rdworks 0.25.7__tar.gz → 0.35.1__tar.gz

{rdworks-0.25.7 → rdworks-0.35.1}/PKG-INFO

@@ -1,7 +1,7 @@
 Metadata-Version: 2.4
 Name: rdworks
-Version: 0.25.7
-Summary: Cheminformatics and AI/ML Work Built on RDKit
+Version: 0.35.1
+Summary: Frequently used tasks built on RDKit and other tools
 Author-email: Sung-Hun Bae <sunghun.bae@gmail.com>
 Maintainer-email: Sung-Hun Bae <sunghun.bae@gmail.com>
 License-Expression: MIT
@@ -10,7 +10,7 @@ Project-URL: Repository, https://github.com/sunghunbae/rdworks.git
 Project-URL: Issues, https://github.com/sunghunbae/rdworks/issues
 Project-URL: Changelog, https://github.com/sunghunbae/rdworks/blob/master/CHANGELOG.md
 Project-URL: Documentation, https://sunghunbae.github.io/rdworks/
-Keywords: neural-network-potential,cheminformatics,rdkit
+Keywords: cheminformatics,rdkit
 Classifier: Development Status :: 3 - Alpha
 Classifier: Intended Audience :: Developers
 Classifier: Programming Language :: Python :: 3
@@ -18,18 +18,15 @@ Classifier: Operating System :: OS Independent
 Requires-Python: >=3.11
 Description-Content-Type: text/markdown
 License-File: LICENSE
-Requires-Dist: numpy
-Requires-Dist: scipy
-Requires-Dist: scikit-learn
+Requires-Dist: rdkit>=2024
+Requires-Dist: cdpkit
 Requires-Dist: pandas
 Requires-Dist: seaborn
-Requires-Dist: networkx
 Requires-Dist: tqdm
-Requires-Dist: psutil
 Requires-Dist: ase
-Requires-Dist: rdkit>=2023
+Requires-Dist: mendeleev
+Requires-Dist: scour
 Requires-Dist: bitarray
-Requires-Dist: cdpkit
 Requires-Dist: pytest
 Dynamic: license-file
 

{rdworks-0.25.7 → rdworks-0.35.1}/pyproject.toml

@@ -7,30 +7,24 @@ name = "rdworks"
 dynamic = ["version"]
 requires-python = ">=3.11"
 dependencies = [
-    "numpy",
-    "scipy",
-    "scikit-learn",
+    "rdkit>=2024",
+    "cdpkit",
     "pandas",
-    "seaborn",
-    "networkx",
+    "seaborn", # Mol.plot_torsion_energies()
     "tqdm",
-    "psutil",
     "ase",
-    "rdkit>=2023",
-    "bitarray",
-    "cdpkit",
+    # "xtb<6.3.0", <--- installation with conda, issue with FORTRAN runtime error
+    "mendeleev",
+    "scour", # SVG optimization
+    "bitarray", # dependencies of bitqt
     "pytest",
     ]
 authors = [{name = "Sung-Hun Bae", email="sunghun.bae@gmail.com"}, ]
 maintainers = [{name = "Sung-Hun Bae", email="sunghun.bae@gmail.com"}, ]
-description = "Cheminformatics and AI/ML Work Built on RDKit"
+description = "Frequently used tasks built on RDKit and other tools"
 readme = "README.md"
 license = "MIT"
-keywords = [
-    "neural-network-potential", 
-    "cheminformatics", 
-    "rdkit",
-    ]
+keywords = ["cheminformatics", "rdkit",]
 classifiers = [
     "Development Status :: 3 - Alpha",
     "Intended Audience :: Developers",
@@ -45,6 +39,8 @@ Issues          = "https://github.com/sunghunbae/rdworks/issues"
 Changelog       = "https://github.com/sunghunbae/rdworks/blob/master/CHANGELOG.md"
 Documentation   = "https://sunghunbae.github.io/rdworks/"
 
+[project.scripts]
+
 [tool.setuptools.dynamic]
 version = {attr = "rdworks.__version__"}
 
@@ -52,7 +48,6 @@ version = {attr = "rdworks.__version__"}
 where = ["src"]
 
 [tool.setuptools.package-data]
-"rdworks.auto3d.models" = [ "*" ]
 "rdworks.predefined" = [ "*.xml" ]
 "rdworks.predefined.Baell2010_PAINS" = [ "*.xml" ]
 "rdworks.predefined.ChEMBL_Walters" = [ "*.xml" ]

{rdworks-0.25.7 → rdworks-0.35.1}/src/rdworks/__init__.py

@@ -1,35 +1,34 @@
-__version__ = '0.25.7'
+__version__ = '0.35.1'
+
+from rdworks.conf    import Conf
+from rdworks.mol     import Mol
+from rdworks.mollibr import MolLibr
 
-from rdworks.xml import list_predefined_xml, get_predefined_xml, parse_xml
-from rdworks.units import ev2kcalpermol, hartree2ev, hartree2kcalpermol, periodictable
-from rdworks.readin import read_csv, merge_csv, read_dataframe, read_smi, read_sdf, read_mae 
-from rdworks.std import desalt_smiles, standardize_smiles, standardize
-from rdworks.tautomers import complete_tautomers
 from rdworks.stereoisomers import complete_stereoisomers
+from rdworks.tautomers import complete_tautomers
 from rdworks.ionized import IonizedStates
+
+from rdworks.readin import read_csv, merge_csv, read_dataframe, read_smi, read_sdf, read_mae 
+from rdworks.std import desalt_smiles, standardize_smiles, standardize
+
 from rdworks.rgroup import expand_rgroup, most_common, most_common_in_NP
 from rdworks.scaffold import scaffold_network, scaffold_tree, BRICS_fragmented, BRICS_fragment_indices
 from rdworks.matchedseries import MatchedSeries
-from rdworks.descriptor import rd_descriptor, rd_descriptor_f
-from rdworks.utils import fix_decimal_places_in_list, fix_decimal_places_in_dict, mae_to_dict, mae_rd_index
-from rdworks.display import svg
-from rdworks.conf import Conf
-from rdworks.mol import Mol
-from rdworks.mollibr import MolLibr
 
-from rdkit import rdBase, RDLogger
-rdkit_logger = RDLogger.logger().setLevel(RDLogger.CRITICAL)
+from rdworks.descriptor import rd_descriptor, rd_descriptor_f
+from rdworks.xml import list_predefined_xml, get_predefined_xml, parse_xml
 
+import rdkit
 import logging
 
+__rdkit_version__ = rdkit.rdBase.rdkitVersion
+
+rdkit_logger = rdkit.RDLogger.logger().setLevel(rdkit.RDLogger.CRITICAL)
+
 main_logger = logging.getLogger()
 main_logger.setLevel(logging.INFO) # level: DEBUG < INFO < WARNING < ERROR < CRITICAL
-logger_formatter = logging.Formatter(
-    fmt='%(asctime)s %(levelname)s %(message)s',
-    datefmt='%Y-%m-%d %H:%M:%S')
+logger_formatter = logging.Formatter(fmt='%(asctime)s %(levelname)s %(message)s', 
+                                     datefmt='%Y-%m-%d %H:%M:%S')
 logger_ch = logging.StreamHandler()
 logger_ch.setFormatter(logger_formatter)
 main_logger.addHandler(logger_ch)
-
-
-__rdkit_version__ = rdBase.rdkitVersion