pythonQEPest 2.0.0a2__py3-none-any.whl → 2.0.0a4__py3-none-any.whl

pythonQEPest/.env.example

@@ -1,4 +1,4 @@
-LOG_LEVEL="INFO"
-LOG_FILE_LOCATION="logs/app.log"
-
+LOG_LEVEL="INFO"
+LOG_FILE_LOCATION="logs/app.log"
+
 APP_DEBUG_ENABLE="false"

pythonQEPest/__init__.py

@@ -1,11 +1,11 @@
-from pythonQEPest.core import QEPest
-from pythonQEPest.dto import QEPestData
-from pythonQEPest.dto import QEPestInput
-from pythonQEPest.dto import QEPestOutput
-
-__all__ = [
-    "QEPest",
-    "QEPestData",
-    "QEPestInput",
-    "QEPestOutput",
-]
+from pythonQEPest.core import QEPest
+from pythonQEPest.dto import QEPestData
+from pythonQEPest.dto import QEPestInput
+from pythonQEPest.dto import QEPestOutput
+
+__all__ = [
+    "QEPest",
+    "QEPestData",
+    "QEPestInput",
+    "QEPestOutput",
+]

pythonQEPest/cli/__init__.py

@@ -1,7 +1,7 @@
-def main():
-    from pythonQEPest.cli.cli import main as _main
-
-    return _main()
-
-
-__all__ = ["main"]
+def main():
+    from pythonQEPest.cli.cli import main as _main
+
+    return _main()
+
+
+__all__ = ["main"]

pythonQEPest/cli/cli.py

@@ -1,101 +1,101 @@
-from __future__ import annotations
-
-import argparse
-import logging
-from importlib.metadata import PackageNotFoundError, version
-from pathlib import Path
-from typing import Sequence
-
-from pythonQEPest.dto import QEPestFile
-from pythonQEPest.services.QEPestFileService import QEPestFileService
-
-logger = logging.getLogger(__name__)
-
-
-def _resolve_package_version() -> str:
-    try:
-        return version("pythonQEPest")
-    except PackageNotFoundError:
-        pass
-
-    try:
-        import tomllib  # py3.11+
-
-        pyproject = Path(__file__).resolve().parents[2] / "pyproject.toml"
-        data = tomllib.loads(pyproject.read_text(encoding="utf-8"))
-        return data["project"]["version"]
-    except Exception:
-        return "0+unknown"
-
-
-def build_parser() -> argparse.ArgumentParser:
-    parser = argparse.ArgumentParser(
-        prog="pythonqepest",
-        description="Compute QEPest scores from a tab-separated input file.",
-    )
-    parser.add_argument(
-        "-v",
-        "--version",
-        action="version",
-        version=f"%(prog)s {_resolve_package_version()}",
-        help="Show program's version number.",
-    )
-    parser.add_argument(
-        "-i",
-        "--input",
-        default="data.txt",
-        help="Path to input tab-separated file with "
-        + "QEPest descriptors (default: data.txt).",
-    )
-
-    parser.add_argument(
-        "-o",
-        "--output",
-        default="data.out.txt",
-        help="Path to output tab-separated file with "
-        + "QEPest descriptors (default: data.txt.out).",
-    )
-
-    parser.add_argument(
-        "-f",
-        "--format",
-        default="txt",
-        help="Format to output file with QEPest (json, txt).",
-    )
-
-    parser.add_argument(
-        "--smiles",
-        action="store_true",
-        help="Input file contains SMILES strings "
-        "(one per line) instead of descriptors.",
-    )
-    return parser
-
-
-def main(argv: Sequence[str] | None = None) -> int:
-    from dotenv import load_dotenv
-
-    from pythonQEPest.core.qepest import QEPest
-    from pythonQEPest.logger import init_logger
-
-    args = build_parser().parse_args(argv)
-
-    load_dotenv()
-    init_logger()
-
-    logger.debug("CLI initiated")
-    logger.info(f"CLI args: {argv}")
-
-    service = QEPestFileService(
-        qepest=QEPest(),
-        qepest_file=QEPestFile(
-            input_file=args.input,
-            output_file=args.output,
-            format=args.format,
-            smiles=args.smiles,
-        ),
-    )
-
-    service.read_file_and_compute_params()
-
-    return 0 if not service.error else 1
+from __future__ import annotations
+
+import argparse
+import logging
+from importlib.metadata import PackageNotFoundError, version
+from pathlib import Path
+from typing import Sequence
+
+from pythonQEPest.dto import QEPestFile
+from pythonQEPest.services.QEPestFileService import QEPestFileService
+
+logger = logging.getLogger(__name__)
+
+
+def _resolve_package_version() -> str:
+    try:
+        return version("pythonQEPest")
+    except PackageNotFoundError:
+        pass
+
+    try:
+        import tomllib  # py3.11+
+
+        pyproject = Path(__file__).resolve().parents[2] / "pyproject.toml"
+        data = tomllib.loads(pyproject.read_text(encoding="utf-8"))
+        return data["project"]["version"]
+    except Exception:
+        return "0+unknown"
+
+
+def build_parser() -> argparse.ArgumentParser:
+    parser = argparse.ArgumentParser(
+        prog="pythonqepest",
+        description="Compute QEPest scores from a tab-separated input file.",
+    )
+    parser.add_argument(
+        "-v",
+        "--version",
+        action="version",
+        version=f"%(prog)s {_resolve_package_version()}",
+        help="Show program's version number.",
+    )
+    parser.add_argument(
+        "-i",
+        "--input",
+        default="data.txt",
+        help="Path to input tab-separated file with "
+        + "QEPest descriptors (default: data.txt).",
+    )
+
+    parser.add_argument(
+        "-o",
+        "--output",
+        default="data.out.txt",
+        help="Path to output tab-separated file with "
+        + "QEPest descriptors (default: data.txt.out).",
+    )
+
+    parser.add_argument(
+        "-f",
+        "--format",
+        default="txt",
+        help="Format to output file with QEPest (json, txt).",
+    )
+
+    parser.add_argument(
+        "--smiles",
+        action="store_true",
+        help="Input file contains SMILES strings "
+        "(one per line) instead of descriptors.",
+    )
+    return parser
+
+
+def main(argv: Sequence[str] | None = None) -> int:
+    from dotenv import load_dotenv
+
+    from pythonQEPest.core.qepest import QEPest
+    from pythonQEPest.logger import init_logger
+
+    args = build_parser().parse_args(argv)
+
+    load_dotenv()
+    init_logger()
+
+    logger.debug("CLI initiated")
+    logger.info(f"CLI args: {argv}")
+
+    service = QEPestFileService(
+        qepest=QEPest(),
+        qepest_file=QEPestFile(
+            input_file=args.input,
+            output_file=args.output,
+            format=args.format,
+            smiles=args.smiles,
+        ),
+    )
+
+    service.read_file_and_compute_params()
+
+    return 0 if not service.error else 1

pythonQEPest/config/__init__.py

@@ -1,11 +1,11 @@
-from pythonQEPest.config.qepest_default import qepest_default
-from pythonQEPest.config.normalise import normalise_default
-from pythonQEPest.config.qepest_config import QEPestConfig
-from pythonQEPest.config.config_provider import ConfigProvider
-
-__all__ = [
-    "normalise_default",
-    "qepest_default",
-    "ConfigProvider",
-    "QEPestConfig",
-]
+from pythonQEPest.config.qepest_default import qepest_default
+from pythonQEPest.config.normalise import normalise_default
+from pythonQEPest.config.qepest_config import QEPestConfig
+from pythonQEPest.config.config_provider import ConfigProvider
+
+__all__ = [
+    "normalise_default",
+    "qepest_default",
+    "ConfigProvider",
+    "QEPestConfig",
+]

pythonQEPest/config/config_provider.py

@@ -1,9 +1,9 @@
-from abc import ABC, abstractmethod
-
-from pythonQEPest.config.qepest_config import QEPestConfig
-
-
-class ConfigProvider(ABC):
-    @abstractmethod
-    def load(self) -> QEPestConfig:
-        pass
+from abc import ABC, abstractmethod
+
+from pythonQEPest.config.qepest_config import QEPestConfig
+
+
+class ConfigProvider(ABC):
+    @abstractmethod
+    def load(self) -> QEPestConfig:
+        pass

pythonQEPest/config/normalise.py

@@ -1,12 +1,12 @@
-normalise_default = {
-    "herb": (69.5849922, 94.4228257, 120.4572352, 228.1589796, 89.7012502, 276.9634213),
-    "insect": (
-        78.2919965,
-        71.2829691,
-        133.9224801,
-        331.170104,
-        70.5540709,
-        193.0023343,
-    ),
-    "fung": (53.3719946, 52.773116, 73.7976536, 144.9887053, 41.4385926, 102.3024319),
-}
+normalise_default = {
+    "herb": (69.5849922, 94.4228257, 120.4572352, 228.1589796, 89.7012502, 276.9634213),
+    "insect": (
+        78.2919965,
+        71.2829691,
+        133.9224801,
+        331.170104,
+        70.5540709,
+        193.0023343,
+    ),
+    "fung": (53.3719946, 52.773116, 73.7976536, 144.9887053, 41.4385926, 102.3024319),
+}

pythonQEPest/config/qepest_config.py

@@ -1,31 +1,31 @@
-from typing import Optional
-
-from pydantic import BaseModel
-
-from pythonQEPest.dto.pest_type.PestTypeConfig import PestTypeConfig
-
-
-class QEPestConfig(BaseModel):
-    name: Optional[str] = "HerbInsectFung"
-    pest_types: list[PestTypeConfig]
-
-    def get_pest_names(self) -> list[str]:
-        return [pest.name for pest in self.pest_types]
-
-    def get_coefficients(
-        self, pest_name: str
-    ) -> list[tuple[float, float, float, float]]:
-        for pest in self.pest_types:
-            if pest.name == pest_name:
-                return pest.coefficients.as_set()
-
-        raise ValueError(f"Pest type '{pest_name}' not found")
-
-    def get_normaliser(
-        self, pest_name: str
-    ) -> tuple[float, float, float, float, float, float]:
-        for pest in self.pest_types:
-            if pest.name == pest_name:
-                return pest.normaliser
-
-        raise ValueError(f"Pest type '{pest_name}' not found")
+from typing import Optional
+
+from pydantic import BaseModel
+
+from pythonQEPest.dto.pest_type.PestTypeConfig import PestTypeConfig
+
+
+class QEPestConfig(BaseModel):
+    name: Optional[str] = "HerbInsectFung"
+    pest_types: list[PestTypeConfig]
+
+    def get_pest_names(self) -> list[str]:
+        return [pest.name for pest in self.pest_types]
+
+    def get_coefficients(
+        self, pest_name: str
+    ) -> list[tuple[float, float, float, float]]:
+        for pest in self.pest_types:
+            if pest.name == pest_name:
+                return pest.coefficients.as_set()
+
+        raise ValueError(f"Pest type '{pest_name}' not found")
+
+    def get_normaliser(
+        self, pest_name: str
+    ) -> tuple[float, float, float, float, float, float]:
+        for pest in self.pest_types:
+            if pest.name == pest_name:
+                return pest.normaliser
+
+        raise ValueError(f"Pest type '{pest_name}' not found")

pythonQEPest/core/__init__.py

@@ -1,7 +1,7 @@
-from .qepest import QEPest
-from .qepest_meta import QEPestMeta
-
-__all__ = [
-    "QEPestMeta",
-    "QEPest",
-]
+from .qepest import QEPest
+from .qepest_meta import QEPestMeta
+
+__all__ = [
+    "QEPestMeta",
+    "QEPest",
+]

pythonQEPest/core/qepest.py

@@ -1,98 +1,98 @@
-import logging
-import math
-from typing import Optional
-
-from pythonQEPest.config import ConfigProvider
-from pythonQEPest.core.qepest_meta import QEPestMeta
-from pythonQEPest.config.qepest_config import QEPestConfig
-from pythonQEPest.dto import QEPestData
-
-from pythonQEPest.dto.QEPestInput import QEPestInput
-from pythonQEPest.dto.QEPestOutput import QEPestOutput
-from pythonQEPest.dto.normalisation.Normaliser import Normaliser
-from pythonQEPest.helpers.check_nan import check_nan
-from pythonQEPest.helpers.compute_df import compute_df
-from pythonQEPest.helpers.get_values_from_line import get_values_from_line
-from pythonQEPest.helpers.round_to_4digs import round_to_4digs
-from pythonQEPest.providers import DefaultConfigProvider
-
-logger = logging.getLogger(__name__)
-
-
-class QEPest(QEPestMeta):
-    def __init__(self, provider: Optional[ConfigProvider] = None, *args, **kwargs):
-        super().__init__(*args, **kwargs)
-
-        self.config: QEPestConfig
-        self.normalisers: dict[str, Normaliser] = {}
-        self.qex: QEPestData = QEPestData({})
-
-        logger.debug("QEPest initialization")
-
-        self.initialise_config(provider)
-
-        logger.debug("QEPest initialization successful")
-
-    def initialise_config(self, provider: Optional[ConfigProvider] = None):
-        logger.debug("Config initialisation")
-        if provider is None:
-            logger.debug("Config is empty. Loading default one.")
-            provider = DefaultConfigProvider()
-
-        self.config = provider.load()
-        logger.debug(f"Config {self.config} loaded")
-
-        for pest in self.config.pest_types:
-            self.normalisers[pest.name] = Normaliser(pest.normaliser)
-
-    def _log_compute_df(
-        self, func, index: int, lst: list[float], data_lst: list
-    ) -> float:
-        df_result = compute_df(lst[index], *data_lst[index])
-        return math.log(func(df_result, index))
-
-    def get_names(self) -> list[str]:
-        return self.config.get_pest_names()
-
-    def compute_params(self, data_input: QEPestInput) -> QEPestOutput:
-        self.get_qex_values(
-            get_values_from_line(list(data_input.model_dump().values()))
-        )
-        return QEPestOutput(data=self.qex, name=data_input.name)
-
-    def get_qex_values(self, d: list[float]) -> QEPestData:
-        names = self.get_names()
-
-        if len(names) == 0:
-            raise ValueError(
-                "No pest types configured. " "Please provide a valid configuration."
-            )
-
-        qe_values = dict.fromkeys(names, 0.0)
-
-        d_num = len(d)
-        for i in range(d_num):
-            for name in names:
-                coeffs = self.config.get_coefficients(name)
-                normaliser = self.normalisers[name]
-                qe_values[name] += self._log_compute_df(
-                    func=normaliser.norm,
-                    index=i,
-                    lst=d,
-                    data_lst=coeffs,
-                )
-
-        result = [round_to_4digs(math.exp(qe_values[name] / d_num)) for name in names]
-
-        result = check_nan(result)
-
-        self.qex = QEPestData(
-            {f"qe_{name}": result[idx] for idx, name in enumerate(names)}
-        )
-
-        return self.qex
-
-
-if __name__ == "__main__":
-    qepest = QEPest()
-    qepest.get_qex_values([1.0, 2.0, 3.0, 4.0, 5.0, 6.0, 7.0])
+import logging
+import math
+from typing import Optional
+
+from pythonQEPest.config import ConfigProvider
+from pythonQEPest.core.qepest_meta import QEPestMeta
+from pythonQEPest.config.qepest_config import QEPestConfig
+from pythonQEPest.dto import QEPestData
+
+from pythonQEPest.dto.QEPestInput import QEPestInput
+from pythonQEPest.dto.QEPestOutput import QEPestOutput
+from pythonQEPest.dto.normalisation.Normaliser import Normaliser
+from pythonQEPest.helpers.check_nan import check_nan
+from pythonQEPest.helpers.compute_df import compute_df
+from pythonQEPest.helpers.get_values_from_line import get_values_from_line
+from pythonQEPest.helpers.round_to_4digs import round_to_4digs
+from pythonQEPest.providers import DefaultConfigProvider
+
+logger = logging.getLogger(__name__)
+
+
+class QEPest(QEPestMeta):
+    def __init__(self, provider: Optional[ConfigProvider] = None, *args, **kwargs):
+        super().__init__(*args, **kwargs)
+
+        self.config: QEPestConfig
+        self.normalisers: dict[str, Normaliser] = {}
+        self.qex: QEPestData = QEPestData({})
+
+        logger.debug("QEPest initialization")
+
+        self.initialise_config(provider)
+
+        logger.debug("QEPest initialization successful")
+
+    def initialise_config(self, provider: Optional[ConfigProvider] = None):
+        logger.debug("Config initialisation")
+        if provider is None:
+            logger.debug("Config is empty. Loading default one.")
+            provider = DefaultConfigProvider()
+
+        self.config = provider.load()
+        logger.debug(f"Config {self.config} loaded")
+
+        for pest in self.config.pest_types:
+            self.normalisers[pest.name] = Normaliser(pest.normaliser)
+
+    def _log_compute_df(
+        self, func, index: int, lst: list[float], data_lst: list
+    ) -> float:
+        df_result = compute_df(lst[index], *data_lst[index])
+        return math.log(func(df_result, index))
+
+    def get_names(self) -> list[str]:
+        return self.config.get_pest_names()
+
+    def compute_params(self, data_input: QEPestInput) -> QEPestOutput:
+        self.get_qex_values(
+            get_values_from_line(list(data_input.model_dump().values()))
+        )
+        return QEPestOutput(data=self.qex, name=data_input.name)
+
+    def get_qex_values(self, d: list[float]) -> QEPestData:
+        names = self.get_names()
+
+        if len(names) == 0:
+            raise ValueError(
+                "No pest types configured. " "Please provide a valid configuration."
+            )
+
+        qe_values = dict.fromkeys(names, 0.0)
+
+        d_num = len(d)
+        for i in range(d_num):
+            for name in names:
+                coeffs = self.config.get_coefficients(name)
+                normaliser = self.normalisers[name]
+                qe_values[name] += self._log_compute_df(
+                    func=normaliser.norm,
+                    index=i,
+                    lst=d,
+                    data_lst=coeffs,
+                )
+
+        result = [round_to_4digs(math.exp(qe_values[name] / d_num)) for name in names]
+
+        result = check_nan(result)
+
+        self.qex = QEPestData(
+            {f"qe_{name}": result[idx] for idx, name in enumerate(names)}
+        )
+
+        return self.qex
+
+
+if __name__ == "__main__":
+    qepest = QEPest()
+    qepest.get_qex_values([1.0, 2.0, 3.0, 4.0, 5.0, 6.0, 7.0])

pythonQEPest/core/qepest_meta.py

@@ -1,28 +1,28 @@
-import os
-from abc import abstractmethod, ABC
-
-from pydantic import BaseModel
-
-from pythonQEPest.dto import QEPestInput, QEPestOutput
-
-
-class QEPestMeta(ABC):
-    def __init__(self, *args, **kwargs):
-        self.qex: BaseModel | None = None
-
-        self.col_number: int = 7
-        self.dir: str = os.getcwd()
-
-    @abstractmethod
-    def compute_params(self, data_input: QEPestInput) -> QEPestOutput:
-        pass
-
-    @abstractmethod
-    def get_qex_values(self, d: list[float]) -> None:
-        pass
-
-    @abstractmethod
-    def _log_compute_df(
-        self, func, index: int, lst: list[float], data_lst: list
-    ) -> float:
-        pass
+import os
+from abc import abstractmethod, ABC
+
+from pydantic import BaseModel
+
+from pythonQEPest.dto import QEPestInput, QEPestOutput
+
+
+class QEPestMeta(ABC):
+    def __init__(self, *args, **kwargs):
+        self.qex: BaseModel | None = None
+
+        self.col_number: int = 7
+        self.dir: str = os.getcwd()
+
+    @abstractmethod
+    def compute_params(self, data_input: QEPestInput) -> QEPestOutput:
+        pass
+
+    @abstractmethod
+    def get_qex_values(self, d: list[float]) -> None:
+        pass
+
+    @abstractmethod
+    def _log_compute_df(
+        self, func, index: int, lst: list[float], data_lst: list
+    ) -> float:
+        pass

pythonQEPest/data.txt

@@ -1,2 +1,2 @@
-Name	MW	LogP	HBA	HBD	RB	arR
+Name	MW	LogP	HBA	HBD	RB	arR
 Nc1nc2CCCC3O[C@H](CCC)C(=O)c(n1)c23	247.29799999999994	1.8178	5	1	2	1

pythonQEPest/data.txt.out

@@ -1,2 +1,2 @@
-Name QEH QEI QEF
-Nc1nc2CCCC3O[C@H](CCC)C(=O)c(n1)c23 0.7387 0.4635 0.5941
+Name QEH QEI QEF
+Nc1nc2CCCC3O[C@H](CCC)C(=O)c(n1)c23 0.7387 0.4635 0.5941