alphapulldown-input-parser 0.2.0__tar.gz → 0.4.0__tar.gz

{alphapulldown_input_parser-0.2.0/src/alphapulldown_input_parser.egg-info → alphapulldown_input_parser-0.4.0}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: alphapulldown-input-parser
-Version: 0.2.0
+Version: 0.4.0
 Summary: Fold specification parser for AlphaPulldown
 Author-email: Kosinski Lab <alphapulldown@embl-hamburg.de>
 License: MIT
@@ -30,7 +30,7 @@ Dynamic: license-file
 Reusable parser for AlphaPulldown-style fold specifications. Install it with:
 
 ```bash
-pip install alphapulldown-input-parser
+pip install "alphapulldown-input-parser>=0.4.0"
 ```
 
 or, for local development:
@@ -48,3 +48,17 @@ The package exposes two helpers:
 
 The parser is dependency-free and works across AlphaPulldown, the Snakemake
 pipeline, or any other tooling that consumes the same fold syntax.
+
+As of `0.4.0`, AF3 JSON feature files support the same copy/range suffixes as
+classic AlphaPulldown feature pickles. For example:
+
+```python
+parse_fold(
+    ["P01258_af3_input.json:1-100:2"],
+    features_directory=["/path/to/features"],
+    protein_delimiter="+",
+)
+```
+
+This expands to two folding entries for the same AF3 JSON feature file, each
+restricted to residues `1-100`.

{alphapulldown_input_parser-0.2.0 → alphapulldown_input_parser-0.4.0}/README.md

@@ -3,7 +3,7 @@
 Reusable parser for AlphaPulldown-style fold specifications. Install it with:
 
 ```bash
-pip install alphapulldown-input-parser
+pip install "alphapulldown-input-parser>=0.4.0"
 ```
 
 or, for local development:
@@ -21,3 +21,17 @@ The package exposes two helpers:
 
 The parser is dependency-free and works across AlphaPulldown, the Snakemake
 pipeline, or any other tooling that consumes the same fold syntax.
+
+As of `0.4.0`, AF3 JSON feature files support the same copy/range suffixes as
+classic AlphaPulldown feature pickles. For example:
+
+```python
+parse_fold(
+    ["P01258_af3_input.json:1-100:2"],
+    features_directory=["/path/to/features"],
+    protein_delimiter="+",
+)
+```
+
+This expands to two folding entries for the same AF3 JSON feature file, each
+restricted to residues `1-100`.

{alphapulldown_input_parser-0.2.0 → alphapulldown_input_parser-0.4.0}/pyproject.toml

@@ -4,7 +4,7 @@ build-backend = "setuptools.build_meta"
 
 [project]
 name = "alphapulldown-input-parser"
-version = "0.2.0"
+version = "0.4.0"
 description = "Fold specification parser for AlphaPulldown"
 readme = "README.md"
 license = {text = "MIT"}

{alphapulldown_input_parser-0.2.0 → alphapulldown_input_parser-0.4.0}/src/alphapulldown_input_parser/parser.py

@@ -72,7 +72,8 @@ class RegionSelection:
         return cls(regions=None)
 
 
-# Either {"json_input": "/path/to.json"} or {"CHAIN_A": RegionSelection(...)}
+# Either {"json_input": "/path/to.json", "regions": RegionSelection(...)?}
+# or {"CHAIN_A": RegionSelection(...)}
 FoldEntry = Dict[str, Union[str, RegionSelection]]
 
 
@@ -309,20 +310,30 @@ def expand_fold_specification(
         if not pf:
             continue
 
-        if pf.endswith(".json"):
-            path_pf = Path(pf)
+        tokens = [token.strip() for token in pf.split(":")]
+        base_token = tokens[0] if tokens else ""
+
+        # JSON inputs: support optional copy number and region ranges.
+        if base_token.endswith(".json"):
+            path_pf = Path(base_token)
             json_path: Optional[str] = None
             for json_key in (path_pf.name, path_pf.stem):
                 json_path = index.json_path(json_key)
                 if json_path:
-                    formatted_folds.append({"json_input": json_path})
+                    copies, region_tokens = _extract_copy_and_regions(tokens, spec)
+                    regions = _parse_regions(region_tokens, spec)
+
+                    for _ in range(copies):
+                        json_entry: FoldEntry = {"json_input": json_path}
+                        if not regions.is_all:
+                            json_entry["regions"] = regions
+                        formatted_folds.append(json_entry)
                     break
             if json_path:
                 continue
             missing_features.append(path_pf.name)
             continue
 
-        tokens = [token.strip() for token in pf.split(":")]
         if not tokens or not tokens[0]:
             _format_error(spec, msg="Protein token is empty.")
 

{alphapulldown_input_parser-0.2.0 → alphapulldown_input_parser-0.4.0/src/alphapulldown_input_parser.egg-info}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: alphapulldown-input-parser
-Version: 0.2.0
+Version: 0.4.0
 Summary: Fold specification parser for AlphaPulldown
 Author-email: Kosinski Lab <alphapulldown@embl-hamburg.de>
 License: MIT
@@ -30,7 +30,7 @@ Dynamic: license-file
 Reusable parser for AlphaPulldown-style fold specifications. Install it with:
 
 ```bash
-pip install alphapulldown-input-parser
+pip install "alphapulldown-input-parser>=0.4.0"
 ```
 
 or, for local development:
@@ -48,3 +48,17 @@ The package exposes two helpers:
 
 The parser is dependency-free and works across AlphaPulldown, the Snakemake
 pipeline, or any other tooling that consumes the same fold syntax.
+
+As of `0.4.0`, AF3 JSON feature files support the same copy/range suffixes as
+classic AlphaPulldown feature pickles. For example:
+
+```python
+parse_fold(
+    ["P01258_af3_input.json:1-100:2"],
+    features_directory=["/path/to/features"],
+    protein_delimiter="+",
+)
+```
+
+This expands to two folding entries for the same AF3 JSON feature file, each
+restricted to residues `1-100`.

{alphapulldown_input_parser-0.2.0 → alphapulldown_input_parser-0.4.0}/test/test_parser.py

@@ -211,6 +211,62 @@ def patch_feature_index(monkeypatch):
             None,
             id="json_in_multiple_dirs",
         ),
+        pytest.param(
+            ["protein1.json:3"],
+            ["dir1"],
+            "+",
+            {"pkl": {}, "json": {"protein1.json": "dir1/protein1.json"}},
+            [
+                [
+                    {"json_input": "dir1/protein1.json"},
+                    {"json_input": "dir1/protein1.json"},
+                    {"json_input": "dir1/protein1.json"},
+                ]
+            ],
+            None,
+            None,
+            id="json_with_copy_number",
+        ),
+        pytest.param(
+            ["protein1.json:1-10"],
+            ["dir1"],
+            "+",
+            {"pkl": {}, "json": {"protein1.json": "dir1/protein1.json"}},
+            [[{"json_input": "dir1/protein1.json", "regions": selection_ranges((1, 10))}]],
+            None,
+            None,
+            id="json_with_range",
+        ),
+        pytest.param(
+            ["protein1.json:2:1-10:20-30"],
+            ["dir1"],
+            "+",
+            {"pkl": {}, "json": {"protein1.json": "dir1/protein1.json"}},
+            [
+                [
+                    {"json_input": "dir1/protein1.json", "regions": selection_ranges((1, 10), (20, 30))},
+                    {"json_input": "dir1/protein1.json", "regions": selection_ranges((1, 10), (20, 30))},
+                ]
+            ],
+            None,
+            None,
+            id="json_with_copy_and_regions",
+        ),
+        pytest.param(
+            ["protein1.json:1-10:20-30:2"],
+            ["dir1"],
+            "+",
+            {"pkl": {}, "json": {"protein1.json": "dir1/protein1.json"}},
+            [
+                [
+                    {"json_input": "dir1/protein1.json", "regions": selection_ranges((1, 10), (20, 30))},
+                    {"json_input": "dir1/protein1.json", "regions": selection_ranges((1, 10), (20, 30))},
+                ]
+            ],
+            None,
+            None,
+            id="json_with_regions_and_copy",
+        ),
     ],
 )
 def test_parse_fold(