, there you may wish to use the following flags to add run time options s
 - `--inference_ckpt_path` [optional] Path for model checkpoint to be used for inference. If not specified, will attempt to find or download parameters in ~/.openfold3/
 
 #### Template arguments
-
 - `--templates`: Flag to enable a template search
 - `--num_templates`: [optional] The number of templates to use (default: 20)
 
@@ -135,19 +134,19 @@ However, there you may wish to use the following flags to add run time options s
 If you wanted to provide a custom template, `custom_a.pdb` for your protein sequence with the ID `A` and you have your template has two chains: chain `A` and chain `B` and chain `B` is what you want the template to be, you could run:
 
 ```bash
-abcfold <input_json>  <output_dir> -abcop --mmseqs2 --custom_template custom_a.pdb  --custom_template_chain B --target_id A
+abcfold <input_json>  <output_dir> -abcopr --mmseqs2 --custom_template custom_a.pdb  --custom_template_chain B --target_id A
 
 ```
 
 If you had multiple IDs in your input sequence, multiple template files and you wanted to provide 3 custom templates, chain `A` from `custom_a.pdb`, chain `B` from `custom_b.pdb`, and chain B from `custom_c.pdb`, where `custom_a.pdb` and `custom_b.pdb` correspond to the ID `A` and `custom_c.pdb` corresponds to the ID `B`, you could run:
 
 ```bash
-abcfold <input_json>  <output_dir> -abcop --mmseqs2 --custom_template custom_a.pdb custom_b.pdb custom_c.pdb --custom_template_chain A B B --target_id A A B
+abcfold <input_json>  <output_dir> -abcopr --mmseqs2 --custom_template custom_a.pdb custom_b.pdb custom_c.pdb --custom_template_chain A B B --target_id A A B
 
 ```
 ### Output
 
-ABCFold will output the AlphaFold, Boltz, Chai, OpenFold3 and Protenix models in the `<output_dir>`, it will also produce an output page containing a results table and informative [PAE viewer](https://gitlab.gwdg.de/general-microbiology/pae-viewer). This is opened automatically in your default browser unless the `--no_server` or `--no_visuals` flags are used.
+ABCFold will output the AlphaFold, Boltz, Chai, OpenFold3, Protenix and RosettaFold3 models in the `<output_dir>`, it will also produce an output page containing a results table and informative [PAE viewer](https://gitlab.gwdg.de/general-microbiology/pae-viewer). This is opened automatically in your default browser unless the `--no_server` or `--no_visuals` flags are used.
 
 Unless the `--no_visuals` flag is used, you can then open the output pages by running:
 
@@ -171,7 +170,7 @@ 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, Chai-1, OpenFold3 and Protenix.
+> These scripts will only modify the input JSON files, I.E. they will NOT run AlphaFold3, Boltz, Chai-1, OpenFold3, Protenix and RosettaFold3.
 
 ### Adding MMseqs2 MSAs and templates
 

abcfold/abcfold.py

@@ -8,6 +8,7 @@
 import tempfile
 import webbrowser
 from pathlib import Path
+from textwrap import dedent
 from typing import Any, Dict, List, Union
 
 from abcfold.alphafold3.run_alphafold3 import run_alphafold3
@@ -19,6 +20,7 @@
                                     prediction_argparse_util,
                                     protenix_argparse_util,
                                     raise_argument_errors,
+                                    rosettafold_argparse_util,
                                     visuals_argparse_util)
 from abcfold.html.html_utils import (PORT, NoCacheHTTPRequestHandler,
                                      get_all_cif_files, get_model_data,
@@ -31,6 +33,7 @@
 from abcfold.output.file_handlers import superpose_models
 from abcfold.output.openfold3 import OpenfoldOutput
 from abcfold.output.protenix import ProtenixOutput
+from abcfold.output.rosettafold3 import RosettafoldOutput
 from abcfold.output.utils import (get_gap_indicies, insert_none_by_minus_one,
                                   make_dummy_m8_file, verify_config_file)
 from abcfold.scripts.abc_script_utils import (check_input_json, make_dir,
@@ -45,7 +48,8 @@
 PLOTS_DIR = ".plots"
 
 ModelOutput = Union[
-    AlphafoldOutput, BoltzOutput, ChaiOutput, ProtenixOutput, OpenfoldOutput
+    AlphafoldOutput, BoltzOutput, ChaiOutput,
+    ProtenixOutput, OpenfoldOutput, RosettafoldOutput
 ]
 
 
@@ -272,6 +276,28 @@ def run(args, config, defaults, config_file):
                 outputs.append(oo)
             successful_runs.append(openfold_success)
 
+        if args.rosettafold3:
+            from abcfold.rosettafold3.run_rosettafold3 import run_rosettafold
+
+            rosettafold_success = run_rosettafold(
+                input_json=run_json,
+                output_dir=args.output_dir,
+                save_input=args.save_input,
+                number_of_models=args.number_of_models,
+                config=rt_config
+            )
+
+            if rosettafold_success:
+                rosettafold_output_dirs = list(
+                    args.output_dir.glob("rosettafold_results*")
+                )
+                ro = RosettafoldOutput(
+                    rosettafold_output_dirs, input_params, name, args.save_input
+                )
+                outputs.append(ro)
+
+            successful_runs.append(rosettafold_success)
+
         if args.no_visuals:
             logger.info("Visuals disabled")
             return
@@ -431,12 +457,41 @@ def run(args, config, defaults, config_file):
                             )
                             protenix_models["models"].append(model_data)
 
+        rosettafold_models: Dict[str, List[Dict[str, Any]]] = {"models": []}
+        if args.rosettafold3:
+            if rosettafold_success:
+                programs_run.append("RosettaFold3")
+                for seed in ro.output.keys():
+                    for idx in ro.output[seed].keys():
+                        if idx >= 0:
+                            model = ro.output[seed][idx]["cif"]
+                            model.check_clashes()
+                            score_file = ro.output[seed][idx]["scores"]
+                            plddt = model.residue_plddts
+                            pae = ro.output[seed][idx]["af3_pae"]
+                            if len(indicies) > 0:
+                                plddt = insert_none_by_minus_one(
+                                    indicies[index_counter], plddt
+                                )
+                            index_counter += 1
+                            model_data = get_model_data(
+                                model,
+                                plot_dict,
+                                "RosettaFold3",
+                                plddt,
+                                pae,
+                                score_file,
+                                args.output_dir,
+                            )
+                            rosettafold_models["models"].append(model_data)
+
         combined_models = (
             alphafold_models["models"] +
             boltz_models["models"] +
             chai_models["models"] +
             openfold_models["models"] +
-            protenix_models["models"]
+            protenix_models["models"] +
+            rosettafold_models["models"]
         )
 
         # Make the output directory for the models
@@ -454,6 +509,8 @@ def run(args, config, defaults, config_file):
                 output_name = "openfold_model_" + model["model_id"][-1] + ".cif"
             elif model["model_source"] == "Protenix":
                 output_name = "protenix_model_" + model["model_id"][-1] + ".cif"
+            elif model["model_source"] == "RosettaFold3":
+                output_name = "rosettafold_model_" + model["model_id"][-1] + ".cif"
             shutil.copy(
                 cif_file,
                 args.output_dir.joinpath("output_models").joinpath(output_name),
@@ -544,7 +601,7 @@ def run(args, config, defaults, config_file):
 
 def main():
     """
-    Run AlphaFold3 / Boltz / Chai-1 / OpenFold3 / Protenix
+    Run AlphaFold3 / Boltz / Chai-1 / OpenFold3 / Protenix / RosettaFold3
     """
     import argparse
 
@@ -553,10 +610,9 @@ def main():
         '--config-file',
         type=str,
         default=str(Path.home() / ".abcfold_config.ini"),
-        help='Path to the config file. '
-        'If not provided, a config file will be created '
-        'at ~/.abcfold_config.ini with default values. '
-        'If a config file already exists at that location, it will be used.'
+        help=dedent('Path to the config file. If not provided, a config file will  \
+        be created at ~/.abcfold_config.ini with default values. \
+        If a config file already exists at that location, it will be used.')
     )
     config_args, remaining = config_parser.parse_known_args()
 
@@ -574,7 +630,8 @@ def main():
         defaults.update(dict(config.items(section)))
 
     parser = argparse.ArgumentParser(
-        description="Run AlphaFold3 / Boltz / Chai-1 / OpenFold3 / Protenix",
+        description=dedent("Run AlphaFold3 / Boltz / Chai-1 / \
+        OpenFold3 / Protenix / RosettaFold3"),
         parents=[config_parser],
     )
 
@@ -584,6 +641,7 @@ def main():
     parser = chai_argparse_util(parser)
     parser = openfold_argparse_util(parser)
     parser = protenix_argparse_util(parser)
+    parser = rosettafold_argparse_util(parser)
     parser = mmseqs2_argparse_util(parser)
     parser = custom_template_argpase_util(parser)
     parser = prediction_argparse_util(parser)

abcfold/argparse_utils.py

@@ -166,6 +166,16 @@ def openfold_argparse_util(parser):
     return parser
 
 
+def rosettafold_argparse_util(parser):
+    parser.add_argument(
+        "-r",
+        "--rosettafold3",
+        action="store_true",
+        help="Run RosettaFold 3",
+    )
+    return parser
+
+
 def alphafold_argparse_util(parser):
     parser.add_argument(
         "--database",
@@ -235,10 +245,11 @@ def raise_argument_errors(args):
         and not args.chai1
         and not args.protenix
         and not args.openfold3
+        and not args.rosettafold3
     ):
         logger.info(
-            dedent("None of AlphaFold3, Boltz, Chai-1, Protenix or OpenFold3 selected. \
-            Running AlphaFold3 by default")
+            dedent("None of AlphaFold3, Boltz, Chai-1, Protenix, OpenFold3 or  \
+            RosettaFold3 selected. Running AlphaFold3 by default")
         )
         args.alphafold3 = True
 

abcfold/data/config.ini

@@ -8,20 +8,23 @@ af3_sif_path = None
 model_params = None
 boltz_weights = None
 openfold_weights = None
+rosettafold_weights = None
 
 [Environments]
 af3_docker_env = alphafold3
 boltz_env = abcfold-boltz-py311
 chai_env = abcfold-chai-py311
 openfold_env = abcfold-openfold-py311
 protenix_env = abcfold-protenix-py311
+rosettafold_env = abcfold-rosetta-py312
 
 [Versions]
 af3_version = 3.0.0
 boltz_version = 2.2.1
 chai_version = 0.6.1
 openfold_version = 0.4.1
 protenix_version = 2.0.0
+rosetta_version = 0.1.12
 
 [Models]
 protenix_model = protenix-v2

abcfold/html/abcfold_vue.js

@@ -62,6 +62,8 @@ Vue.component('abc-table', {
                     return 'btn-source4';
                 case 'OpenFold3':
                     return 'btn-source5';
+                case 'RosettaFold3':
+                    return 'btn-source6';
                 default:
                     return 'btn-default';
             }

abcfold/html/html_utils.py

@@ -16,6 +16,7 @@
 from abcfold.output.file_handlers import ConfidenceJsonFile, NpzFile
 from abcfold.output.openfold3 import OpenfoldOutput
 from abcfold.output.protenix import ProtenixOutput
+from abcfold.output.rosettafold3 import RosettafoldOutput
 from abcfold.plots.pae_plot import create_pae_plots
 from abcfold.plots.plddt_plot import plot_plddt
 from abcfold.scripts.ipsae import Ipsae
@@ -293,6 +294,11 @@ def get_all_cif_files(outputs) -> Dict[str, list]:
                 if "Protenix" not in method_cif_objs:
                     method_cif_objs["Protenix"] = []
                 method_cif_objs["Protenix"].extend(output.cif_files[seed])
+        elif isinstance(output, RosettafoldOutput):
+            for seed in output.seeds:
+                if "RosettaFold3" not in method_cif_objs:
+                    method_cif_objs["RosettaFold3"] = []
+                method_cif_objs["RosettaFold3"].extend(output.cif_files[seed])
 
     return method_cif_objs
 

abcfold/html/style.css

@@ -496,6 +496,16 @@ rect{
     transition: background-color 0.3s ease;
 }
 
+.btn-source6 {
+    background-color: #49aaa1eb;
+    color: #F8F9FA;
+    border: none;
+    border-radius: 12px;
+    padding: 7px 15px;
+    cursor: pointer;
+    transition: background-color 0.3s ease;
+}
+
 .btn-default {
     background-color: rgb(199, 195, 195);
     color: white;

abcfold/openfold3/run_openfold3.py

@@ -19,7 +19,7 @@ def run_openfold(
     save_input: bool = False,
     test: bool = False,
     number_of_models: int = 5,
-    template_hits_path: Path | None = None,
+    template_hits_path: Optional[Path] = None,
     input_ckpt: Optional[Union[str, Path]] = None,
 ) -> bool:
     """