Adapt upstream OpenFold and RosettaFold updates

abcfold/abcfold.py

@@ -18,6 +18,7 @@
                                     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,
@@ -30,6 +31,7 @@
 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,
@@ -44,7 +46,12 @@
 PLOTS_DIR = ".plots"
 
 ModelOutput = Union[
-    AlphafoldOutput, BoltzOutput, ChaiOutput, ProtenixOutput, OpenfoldOutput
+    AlphafoldOutput,
+    BoltzOutput,
+    ChaiOutput,
+    ProtenixOutput,
+    OpenfoldOutput,
+    RosettafoldOutput,
 ]
 
 
@@ -281,6 +288,27 @@ 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
@@ -440,12 +468,41 @@ 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"]
+            + rosettafold_models["models"]
         )
 
         # Make the output directory for the models
@@ -463,6 +520,8 @@ 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),
@@ -551,7 +610,7 @@ 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
 
@@ -581,7 +640,9 @@ def main():
         defaults.update(dict(config.items(section)))
 
     parser = argparse.ArgumentParser(
-        description="Run AlphaFold3 / Boltz / Chai-1 / OpenFold3 / Protenix",
+        description=(
+            "Run AlphaFold3 / Boltz / Chai-1 / OpenFold3 / Protenix / RosettaFold3"
+        ),
         parents=[config_parser],
     )
 
@@ -591,6 +652,7 @@ 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

@@ -267,6 +267,16 @@ 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",
@@ -336,10 +346,11 @@ 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 = /mnt/ligandpro/soft/protein/alphafold3/models
 boltz_weights = None
 openfold_weights = None
+rosettafold_weights = None
 
 [Environments]
 af3_docker_env = romerolabduke/alphafast:latest
 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 = 0.3.1
+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: #FFA533;
+    color: #3b3b3d;
+    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;
@@ -506,6 +516,6 @@ rect{
     transition: background-color 0.3s ease;
 }
 
-.btn-source1:hover, .btn-source2:hover, .btn-source3:hover, .btn-default:hover {
+.btn-source1:hover, .btn-source2:hover, .btn-source3:hover, .btn-source4:hover, .btn-source5:hover, .btn-source6:hover, .btn-default:hover {
     opacity: 0.8;
 }

abcfold/output/file_handlers.py

@@ -848,6 +848,26 @@ def from_openfold(cls,
         cls._fix_openfold_mmcif(str(openfold_path), str(tmp_path))
         return cls(str(tmp_path), input_params)
 
+    @classmethod
+    def from_rosettafold(cls,
+                         rosettafold_cif: Union[str, Path],
+                         input_params: Optional[dict] = None) -> "CifFile":
+        """
+        Create a CifFile from a RosettaFold3 mmCIF and convert pLDDT scores
+        stored in the B-factor field from 0-1 scale to 0-100 scale.
+        """
+        rosettafold_path = Path(rosettafold_cif)
+        tmp_path = rosettafold_path.parent / f"{rosettafold_path.stem}_fixed.cif"
+        parser = MMCIFParser(QUIET=True)
+        model = parser.get_structure(rosettafold_path.stem, rosettafold_path)
+        for atom in model.get_atoms():
+            atom.bfactor = atom.bfactor * 100.0
+        io = MMCIFIO()
+        io.set_structure(model)
+        io.save(str(tmp_path))
+
+        return cls(str(tmp_path), input_params)
+
 
 class ConfidenceJsonFile(FileBase):
     def __init__(self, json_file: Union[str, Path]):