pxmeter 0.0.1__tar.gz → 0.1.0__tar.gz

{pxmeter-0.0.1/pxmeter.egg-info → pxmeter-0.1.0}/PKG-INFO

@@ -1,7 +1,7 @@
 Metadata-Version: 2.1
 Name: pxmeter
-Version: 0.0.1
-Summary: PXMeter is a tool crafted to assess the structural quality derived from Biomolecular Folding Models
+Version: 0.1.0
+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
 License: Apache 2.0 License

{pxmeter-0.0.1 → pxmeter-0.1.0}/pxmeter/cli.py

@@ -12,13 +12,19 @@
 # See the License for the specific language governing permissions and
 # limitations under the License.
 
+import sys
 from pathlib import Path
 
 import click
 
-from pxmeter.configs.data_config import COMPONENTS_FILE, download_ccd_cif
+from pxmeter.configs.data_config import (
+    COMPONENTS_FILE,
+    download_ccd_cif,
+    make_one_letter_code_json_from_ccd,
+    ONE_LETTER_CODE_JSON,
+)
 from pxmeter.eval import evaluate, MetricResult
-from pxmeter.utils import none_or_str, read_chain_id_to_mol_from_json
+from pxmeter.utils import read_chain_id_to_mol_from_json
 
 
 def run_eval_cif(
@@ -29,14 +35,14 @@ def run_eval_cif(
     ref_assembly_id: str | None = None,
     ref_altloc: str = "first",
     interested_lig_label_asym_id: str | None = None,
-    chain_id_to_mol_json: str | None = None,
+    chain_id_to_mol_json: Path | None = None,
     output_mapped_cif: bool = False,
 ) -> MetricResult:
     """
-    Evaluate the performance of a model CIF file against a reference CIF file.
-    And save the result to a JSON file.
+    Evaluate the performance of a model CIF file by comparing it to a reference CIF file,
+    and save the results in a JSON file.
     """
-    if chain_id_to_mol_json:
+    if chain_id_to_mol_json is not None:
         chain_id_to_mol = read_chain_id_to_mol_from_json(chain_id_to_mol_json)
     else:
         chain_id_to_mol = None
@@ -68,37 +74,9 @@ def run_eval_cif(
     return metric_result
 
 
-@click.group()
-def ccd_cli():
-    """
-    CCD Options.
-    """
-    return
-
-
-@ccd_cli.command(name="update")
-def update():
-    """
-    Update the CCD database.
-    """
-    download_ccd_cif(output_path=COMPONENTS_FILE.parent)
-
-
-@click.group()
-def eval_cif():
-    """
-    Evaluate the performance of a model CIF file against a reference CIF file.
-    """
-    return
-
-
 @click.group(invoke_without_command=True)
-@click.option(
-    "-r", "--ref_cif", type=Path, required=True, help="Path to the reference CIF file."
-)
-@click.option(
-    "-m", "--model_cif", type=Path, required=True, help="Path to the model CIF file."
-)
+@click.option("-r", "--ref_cif", type=Path, help="Path to the reference CIF file.")
+@click.option("-m", "--model_cif", type=Path, help="Path to the model CIF file.")
 @click.option(
     "-o",
     "--output_json",
@@ -114,7 +92,7 @@ def eval_cif():
 )
 @click.option(
     "--ref_assembly_id",
-    type=none_or_str,
+    type=str,
     default=None,
     help="Assembly ID in the reference CIF file. Defaults to None.",
 )
@@ -127,15 +105,15 @@ def eval_cif():
 @click.option(
     "-l",
     "--interested_lig_label_asym_id",
-    type=none_or_str,
+    type=str,
     default=None,
     help="The label_asym_id of the ligand of interest in the reference structure (for ligand RMSD metrics). \
-            If multiple ligands are present, separate them by comma. Defaults to None.",
+        If multiple ligands are present, separate them by comma. Defaults to None.",
 )
 @click.option(
     "-c",
     "--chain_id_to_mol_json",
-    type=none_or_str,
+    type=Path,
     default=None,
     help="Path to a JSON file containing a mapping of chain IDs to molecular input (SMILES). \
         E.g. {'B': 'c1ccccc1', 'D':'CCCC'}",
@@ -145,7 +123,9 @@ def eval_cif():
     is_flag=True,
     help="Whether to output the mapped CIF file. Defaults to False.",
 )
-def run_eval_cif_cli(
+@click.pass_context
+def cli(
+    ctx,
     ref_cif: Path,
     model_cif: Path,
     output_json: Path,
@@ -153,21 +133,47 @@ def run_eval_cif_cli(
     ref_assembly_id: str | None = None,
     ref_altloc: str = "first",
     interested_lig_label_asym_id: str | None = None,
-    chain_id_to_mol_json: str | None = None,
+    chain_id_to_mol_json: Path | None = None,
     output_mapped_cif: bool = False,
 ):
     """
-    Evaluate the performance of a model CIF file against a reference CIF file.
-    And save the result to a JSON file.
+    Evaluate the performance of a model CIF file by comparing it to a reference CIF file,
+    and save the results in a JSON file.
     """
-    run_eval_cif(
-        ref_cif,
-        model_cif,
-        output_json,
-        ref_model,
-        ref_assembly_id,
-        ref_altloc,
-        interested_lig_label_asym_id,
-        chain_id_to_mol_json,
-        output_mapped_cif,
-    )
+    if ctx.invoked_subcommand is None:
+        if len(sys.argv) == 1:
+            click.echo(ctx.get_help())
+            ctx.exit()
+
+        if ref_cif is None or model_cif is None:
+            click.echo("Error: --ref_cif and --model_cif are required.")
+            ctx.exit()
+
+        run_eval_cif(
+            ref_cif,
+            model_cif,
+            output_json,
+            ref_model,
+            ref_assembly_id,
+            ref_altloc,
+            interested_lig_label_asym_id,
+            chain_id_to_mol_json,
+            output_mapped_cif,
+        )
+
+
+@cli.group(name="ccd")
+def ccd_cli():
+    """
+    CCD Options.
+    """
+    return
+
+
+@ccd_cli.command(name="update")
+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)

{pxmeter-0.0.1 → pxmeter-0.1.0}/pxmeter/configs/data_config.py

@@ -52,7 +52,7 @@ def download_ccd_cif(output_path: Path):
 
     sp.run(f"gunzip -d {output_cif_gz}", shell=True, check=True)
 
-    logging.info("Download CCD CIF file successfully.")
+    logging.info("Download CCD CIF file successfully: %s", output_cif)
 
 
 def make_one_letter_code_json_from_ccd(components_file: Path, output_json: Path):

{pxmeter-0.0.1 → pxmeter-0.1.0}/pxmeter/utils.py

@@ -13,30 +13,18 @@
 # limitations under the License.
 
 import json
+from pathlib import Path
 
 from rdkit import Chem
 
 
-def none_or_str(value: str | None) -> str | None:
-    """
-    Converts the string "None" to a NoneType, otherwise returns the input string.
-    Args:
-        value (str, optional): The input string which may be "None".
-    Returns:
-        str or None: None if the input is the string "None", otherwise the input string.
-    """
-    if value == "None":
-        return None
-    return value
-
-
-def read_chain_id_to_mol_from_json(json_f: str) -> dict[str, Chem.Mol]:
+def read_chain_id_to_mol_from_json(json_f: Path | str) -> dict[str, Chem.Mol]:
     """
     Reads a JSON file containing chain IDs and their corresponding SMILES representations,
     and returns a dictionary mapping chain IDs to RDKit Mol objects.
 
     Args:
-        json_f (str): The path to the JSON file.
+        json_f (Path | str): The path to the JSON file.
 
     Returns:
         dict[str, Chem.Mol]: A dictionary mapping chain IDs to RDKit Mol objects.

{pxmeter-0.0.1 → pxmeter-0.1.0/pxmeter.egg-info}/PKG-INFO

@@ -1,7 +1,7 @@
 Metadata-Version: 2.1
 Name: pxmeter
-Version: 0.0.1
-Summary: PXMeter is a tool crafted to assess the structural quality derived from Biomolecular Folding Models
+Version: 0.1.0
+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
 License: Apache 2.0 License

pxmeter-0.1.0/pxmeter.egg-info/entry_points.txt

@@ -0,0 +1,2 @@
+[console_scripts]
+pxm = pxmeter.cli:cli

{pxmeter-0.0.1 → pxmeter-0.1.0}/setup.py

@@ -20,8 +20,9 @@ with open("requirements.txt") as f:
 setup(
     name="pxmeter",
     python_requires=">=3.11",
-    version="0.0.1",
-    description="PXMeter is a tool crafted to assess the structural quality derived from Biomolecular Folding Models",
+    version="0.1.0",
+    description="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",
     packages=find_packages(
@@ -41,7 +42,7 @@ setup(
     platforms="manylinux1",
     entry_points={
         "console_scripts": [
-            "pxm = pxmeter.cli:run_eval_cif_cli",
+            "pxm = pxmeter.cli:cli",
         ],
     },
 )

pxmeter-0.0.1/pxmeter.egg-info/entry_points.txt

@@ -1,2 +0,0 @@
-[console_scripts]
-pxm = pxmeter.cli:run_eval_cif_cli