pxmeter 0.1.1__tar.gz → 0.1.2__tar.gz

{pxmeter-0.1.1/pxmeter.egg-info → pxmeter-0.1.2}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: pxmeter
-Version: 0.1.1
+Version: 0.1.2
 Summary: PXMeter is a comprehensive toolkit for evaluating the quality of         structures generated by biomolecular structure prediction models.
 Author: Bytedance Inc.
 Author-email: ai4s-bio@bytedance.com

{pxmeter-0.1.1 → pxmeter-0.1.2}/pxmeter/cli.py

@@ -18,9 +18,10 @@ from pathlib import Path
 import click
 
 from pxmeter.configs.data_config import (
+    CCD_BLOCKS_JSON,
     COMPONENTS_FILE,
     download_ccd_cif,
-    make_one_letter_code_json_from_ccd,
+    make_precomputed_json_from_ccd,
     ONE_LETTER_CODE_JSON,
 )
 from pxmeter.eval import evaluate, MetricResult
@@ -176,4 +177,6 @@ def update():
     Update the CCD database.
     """
     download_ccd_cif(output_path=COMPONENTS_FILE.parent)
-    make_one_letter_code_json_from_ccd(COMPONENTS_FILE, ONE_LETTER_CODE_JSON)
+    make_precomputed_json_from_ccd(
+        COMPONENTS_FILE, CCD_BLOCKS_JSON, ONE_LETTER_CODE_JSON
+    )

{pxmeter-0.1.1 → pxmeter-0.1.2}/pxmeter/configs/data_config.py

@@ -55,7 +55,9 @@ def download_ccd_cif(output_path: Path):
     logging.info("Download CCD CIF file successfully: %s", output_cif)
 
 
-def make_one_letter_code_json_from_ccd(components_file: Path, output_json: Path):
+def make_precomputed_json_from_ccd(
+    components_file: Path, ccd_blocks_json: Path, one_letter_code_json: Path
+):
     """
     Make a one-letter code JSON file from the CCD CIF file.
 
@@ -65,17 +67,23 @@ def make_one_letter_code_json_from_ccd(components_file: Path, output_json: Path)
     ccd_cif = gemmi.cif.read(str(components_file))
 
     ccd_code_to_one_letter_code = {}
+    ccd_code_to_block = {}
     for block in ccd_cif:
         ccd_code = block.find_value("_chem_comp.id")
         one_letter_code = block.find_value("_chem_comp.one_letter_code")
+        ccd_code_to_block[ccd_code] = block.as_string()
         if one_letter_code is None or one_letter_code == "?":
             continue
         ccd_code_to_one_letter_code[ccd_code] = one_letter_code
 
-    with open(output_json, "w") as f:
-        json.dump(ccd_code_to_one_letter_code, f, indent=4)
+    with open(ccd_blocks_json, "w") as f:
+        json.dump(ccd_code_to_block, f, indent=4)
+
+    logging.info("Make CCD_BLOCKS_JSON successfully: %s", ccd_blocks_json)
 
-    logging.info("Make ONE_LETTER_CODE_JSON successfully: %s", output_json)
+    with open(one_letter_code_json, "w") as f:
+        json.dump(ccd_code_to_one_letter_code, f, indent=4)
+    logging.info("Make ONE_LETTER_CODE_JSON successfully: %s", one_letter_code_json)
 
 
 # default is <repo_dir>/ccd_cache/components.cif Your path for components file
@@ -84,20 +92,30 @@ def make_one_letter_code_json_from_ccd(components_file: Path, output_json: Path)
 repo_dir = Path(__file__).absolute().parent.parent.parent
 ccd_file_in_repo = repo_dir / "ccd_cache" / "components.cif"
 COMPONENTS_FILE = Path(os.environ.get("PXM_CCD_FILE", ccd_file_in_repo))
-ONE_LETTER_CODE_JSON = COMPONENTS_FILE.with_suffix(".json")
+
+CCD_BLOCKS_JSON = COMPONENTS_FILE.with_suffix(".json")
+ONE_LETTER_CODE_JSON = COMPONENTS_FILE.parent / "one_letter_code.json"
 
 if not COMPONENTS_FILE.exists():
     logging.debug(
         "CCD CIF file not found. Downloading CCD CIF file to %s", COMPONENTS_FILE.parent
     )
     download_ccd_cif(output_path=COMPONENTS_FILE.parent)
-    make_one_letter_code_json_from_ccd(COMPONENTS_FILE, ONE_LETTER_CODE_JSON)
+    make_precomputed_json_from_ccd(
+        COMPONENTS_FILE, CCD_BLOCKS_JSON, ONE_LETTER_CODE_JSON
+    )
 else:
     logging.debug("Load CCD CIF file from: %s", COMPONENTS_FILE)
 
-if not ONE_LETTER_CODE_JSON.exists():
-    make_one_letter_code_json_from_ccd(COMPONENTS_FILE, ONE_LETTER_CODE_JSON)
+if not ONE_LETTER_CODE_JSON.exists() or not CCD_BLOCKS_JSON.exists():
+    make_precomputed_json_from_ccd(
+        COMPONENTS_FILE, CCD_BLOCKS_JSON, ONE_LETTER_CODE_JSON
+    )
 
 logging.debug("Load CCD one-letter code from: %s", ONE_LETTER_CODE_JSON)
 with open(ONE_LETTER_CODE_JSON, "r") as f:
     CCD_ONE_LETTER_CODE = json.load(f)
+
+
+with open(CCD_BLOCKS_JSON, "r") as f:
+    CCD_BLOCKS = json.load(f)

{pxmeter-0.1.1 → pxmeter-0.1.2}/pxmeter/data/ccd.py

@@ -24,7 +24,7 @@ from pdbeccdutils.core import ccd_reader
 from rdkit import Chem
 from rdkit.Geometry import Point3D
 
-from pxmeter.configs.data_config import COMPONENTS_FILE
+from pxmeter.configs.data_config import CCD_BLOCKS
 from pxmeter.data.utils import (
     get_inter_residue_bonds,
     get_mol_graph_matches,
@@ -34,17 +34,6 @@ from pxmeter.data.utils import (
 logging.getLogger("rdkit").setLevel(logging.ERROR)
 
 
-@functools.lru_cache
-def _gemmi_load_ccd_cif() -> gemmi.cif.Document:
-    """
-    Load the CCD components file using the gemmi library.
-
-    Returns:
-        gemmi.cif.Document: gemmi ccd components file
-    """
-    return gemmi.cif.read(str(COMPONENTS_FILE))
-
-
 @functools.lru_cache
 def get_ccd_mol_from_cif(ccd_code: str) -> Chem.Mol:
     """
@@ -57,10 +46,8 @@ def get_ccd_mol_from_cif(ccd_code: str) -> Chem.Mol:
         mol (Chem.Mol): The RDKit molecule object corresponding to the given CCD code.
                               Returns None if the CCD code is not found.
     """
-    ccd_cif = _gemmi_load_ccd_cif()
-
     try:
-        ccd_block = ccd_cif[ccd_code]
+        ccd_block = gemmi.cif.read_string(CCD_BLOCKS[ccd_code])[0]
     except KeyError:
         return
     ccd_reader_result = ccd_reader._parse_pdb_mmcif(ccd_block, sanitize=True)

{pxmeter-0.1.1 → pxmeter-0.1.2/pxmeter.egg-info}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: pxmeter
-Version: 0.1.1
+Version: 0.1.2
 Summary: PXMeter is a comprehensive toolkit for evaluating the quality of         structures generated by biomolecular structure prediction models.
 Author: Bytedance Inc.
 Author-email: ai4s-bio@bytedance.com

{pxmeter-0.1.1 → pxmeter-0.1.2}/setup.py

@@ -20,7 +20,7 @@ with open("requirements.txt") as f:
 setup(
     name="pxmeter",
     python_requires=">=3.11",
-    version="0.1.1",
+    version="0.1.2",
     description="PXMeter is a comprehensive toolkit for evaluating the quality of \
         structures generated by biomolecular structure prediction models.",
     author="Bytedance Inc.",