ligandparam 0.3.2__tar.gz → 0.3.4__tar.gz

{ligandparam-0.3.2 → ligandparam-0.3.4}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: ligandparam
-Version: 0.3.2
+Version: 0.3.4
 Summary: A ligand parameterization package for Amber
 Author-email: Zeke Piskulich <piskulichz@gmail.com>
 License: MIT
@@ -16,8 +16,9 @@ Requires-Dist: requests
 Requires-Dist: MDAnalysis>2.7.0
 Requires-Dist: pathlib
 Requires-Dist: parmed
+Requires-Dist: ase
+Requires-Dist: openff-toolkit
 Provides-Extra: ml
-Requires-Dist: ase; extra == "ml"
 Requires-Dist: deepmd-kit; extra == "ml"
 Requires-Dist: tensorflow; extra == "ml"
 Requires-Dist: tblite; extra == "ml"
@@ -41,3 +42,14 @@ key features encountered by users, including...
 
 The online documentation is located here: https://ligandparam.readthedocs.io/en/latest/
 
+
+
+### Developing
+
+#### Releasing a new version
+
+1. update `version` at `pyproject.toml`. Eg: `0.3.2`
+2. Add and commit the change. Then tag the commit: `git tag 0.3.2`
+3. `git push origin --tags`
+
+gitlab's CI/CD will publish the new version automatically

{ligandparam-0.3.2 → ligandparam-0.3.4}/README.md

@@ -8,3 +8,14 @@ key features encountered by users, including...
 
 The online documentation is located here: https://ligandparam.readthedocs.io/en/latest/
 
+
+
+### Developing
+
+#### Releasing a new version
+
+1. update `version` at `pyproject.toml`. Eg: `0.3.2`
+2. Add and commit the change. Then tag the commit: `git tag 0.3.2`
+3. `git push origin --tags`
+
+gitlab's CI/CD will publish the new version automatically

{ligandparam-0.3.2 → ligandparam-0.3.4}/pyproject.toml

@@ -4,7 +4,7 @@ build-backend = "setuptools.build_meta"
 
 [project]
 name = "ligandparam"
-version = "0.3.2"
+version = "0.3.4"
 description = "A ligand parameterization package for Amber"
 readme = "README.md"
 requires-python = ">=3.6"
@@ -23,7 +23,9 @@ dependencies = [
   "requests",
   "MDAnalysis>2.7.0",
   "pathlib",
-  "parmed"
+  "parmed",
+  "ase",
+  "openff-toolkit"
 ]
 
 urls = { "Homepage" = "https://github.com/piskulichz/ligandparam" }
@@ -31,7 +33,6 @@ urls = { "Homepage" = "https://github.com/piskulichz/ligandparam" }
 [project.optional-dependencies]
 
 ml = [
-  "ase",
   "deepmd-kit",
   "tensorflow",
   "tblite"
@@ -56,6 +57,7 @@ all = [
 lighfix = "ligandparam.cli.cli_lighfix:lighfix"
 lig-getparam = "ligandparam.cli.ligandparam_getparam:main"
 smiles-to-pdb = "ligandparam.cli.smiles_to_pdb:main"
+lig-to-sage = "ligandparam.cli.mol2_to_sage:main"
 
 
 [tool.ruff]

ligandparam-0.3.4/src/ligandparam/cli/mol2_to_sage.py

@@ -0,0 +1,20 @@
+from openff.toolkit import Molecule, ForceField, Topology, Quantity
+from openff.interchange import Interchange
+from openff.units import unit
+from rdkit import Chem
+from rdkit.Chem import AllChem
+import os
+ 
+from ligandparam.stages import StageSageCreate
+
+def main():
+    import argparse
+    parser = argparse.ArgumentParser(description="Generate AMBER parameters from a mol2 file.")
+    parser.add_argument("input_mol2", type=str, help="Path to the input mol2 file.")
+    parser.add_argument("output_tag", type=str, help="Tag for the output files.")
+    args = parser.parse_args()
+    stage = StageSageCreate("sage_creation", args.input_mol2, os.getcwd(), out_parm=f"{args.output_tag}.parm7")
+    stage.execute()
+ 
+if __name__ == "__main__":
+    main()

{ligandparam-0.3.2 → ligandparam-0.3.4}/src/ligandparam/driver.py

@@ -4,6 +4,33 @@ from pathlib import Path
 
 
 class Driver:
+    """ Base class for all parametrization drivers.
+    
+    This class is the base class for all parametrizations. It is designed to be subclassed, and the subclass should
+    implement the stages that are needed to complete the parametrization.
+
+    Parameters
+    ----------
+    in_filename : str or Path
+        The input filename for the parametrization.
+    cwd : str or Path
+        The current working directory for the parametrization.
+    *args : list
+        Additional arguments to pass to the subclass.
+    **kwargs : dict
+        Additional keyword arguments to pass to the subclass.
+    
+    
+    Attributes
+    ----------
+    in_filename : str or Path
+        The input filename for the parametrization.
+    cwd : str or Path
+        The current working directory for the parametrization.
+    stages : list
+        The list of stages to run for the parametrization.
+    
+    """
     @abstractmethod
     def __init__(self, in_filename: Union[Path, str], cwd: Union[Path, str], *args, **kwargs):
         """Initialize the Driver class object.
@@ -50,10 +77,21 @@ class Driver:
         ----------
         dry_run : bool, optional
             If True, the stages will not be executed, but the function will print the commands that would be executed.
+        nproc : int, optional
+            The number of processors to use for the stages that support parallel execution.
+        mem : int, optional
+            The amount of memory to use for the stages that support memory specification.
 
         Returns
         -------
         None
+
+        Raises
+        ------
+        RuntimeError
+            If a stage fails, a RuntimeError is raised with the error message from the stage.
+        
+            
         """
         for stage in self.stages:
             try:
@@ -72,6 +110,12 @@ class Driver:
         Returns
         -------
         None
+
+        Raises
+        ------
+        RuntimeError
+            If a stage fails, a RuntimeError is raised with the error message from the stage.
+        
         """
 
         for stage in reversed(self.stages):
@@ -96,6 +140,7 @@ class Driver:
         Returns
         -------
         None
+
         """
         print("List of Stages to Run")
         for stage in self.stages:
@@ -116,6 +161,7 @@ class Driver:
         Returns
         -------
         None
+
         """
         for stage in self.stages:
             if stage.stage_name == stage_name:
@@ -136,6 +182,20 @@ class Driver:
         ----------
         stage_name : str
             The name of the stage to insert into the list of stages to run.
+        newstage : Stage
+            The stage object to insert into the list of stages to run.
+        print_info : bool, optional
+            If True, the function will print the list of stages after the new stage is inserted.
+        
+        Returns
+        -------
+        None
+
+        Raises
+        ------
+        ValueError
+            If the specified stage is not in the list, a ValueError is raised.
+            
         """
         idx = -1
         for stage in self.stages:

{ligandparam-0.3.2 → ligandparam-0.3.4}/src/ligandparam/interfaces.py

@@ -9,22 +9,68 @@ from ligandparam.log import get_logger
 
 
 class SimpleInterface:
+    """
+    A simple interface to call external programs.
+
+    This class is designed to be subclassed, with the `method` attribute set to the desired program. The `call` method will then execute the program with the specified arguments.
+
+    Parameters
+    ----------
+    *args : list
+        Additional arguments to pass to the subclass.
+    **kwargs : dict
+        Additional keyword arguments to pass to the subclass.
+
+    Attributes
+    ----------
+    method : str
+        The method to call the external program.
+    logger : logging.Logger
+        The logger to use for logging.
+    cwd : Path
+        The current working directory to run the program in.
+    nproc : int
+        The number of processors to use for the program.
+    """
+
     @abstractmethod
     def __init__(self, *args, **kwargs) -> None:
-        """This class is a simple interface to call external programs.
-
-        This class is a simple interface to call external programs. It is designed to be subclassed
-        and the method attribute set to the desired program. The call method will then call the program
-        with the specified arguments.
+        """
+        Initialize the SimpleInterface class.
 
+        This class is designed to be subclassed, with the `method` attribute set to the desired program. The `call` method will then execute the program with the specified arguments.
         """
         pass
 
     def set_method(self, method):
+        """
+        Set the method to call the external program.
+
+        Parameters
+        ----------
+        method : str
+            The name of the external program to call.
+        """
         self.method = method
         return
 
     def call(self, **kwargs):
+        """
+        Call the external program with the specified arguments.
+
+        Parameters
+        ----------
+        **kwargs : dict
+            Keyword arguments to pass to the external program. Special keys include:
+            - `dry_run` (bool): If True, log the command without executing it.
+            - `inp_pipe` (str): Input file to pipe into the program.
+            - `out_pipe` (str): Output file to pipe the program's output.
+
+        Raises
+        ------
+        RuntimeError
+            If the external program returns a non-zero exit code.
+        """
         dry_run = False
         if "dry_run" in kwargs:
             dry_run = kwargs["dry_run"]
@@ -34,10 +80,10 @@ class SimpleInterface:
         shell = False
         for key, value in kwargs.items():
             if key == "inp_pipe":
-                command.extend([f"<", str(value)])
+                command.extend(["<", str(value)])
                 shell = True
             elif key == "out_pipe":
-                command.extend([f">", str(value)])
+                command.extend([">", str(value)])
                 shell = True
             else:
                 if value is not None:
@@ -70,9 +116,47 @@ class SimpleInterface:
 
 
 class Antechamber(SimpleInterface):
+    """
+    Interface to call the Antechamber program.
+
+    This class provides a simple interface to execute the Antechamber program.
+
+    Parameters
+    ----------
+    *args : list
+        Additional arguments to pass to the interface.
+    **kwargs : dict
+        Additional keyword arguments. Must include:
+        - `cwd` (str): Path to the working directory.
+
+    Attributes
+    ----------
+    cwd : Path
+        The current working directory to run the program in.
+    logger : logging.Logger
+        The logger to use for logging.
+    nproc : int
+        The number of processors to use for the program.
+    """
+
     @override
     def __init__(self, *args, **kwargs) -> None:
-        """This class is a simple interface to call the Antechamber program."""
+        """
+        Initialize the Antechamber interface.
+
+        Parameters
+        ----------
+        *args : list
+            Additional arguments to pass to the interface.
+        **kwargs : dict
+            Additional keyword arguments. Must include:
+            - `cwd` (str): Path to the working directory.
+
+        Raises
+        ------
+        ValueError
+            If the `cwd` argument is missing.
+        """
         try:
             self.cwd = Path(kwargs["cwd"])
         except KeyError:

{ligandparam-0.3.2 → ligandparam-0.3.4}/src/ligandparam/io/gaussianIO.py

@@ -251,10 +251,11 @@ class GaussianReader:
         multiplicity : int
             The multiplicity of the molecule
 
-        To Do
+        Notes
         -----
-        - Add error handling for missing data
-        - Check that this reads only the FINAL geometry
+        .. todo::
+            - Add error handling for missing data
+            - Check that this reads only the FINAL geometry
 
         """
         atn, coords = [], []

ligandparam-0.3.4/src/ligandparam/log.py

@@ -0,0 +1,91 @@
+"""
+This module provides logging utilities for the ligandparam package.
+
+Functions
+---------
+get_logger() -> logging.Logger
+    Returns a logger with a null handler.
+
+set_stream_logger(logging_level: int = logging.INFO) -> logging.Logger
+    Sets up a logger to output to the standard output stream.
+
+set_file_logger(logfilename: Path, logname: str = None, filemode: str = 'a') -> logging.Logger
+    Sets up a logger to output to a file.
+"""
+
+import sys
+import logging
+from pathlib import Path
+
+from . import __logging_name__
+
+
+def get_logger() -> logging.Logger:
+    """
+    Get a logger with a null handler.
+
+    Returns
+    -------
+    logging.Logger
+        A logger instance with a null handler.
+    """
+    logger = logging.getLogger(__logging_name__)
+    logger.setLevel(logging.INFO)
+    logger.addHandler(logging.NullHandler())
+    return logger
+
+def set_stream_logger(logging_level: int = logging.INFO) -> logging.Logger:
+    """
+    Set up a logger to output to the standard output stream.
+
+    Parameters
+    ----------
+    logging_level : int, optional
+        The logging level to set for the logger, by default logging.INFO.
+
+    Returns
+    -------
+    logging.Logger
+        A logger instance configured to output to the standard output stream.
+    """
+    logger = logging.getLogger(__logging_name__)
+    logger.setLevel(logging_level)
+    stream_handler = logging.StreamHandler(sys.stdout)
+    stream_handler.setLevel(logging_level)
+    logger.addHandler(stream_handler)
+
+    return logger
+
+def set_file_logger(logfilename: Path, logname: str = None, filemode: str = 'a') -> logging.Logger:
+    """
+    Set up a logger to output to a file.
+
+    Parameters
+    ----------
+    logfilename : Path
+        The path to the log file.
+    logname : str, optional
+        The name of the logger, by default None. If None, the module's logging name is used.
+    filemode : str, optional
+        The mode to open the log file, by default 'a'.
+
+    Returns
+    -------
+    logging.Logger
+        A logger instance configured to output to the specified file.
+    """
+    if logname is None:
+        logname = __logging_name__
+    logger = logging.getLogger(logname)
+    logger.setLevel(logging.INFO)
+    formatter = logging.Formatter(
+        "{asctime} - {levelname} - {message}",
+        style="{",
+        datefmt="%Y-%m-%d %H:%M:%S",
+    )
+    file_handler = logging.FileHandler(filename=logfilename, mode=filemode)
+    file_handler.setLevel(logging.INFO)
+    file_handler.setFormatter(formatter)
+    logger.addHandler(file_handler)
+
+    return logger

ligandparam-0.3.4/src/ligandparam/parametrization.py

@@ -0,0 +1,135 @@
+"""
+This module provides classes for parametrizing ligands and managing recipes.
+
+Classes
+-------
+Parametrization
+    A class for parametrizing ligands using various stages.
+
+Recipe
+    A subclass of Parametrization for managing ligand recipes.
+"""
+
+import logging
+from pathlib import Path
+from typing import Optional, Union
+from typing_extensions import override
+
+from ligandparam.driver import Driver
+from ligandparam.log import get_logger, set_stream_logger, set_file_logger
+
+
+class Parametrization(Driver):
+    """
+    A class for parametrizing ligands using various stages.
+
+    Parameters
+    ----------
+    in_filename : Union[Path, str]
+        The input filename of the ligand.
+    cwd : Union[Path, str]
+        The current working directory.
+    *args : tuple
+        Additional positional arguments.
+    **kwargs : dict
+        Additional keyword arguments.
+
+    Keyword Args
+    ------------
+    label : str, optional
+        A label for the ligand, by default the stem of `in_filename`.
+    leaprc : list, optional
+        A list of leaprc files to use, by default ["leaprc.gaff2"].
+    logger : Union[str, logging.Logger], optional
+        The logger to use. Can be "file", "stream", or a logging.Logger instance.
+
+    Attributes
+    ----------
+    in_filename : Path
+        The resolved path to the input file.
+    label : str
+        The label for the ligand.
+    cwd : Path
+        The current working directory.
+    stages : list
+        A list of stages to run.
+    leaprc : list
+        A list of leaprc files to use.
+    logger : logging.Logger
+        The logger instance.
+
+    Raises
+    ------
+    ValueError
+        If an invalid logger type is provided.
+    """
+
+    @override
+    def __init__(self, in_filename: Union[Path, str], cwd: Union[Path, str], *args, **kwargs):
+        """
+        The rough approach to using this class is to generate a new Parametrization class, and then generate self.stages as a list
+        of stages that you want to run.
+
+        Parameters
+        ----------
+        in_filename : Union[Path, str]
+            The input filename of the ligand.
+        cwd : Union[Path, str]
+            The current working directory.
+        *args : tuple
+            Additional positional arguments.
+        **kwargs : dict
+            Additional keyword arguments.
+
+        Keyword Args
+        ------------
+        label : str, optional
+            A label for the ligand, by default the stem of `in_filename`.
+        leaprc : list, optional
+            A list of leaprc files to use, by default ["leaprc.gaff2"].
+        logger : Union[str, logging.Logger], optional
+            The logger to use. Can be "file", "stream", or a logging.Logger instance.
+
+        Raises
+        ------
+        ValueError
+            If an invalid logger type is provided.
+        """
+        self.in_filename = Path(in_filename).resolve()
+        self.label = kwargs.get("label", self.in_filename.stem)
+        self.cwd = Path(cwd)
+        self.stages = []
+        self.leaprc = kwargs.get("leaprc", ["leaprc.gaff2"])
+        try:
+            logger = kwargs.pop("logger")
+            if isinstance(logger, str):
+                if logger == "file":
+                    self.logger = set_file_logger(self.cwd / f"{self.label}.log")
+                elif logger == "stream":
+                    self.logger = set_stream_logger()
+                else:
+                    raise ValueError("Invalid input string for logger. Must be either 'file' or 'stream'.")
+            elif isinstance(logger, logging.Logger):
+                self.logger = logger
+            else:
+                raise ValueError("logger must be a string or a logging.Logger instance.")
+        except KeyError:
+            self.logger = get_logger()
+
+    def add_leaprc(self, leaprc) -> None:
+        """
+        Add a leaprc file to the list of leaprc files.
+
+        Parameters
+        ----------
+        leaprc : str
+            The name of the leaprc file to add.
+        """
+        self.leaprc.append(leaprc)
+
+
+class Recipe(Parametrization):
+    """
+    A subclass of Parametrization for managing ligand recipes.
+    """
+    pass

{ligandparam-0.3.2 → ligandparam-0.3.4}/src/ligandparam/recipes/freeligand.py

@@ -27,8 +27,8 @@ class FreeLigand(Recipe):
     Initializing from a pdb file, assigning atom types, running gaussian optimization, rotating and calculating grid effects on RESP charges, and then generating the final mol2/lib/frcmod files
     with RESP charges.
 
-    Attributes:
-    -----------
+    Attributes
+    ----------
     in_filename : Union[Path, str]
         The input file containing the ligand structure, typically in PDB format.
     cwd : Union[Path, str]
@@ -56,8 +56,8 @@ class FreeLigand(Recipe):
     kwargs : dict
         Additional keyword arguments that can be passed to the stages.
     
-    Parameters:
-    -----------
+    Parameters
+    ----------
     in_filename : Union[Path, str]
         The input file containing the ligand structure, typically in PDB format.
     cwd : Union[Path, str]
@@ -85,8 +85,8 @@ class FreeLigand(Recipe):
     kwargs : dict, optional
         Additional keyword arguments that can be passed to the stages.
 
-    Raises:
-    -------
+    Raises
+    ------
     KeyError
         If a required option is missing from the keyword arguments.
     ValueError
@@ -96,7 +96,7 @@ class FreeLigand(Recipe):
     AttributeError
         If a required attribute is not set during initialization.
     
-    Example:
+    Examples
     --------
     >>> from ligandparam.recipes import FreeLigand
     >>> from pathlib import Path

{ligandparam-0.3.2 → ligandparam-0.3.4}/src/ligandparam/recipes/lazyligand.py

@@ -23,8 +23,8 @@ class LazyLigand(Recipe):
     Initializing from a pdb file, assigning atom types, running gaussian optimization, and calculating RESP charges, and then generating the final mol2/lib/frcmod files
     with RESP charges.
 
-    Attributes:
-    -----------
+    Attributes
+    ----------
     in_filename : Union[Path, str]
         The input file containing the ligand structure, typically in PDB format.
     cwd : Union[Path, str]
@@ -51,9 +51,9 @@ class LazyLigand(Recipe):
         The directory for Gaussian scratch files, if not set, will use the environment variable.
     kwargs : dict
         Additional keyword arguments that can be passed to the stages.
-    
-    Parameters:
-    -----------
+
+    Parameters
+    ----------
     in_filename : Union[Path, str]
         The input file containing the ligand structure, typically in PDB format.
     cwd : Union[Path, str]
@@ -81,8 +81,8 @@ class LazyLigand(Recipe):
     kwargs : dict, optional
         Additional keyword arguments that can be passed to the stages.
 
-    Raises:
-    -------
+    Raises
+    ------
     KeyError
         If a required option is missing from the keyword arguments.
     ValueError
@@ -92,7 +92,7 @@ class LazyLigand(Recipe):
     AttributeError
         If a required attribute is not set during initialization.
     
-    Example:
+    Examples
     --------
     >>> from ligandparam.recipes import LazyLigand
     >>> from pathlib import Path
@@ -302,7 +302,7 @@ class LazyLigand(Recipe):
         
         This method executes the LazyLigand recipe, which includes running all the stages defined in the setup method.
         
-        Parameters:
+        Parameters
         ----------
         dry_run : bool, optional
             If True, the stages will not be executed, but the commands that would be run will be printed.
@@ -311,7 +311,7 @@ class LazyLigand(Recipe):
         mem : Optional[int], optional
             The amount of memory (in GB) to allocate for the calculations. If None, will use the value set in the recipe.
         
-        Returns:
+        Returns
         -------
         None
         """

{ligandparam-0.3.2 → ligandparam-0.3.4}/src/ligandparam/stages/__init__.py

@@ -12,4 +12,5 @@ from .smilestopdb import StageSmilesToPDB
 from .lighfix import LigHFix
 from .displacemol import StageDisplaceMol
 from .pdb_names import PDB_Name_Fixer
-from .deepmd import DPMinimize
+from .deepmd import DPMinimize
+from .generate_sage_params import StageSageCreate