ppqm 0.1.0__py3-none-any.whl

env/bin/activate_this.py

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+# Copyright (c) 2020-202x The virtualenv developers
+#
+# Permission is hereby granted, free of charge, to any person obtaining
+# a copy of this software and associated documentation files (the
+# "Software"), to deal in the Software without restriction, including
+# without limitation the rights to use, copy, modify, merge, publish,
+# distribute, sublicense, and/or sell copies of the Software, and to
+# permit persons to whom the Software is furnished to do so, subject to
+# the following conditions:
+#
+# The above copyright notice and this permission notice shall be
+# included in all copies or substantial portions of the Software.
+#
+# THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
+# EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF
+# MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
+# NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE
+# LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION
+# OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION
+# WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.
+
+"""
+Activate virtualenv for current interpreter:
+
+import runpy
+runpy.run_path(this_file)
+
+This can be used when you must use an existing Python interpreter, not the virtualenv bin/python.
+"""  # noqa: D415
+
+from __future__ import annotations
+
+import os
+import site
+import sys
+
+try:
+    abs_file = os.path.abspath(__file__)
+except NameError as exc:
+    msg = "You must use import runpy; runpy.run_path(this_file)"
+    raise AssertionError(msg) from exc
+
+bin_dir = os.path.dirname(abs_file)
+base = bin_dir[: -len("bin") - 1]  # strip away the bin part from the __file__, plus the path separator
+
+# prepend bin to PATH (this file is inside the bin directory)
+os.environ["PATH"] = os.pathsep.join([bin_dir, *os.environ.get("PATH", "").split(os.pathsep)])
+os.environ["VIRTUAL_ENV"] = base  # virtual env is right above bin directory
+os.environ["VIRTUAL_ENV_PROMPT"] = "" or os.path.basename(base)  # noqa: SIM222
+
+# add the virtual environments libraries to the host python import mechanism
+prev_length = len(sys.path)
+for lib in "../lib/python3.12/site-packages".split(os.pathsep):
+    path = os.path.realpath(os.path.join(bin_dir, lib))
+    site.addsitedir(path)
+sys.path[:] = sys.path[prev_length:] + sys.path[0:prev_length]
+
+sys.real_prefix = sys.prefix
+sys.prefix = base

ppqm/__init__.py

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+from ppqm import chembridge
+from ppqm.gamess import GamessCalculator
+from ppqm.gaussian import GaussianCalculator
+from ppqm.mopac import MopacCalculator
+from ppqm.orca import OrcaCalculator
+from ppqm.utils.files import WorkDir
+from ppqm.xtb import XtbCalculator

ppqm/calculator.py

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+import abc
+import copy
+import logging
+from collections import ChainMap
+from pathlib import Path
+from typing import Any
+
+from ppqm import chembridge, constants
+from ppqm.chembridge import Mol
+
+_logger = logging.getLogger(__name__)
+
+
+class BaseCalculator(abc.ABC):
+    """Base class for quantum calculators
+
+    This class should not be used directly, use a class appropriate for your
+    quantum calculations (e.g. MopacCalculator or GamessCalculator) instead.
+    """
+
+    def __init__(self, scr: Path = constants.SCR) -> None:
+        self.scr = Path(scr)
+        # Ensure scrdir
+        self.set_scratch_directory()
+
+    def _health_check(self) -> None:
+        raise NotImplementedError
+
+    def _generate_options(self, **kwargs: Any) -> dict:
+        """to be implemented by individual programs"""
+        raise NotImplementedError
+
+    def calculate(self, molobj: Mol, options: dict) -> list[dict | None]:
+        raise NotImplementedError
+
+    def optimize(self, molobj: Mol, options: dict | None = None, return_copy: bool = True) -> Mol:
+        """
+
+        Parameters
+        ----------
+        molobj: Mol
+            A RDkit Molobj
+
+        return_copy: Bool
+            Return a new copy of molobj, instead of overwriting it
+
+        return_properties: Bool
+            Return list of properties for molobj conformers
+
+        Examples
+        --------
+        >>> molobj_prime = calc.optimize(molobj)
+
+        Returns
+        -------
+        molobj: Mol
+            RDKit molobj with updated conformer coordinates
+
+        properties: List(Dict(Str, Any))
+            Properties associated with each conformer
+
+        """
+
+        # TODO Embed properties into conformres
+
+        # Merge options
+        if options is None:
+            options = {}
+        options_ = self._generate_options(optimize=True)
+        options_prime = dict(ChainMap(options, options_))
+
+        if return_copy:
+            molobj = copy.deepcopy(molobj)
+
+        result_properties: list[dict] = self.calculate(molobj, options_prime)  # type: ignore
+
+        for i, properties in enumerate(result_properties):
+            # TODO Check if unconverged
+            # TODO Check number of steps?
+
+            if constants.COLUMN_COORDINATES not in properties:
+                # TODO Unable to set coordinates, skip for now
+                _logger.error(f"Unable to optimize, conformer {i} skipped")
+                continue
+
+            coord = properties[constants.COLUMN_COORDINATES]
+
+            # Set coord on conformer
+            chembridge.molobj_set_coordinates(molobj, coord, confid=i)
+
+        return molobj
+
+    def get_gradient(self, molobj: Mol) -> None:
+        raise NotImplementedError
+
+    def get_hessian(self, molobj: Mol) -> None:
+        raise NotImplementedError
+
+    def set_energy_unit(self, unit: Mol) -> None:
+        raise NotImplementedError
+        # TODO set unit.convert(value, X, to)
+
+    def set_scratch_directory(self) -> None:
+        self.scr.mkdir(parents=True, exist_ok=True)
+
+    def health_check(self) -> None:
+        raise NotImplementedError
+
+    def __repr__(self) -> str:
+        return "CalculatorSkeleton()"