ppqm 0.1.0__tar.gz

ppqm-0.1.0/LICENSE

@@ -0,0 +1,21 @@
+MIT License
+
+Copyright (c) 2020 Psi Phi Quantum Mechanics
+
+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.

ppqm-0.1.0/PKG-INFO

@@ -0,0 +1,115 @@
+Metadata-Version: 2.4
+Name: ppqm
+Version: 0.1.0
+Summary: Utilities for running QM calculations with RDKit
+Maintainer: Jimmy Kromann, Hagen Muenkler
+License: MIT
+Classifier: Intended Audience :: Science/Research
+Classifier: License :: OSI Approved :: MIT License
+Classifier: Programming Language :: Python :: 3
+Requires-Python: >=3.10
+Description-Content-Type: text/markdown
+License-File: LICENSE
+Requires-Dist: numpy
+Requires-Dist: tqdm
+Requires-Dist: rmsd
+Requires-Dist: rdkit
+Provides-Extra: test
+Requires-Dist: pytest; extra == "test"
+Requires-Dist: pytest-cov; extra == "test"
+Provides-Extra: dev
+Requires-Dist: build; extra == "dev"
+Requires-Dist: ipython; extra == "dev"
+Requires-Dist: ipywidgets; extra == "dev"
+Requires-Dist: jupytext; extra == "dev"
+Requires-Dist: matplotlib; extra == "dev"
+Requires-Dist: nglview; extra == "dev"
+Requires-Dist: pandas; extra == "dev"
+Requires-Dist: pip; extra == "dev"
+Requires-Dist: pre-commit; extra == "dev"
+Requires-Dist: ruff; extra == "dev"
+Requires-Dist: twine; extra == "dev"
+Requires-Dist: ty; extra == "dev"
+Dynamic: license-file
+
+# Psi Phi Package
+
+Do you need RDKit? Do you need quantum chemistry? We got you.
+This package is a simple bridge between RDKit and quantum chemistry (QC) packages
+that lack Python interfaces.
+
+Current version has calculator wrappers for
+
+- GAMESS
+- Gaussian
+- MNDO
+- MOPAC
+- Orca
+- xTB
+
+## Example
+
+Assume all codesnippets below are using RDKit molecule objs.
+
+```python
+molecule = Chem.MolFromSmiles("O")
+Chem.AddHydrogens(molecule)
+AllChem.UFFOptimizeMolecule(molecule)
+```
+
+The simple usage is to make an instance of a QC software.
+For example, using the popular package xTB, you can define the amount of cores
+to allocate and the exact path to the executable.
+
+```python
+from ppqm import XtbCalculator
+
+xtb = XtbCalculator(cmd="xtb", cores=4)
+```
+
+The format for running calculations are based on Python dictionaries, which are
+translated into the right format. So for example running a GFN2 optimization in
+water, the input would be
+
+```python
+# Define the calculation
+optimize_options = {
+    "gfn": 2,
+    "alpb": "h2o",
+    "opt": None,
+}
+
+# Run the calculation
+results = xtb.calculate(molecule, optimize_options)
+
+# Results is a List of Dict properties
+for i, propeties in enumerate(results):
+    print(f"Conformer {i} properties: {properties}")
+```
+
+For more documentation by example, checkout the `notebooks/` directory.
+
+## Contributions
+
+Fork, branch and use pre-commit.
+
+## Other code bases
+
+"is this the first python wrapper for quantum chemistry?" No, check the others
+and find the one right for your project. Know one, not on the list? Add it. In
+alphabetic order.
+
+- [Moleculekit](https://github.com/Acellera/moleculekit)
+- [stko](https://github.com/JelfsMaterialsGroup/stko)
+- [MolSSI](https://github.com/MolSSI)
+- [cclib](https://github.com/cclib/cclib)
+- [datamol](https://github.com/datamol-org/datamol)
+- [autodE](https://github.com/duartegroup/autodE/)
+- [cctk](https://github.com/ekwan/cctk)
+- [pygamess](https://github.com/kzfm/pygamess)
+- [stk](https://github.com/lukasturcani/stk)
+- [ASE](https://gitlab.com/ase/ase)
+
+## Future work
+
+- Separation of concern. The ppqm package should adapt to using `cclib` or similar to collect quantum output.

ppqm-0.1.0/env/bin/activate_this.py

@@ -0,0 +1,59 @@
+# 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-0.1.0/ppqm/__init__.py

@@ -0,0 +1,7 @@
+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-0.1.0/ppqm/calculator.py

@@ -0,0 +1,110 @@
+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()"