Completely removed python version restrictions.

README.md

@@ -1,4 +1,4 @@
-[![made-with-python](https://img.shields.io/badge/Made%20with-Python-1f425f.svg)](https://www.python.org/) [![License: LGPL v2.1](https://img.shields.io/badge/License-LGPL_v2.1-green.svg)](https://www.gnu.org/licenses/old-licenses/lgpl-2.1.en.html) [![PyPI - Version](https://img.shields.io/pypi/v/cosolvkit)](https://pypi.org/project/cosolvkit/0.4.5/) [![Powered by RDKit](https://img.shields.io/badge/Powered%20by-RDKit-3838ff.svg?logo=data:image/png;base64,iVBORw0KGgoAAAANSUhEUgAAABAAAAAQBAMAAADt3eJSAAAABGdBTUEAALGPC/xhBQAAACBjSFJNAAB6JgAAgIQAAPoAAACA6AAAdTAAAOpgAAA6mAAAF3CculE8AAAAFVBMVEXc3NwUFP8UPP9kZP+MjP+0tP////9ZXZotAAAAAXRSTlMAQObYZgAAAAFiS0dEBmFmuH0AAAAHdElNRQfmAwsPGi+MyC9RAAAAQElEQVQI12NgQABGQUEBMENISUkRLKBsbGwEEhIyBgJFsICLC0iIUdnExcUZwnANQWfApKCK4doRBsKtQFgKAQC5Ww1JEHSEkAAAACV0RVh0ZGF0ZTpjcmVhdGUAMjAyMi0wMy0xMVQxNToyNjo0NyswMDowMDzr2J4AAAAldEVYdGRhdGU6bW9kaWZ5ADIwMjItMDMtMTFUMTU6MjY6NDcrMDA6MDBNtmAiAAAAAElFTkSuQmCC)](https://www.rdkit.org/)
+[![made-with-python](https://img.shields.io/badge/Made%20with-Python-1f425f.svg)](https://www.python.org/) [![License: LGPL v2.1](https://img.shields.io/badge/License-LGPL_v2.1-green.svg)](https://www.gnu.org/licenses/old-licenses/lgpl-2.1.en.html) [![PyPI - Version](https://img.shields.io/pypi/v/cosolvkit)](https://pypi.org/project/cosolvkit/0.4.6/) [![Powered by RDKit](https://img.shields.io/badge/Powered%20by-RDKit-3838ff.svg?logo=data:image/png;base64,iVBORw0KGgoAAAANSUhEUgAAABAAAAAQBAMAAADt3eJSAAAABGdBTUEAALGPC/xhBQAAACBjSFJNAAB6JgAAgIQAAPoAAACA6AAAdTAAAOpgAAA6mAAAF3CculE8AAAAFVBMVEXc3NwUFP8UPP9kZP+MjP+0tP////9ZXZotAAAAAXRSTlMAQObYZgAAAAFiS0dEBmFmuH0AAAAHdElNRQfmAwsPGi+MyC9RAAAAQElEQVQI12NgQABGQUEBMENISUkRLKBsbGwEEhIyBgJFsICLC0iIUdnExcUZwnANQWfApKCK4doRBsKtQFgKAQC5Ww1JEHSEkAAAACV0RVh0ZGF0ZTpjcmVhdGUAMjAyMi0wMy0xMVQxNToyNjo0NyswMDowMDzr2J4AAAAldEVYdGRhdGU6bW9kaWZ5ADIwMjItMDMtMTFUMTU6MjY6NDcrMDA6MDBNtmAiAAAAAElFTkSuQmCC)](https://www.rdkit.org/)
 [![Documentation Status](https://readthedocs.org/projects/cosolvkit/badge/?version=latest)](https://cosolvkit.readthedocs.io/en/latest/?badge=latest)
 
 

cosolvkit/cosolvent_system.py

@@ -3,7 +3,7 @@
 import sys
 import io
 from collections import defaultdict
-from typing import Union
+from typing import Union, Tuple
 import numpy as np
 from scipy import spatial
 from scipy.stats import qmc
@@ -635,7 +635,7 @@ def _create_system(self, forcefield: app.forcefield, topology: app.Topology) ->
 #region FillTheVoid
     def add_cosolvents(self, 
                        cosolvents: dict, 
-                       vectors: tuple[Vec3, Vec3, Vec3], 
+                       vectors: Tuple[Vec3, Vec3, Vec3], 
                        lowerBound: Union[openmmunit.Quantity, Vec3], 
                        upperBound: Union[openmmunit.Quantity, Vec3],
                        receptor_positions: list) -> dict:
@@ -647,7 +647,7 @@ def add_cosolvents(self,
         :param cosolvents: keys are cosolvent molecules and values are 3D coordinates of the molecule
         :type cosolvents: dict
         :param vectors: vectors defining the simulation box
-        :type vectors: tuple[openmm.Vec3, openmm.Vec3, openmm.Vec3]
+        :type vectors: Tuple[openmm.Vec3, openmm.Vec3, openmm.Vec3]
         :param lowerBound: lower bound of the simulation box
         :type lowerBound: Union[openmm.unit.Quantity, Vec3]
         :param upperBound: upper bound of the simulation box
@@ -761,7 +761,7 @@ def accept_reject(self,
                       valid_ids: list, 
                       lowerBound: Union[openmmunit.Quantity, Vec3], 
                       upperBound: Union[openmmunit.Quantity, Vec3], 
-                      protein_kdtree: spatial.cKDTree) -> tuple[np.ndarray, list]:
+                      protein_kdtree: spatial.cKDTree) -> Tuple[np.ndarray, list]:
         """Accepts or reject the halton move. A random halton point is selected and checked, if accepted
         the cosolvent is placed there, otherwise a local search is performed in the neighbors of the point 
         (1 tile). If the local search produces no clashes the new position is accepted, otherwise a new 
@@ -783,7 +783,7 @@ def accept_reject(self,
         :param protein_kdtree: tree of the protein's positions
         :type protein_kdtree: spatial.cKDTree
         :return: accepted coordinates for the cosolvent and the used halton ids
-        :rtype: tuple[np.ndarray, list]
+        :rtype: Tuple[np.ndarray, list]
         """        
         trial = 0
         accepted = False
@@ -1005,7 +1005,7 @@ def _parametrize_cosolvents(self, cosolvents: dict, small_molecule_ff="espaloma"
     def _build_box(self, 
                    positions: np.ndarray, 
                    padding: openmmunit.Quantity, 
-                   radius: openmmunit.Quantity = None) -> tuple[tuple[Vec3, Vec3, Vec3], 
+                   radius: openmmunit.Quantity = None) -> Tuple[Tuple[Vec3, Vec3, Vec3], 
                                                                 Vec3, 
                                                                 Union[openmmunit.Quantity, Vec3],
                                                                 Union[openmmunit.Quantity, Vec3]]:

cosolvkit/utils.py

@@ -12,6 +12,7 @@
 import shutil
 import subprocess
 import importlib
+from typing import List, Tuple
 from collections import defaultdict
 
 import numpy as np
@@ -89,7 +90,7 @@ class MutuallyExclusiveParametersError(Exception):
 
 #     simulation.context.setParameter('k', k)
 
-def fix_pdb(pdbfile: str, pdbxfile: str, keep_heterogens: bool=False) -> tuple[Topology, list]:
+def fix_pdb(pdbfile: str, pdbxfile: str, keep_heterogens: bool=False) -> Tuple[Topology, List]:
     """Fixes common problems in PDB such as:
             - missing atoms
             - missing residues
@@ -123,7 +124,7 @@ def fix_pdb(pdbfile: str, pdbxfile: str, keep_heterogens: bool=False) -> tuple[T
     fixer.addMissingHydrogens(7)
     return fixer.topology, fixer.positions
 
-def add_variants(topology: Topology, positions: list, variants: list=list()) -> tuple[Topology, list]:
+def add_variants(topology: Topology, positions: list, variants: list=list()) -> Tuple[Topology, List]:
     """Adds variants for specific protonation states.
 
     :param topology: openmm topology

setup.py

@@ -18,7 +18,7 @@ def find_files(directory):
 
 
 setup(name="cosolvkit",
-      version='0.4.5',
+      version='0.4.6',
       description="CosolvKit",
       author="Niccolo Bruciaferri, Jerome Eberhardt",
       author_email="[email protected]",
@@ -28,7 +28,6 @@ def find_files(directory):
       data_files=[("", ["README.md", "LICENSE"])],
       include_package_data=True,
       zip_safe=False,
-      python_requires=">=3.9",
       license="LGPL-2.1",
       keywords=["molecular modeling", "drug design",
                 "cosolvent", "MD simulations"],