Addition of an internal meeko

.github/workflows/tests.yml

@@ -30,7 +30,7 @@ jobs:
       fail-fast: false
       matrix:
         os: [ubuntu-latest, macOS-latest] #windows-latest (vina is not available for windows in conda-forge),m think about use bioconda autodock-vina
-        python-version: [3.8, 3.9, '3.10', 3.11]
+        python-version: [3.8, 3.9, '3.10', 3.11, 3.12, 3.13]
     steps:
     - uses: actions/checkout@v4
     - name: Set up Python ${{ matrix.python-version }}

pyproject.toml

@@ -44,18 +44,16 @@ keywords = [
     "genetic algorithm",
 ]
 
-requires-python = ">= 3.8 , < 3.12"
+requires-python = ">= 3.8"
 dependencies = [
     "crem",
     "tqdm",
     "numpy",
     "pandas",
     "pyyaml",
     "dill",
-    "meeko>=0.4.0,<0.6.0",
-    "six",
+    "scipy",
     "rdkit>=2022.3.5",
-    "scipy",  # a meeko dependency
 ]
 
 [project.license]
@@ -68,9 +66,9 @@ dev = ["requests", "pytest"]
 default-version = "1+unknown"
 
 [tool.versioningit.format]
-distance = "{base_version}"
-dirty = "{base_version}"
-distance-dirty = "{base_version}"
+distance = "{base_version}.post{distance}"
+dirty = "{base_version}.post{distance}.dev0"
+distance-dirty = "{base_version}.post{distance}.dev0"
 
 [tool.versioningit.vcs]
 method = "git"
@@ -95,6 +93,7 @@ moldrug = [
     "data/*/*.smi",
     "data/*/*.pdb",
     "data/*/*.pdbqt",
+    "meeko_light/data/params/*.json"
 
 ]
 

src/moldrug/fitness.py

@@ -6,8 +6,8 @@
 
 import numpy as np
 # from warnings import import warn
-from meeko import (MoleculePreparation, PDBQTMolecule, PDBQTWriterLegacy,
-                   RDKitMolCreate)
+from moldrug.meeko_light import (MoleculePreparation,
+                                 PDBQTMolecule, PDBQTWriterLegacy, RDKitMolCreate)
 from rdkit import Chem
 from rdkit.Chem import QED, Descriptors
 

src/moldrug/meeko_light/__init__.py

@@ -0,0 +1,28 @@
+#!/usr/bin/env python
+# -*- coding: utf-8 -*-
+#
+# This module was taken from Meeko 0.6.1
+# https://github.com/forlilab/meeko
+# Only unnecessary functionalities were removed.
+
+__meeko_original_version__ = "0.6.1"
+
+from .preparation import MoleculePreparation
+from .molecule_pdbqt import PDBQTMolecule
+from .rdkit_mol_create import RDKitMolCreate
+from .writer import PDBQTWriterLegacy
+
+import logging
+from rdkit import rdBase
+rdkit_logger = logging.getLogger("rdkit")
+rdkit_logger.handlers[0].setLevel("WARNING")
+rdkit_logger.handlers[0].setFormatter(
+    logging.Formatter('[RDKit] %(levelname)s:%(message)s'),
+)
+rdBase.LogToPythonLogger()
+
+__all__ = ['MoleculePreparation',
+           'PDBQTMolecule',
+           'RDKitMolCreate',
+           'PDBQTWriterLegacy',
+           ]