rdworks 0.40.1__tar.gz → 0.41.1__tar.gz

{rdworks-0.40.1 → rdworks-0.41.1}/PKG-INFO

@@ -1,7 +1,7 @@
 Metadata-Version: 2.4
 Name: rdworks
-Version: 0.40.1
-Summary: Frequently used tasks built on RDKit and other tools
+Version: 0.41.1
+Summary: Routine 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: cheminformatics,rdkit
+Keywords: cheminformatics,rdkit,cdpkit
 Classifier: Development Status :: 3 - Alpha
 Classifier: Intended Audience :: Developers
 Classifier: Programming Language :: Python :: 3
@@ -30,5 +30,45 @@ Requires-Dist: bitarray
 Requires-Dist: pytest
 Dynamic: license-file
 
-# rdworks
-Higher level wrapper using RDKit
+# Rdworks - routine tasks made easy
+
+Rdworks is designed to perform routine cheminformatics tasks easily. It is built on RDKit and other tools. 
+
+## Install
+
+```sh
+$ pip install rdworks
+```
+
+OR
+
+```sh
+$ pip install git+https://github.com/sunghunbae/rdworks.git
+```
+
+## Getting started
+
+```py
+from rdworks import Mol
+
+version = rdworks.__version__
+
+mol = Mol('CC(=O)Nc1ccc(O)cc1', 'acetaminophen')
+
+mol = mol.make_confs(n=5)
+mol.to_sdf('acetaminophen.sdf')
+
+torsion_dict = mol.torsion_atoms() 
+# torsion_dict = {0: (5,4,3,1)}
+
+mol = mol.torsion_energies(calculator='MMFF94', simplify=True)
+
+mol.plot_torsion_energies(0, figsize=(6,4))
+
+mol.to_png(300, 300, atom_index=True, highlight_atoms=torsion_dict.get(0))
+
+serialized = mol.serialize(compress=True)
+mol2 = Mol().deserialize(serialized, compress=True)
+
+mol3 = mol.copy()
+```

rdworks-0.41.1/README.md

@@ -0,0 +1,42 @@
+# Rdworks - routine tasks made easy
+
+Rdworks is designed to perform routine cheminformatics tasks easily. It is built on RDKit and other tools. 
+
+## Install
+
+```sh
+$ pip install rdworks
+```
+
+OR
+
+```sh
+$ pip install git+https://github.com/sunghunbae/rdworks.git
+```
+
+## Getting started
+
+```py
+from rdworks import Mol
+
+version = rdworks.__version__
+
+mol = Mol('CC(=O)Nc1ccc(O)cc1', 'acetaminophen')
+
+mol = mol.make_confs(n=5)
+mol.to_sdf('acetaminophen.sdf')
+
+torsion_dict = mol.torsion_atoms() 
+# torsion_dict = {0: (5,4,3,1)}
+
+mol = mol.torsion_energies(calculator='MMFF94', simplify=True)
+
+mol.plot_torsion_energies(0, figsize=(6,4))
+
+mol.to_png(300, 300, atom_index=True, highlight_atoms=torsion_dict.get(0))
+
+serialized = mol.serialize(compress=True)
+mol2 = Mol().deserialize(serialized, compress=True)
+
+mol3 = mol.copy()
+```

{rdworks-0.40.1 → rdworks-0.41.1}/pyproject.toml

@@ -14,17 +14,17 @@ dependencies = [
     "tqdm",
     "ase",
     # "xtb<6.3.0", <--- installation with conda, issue with FORTRAN runtime error
-    "mendeleev",
+    "mendeleev", # periodic table
     "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 = "Frequently used tasks built on RDKit and other tools"
+description = "Routine tasks built on RDKit and other tools"
 readme = "README.md"
 license = "MIT"
-keywords = ["cheminformatics", "rdkit",]
+keywords = ["cheminformatics", "rdkit", "cdpkit"]
 classifiers = [
     "Development Status :: 3 - Alpha",
     "Intended Audience :: Developers",

{rdworks-0.40.1 → rdworks-0.41.1}/src/rdworks/__init__.py

@@ -1,4 +1,4 @@
-__version__ = '0.40.1'
+__version__ = '0.41.1'
 
 from rdworks.conf    import Conf
 from rdworks.mol     import Mol

{rdworks-0.40.1 → rdworks-0.41.1}/src/rdworks/conf.py

@@ -27,12 +27,17 @@ from rdworks.display import render_png, render_svg
 class Conf:
     """Container for 3D conformers."""
     
-    def __init__(self, molecule: str | Chem.Mol | None = None, name: str='') -> None:
+    def __init__(self, 
+                 molecule: str | Chem.Mol | None = None, 
+                 name: str = '',
+                 compressed: bool = False) -> None:
         """Initialize.
 
         Args:
             molecule (Chem.Mol | MolBlock string): Molecule for 3D conformer.
             name (str): Name prefix of the generated conformers. Defaults to ''.
+            compressed (bool): whether the MolBlock string is compressed or not. 
+                Defaults to False.
 
         Raises:
             ValueError: if `molecule` is not rdkit.Chem.Mol object.
@@ -59,8 +64,13 @@ class Conf:
             return
 
         if isinstance(molecule, str): # 3-D MolBLock string
+            if compressed:
+                molecule = decompress_string(molecule)
             try:
-                self.rdmol = Chem.MolFromMolBlock(molecule)
+                self.rdmol = Chem.MolFromMolBlock(molecule, 
+                                                  sanitize=False, 
+                                                  removeHs=False, 
+                                                  strictParsing=True)
             except:
                 ValueError(f'Conf() Error: invalid MolBlock string')
 

{rdworks-0.40.1 → rdworks-0.41.1}/src/rdworks.egg-info/PKG-INFO

@@ -1,7 +1,7 @@
 Metadata-Version: 2.4
 Name: rdworks
-Version: 0.40.1
-Summary: Frequently used tasks built on RDKit and other tools
+Version: 0.41.1
+Summary: Routine 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: cheminformatics,rdkit
+Keywords: cheminformatics,rdkit,cdpkit
 Classifier: Development Status :: 3 - Alpha
 Classifier: Intended Audience :: Developers
 Classifier: Programming Language :: Python :: 3
@@ -30,5 +30,45 @@ Requires-Dist: bitarray
 Requires-Dist: pytest
 Dynamic: license-file
 
-# rdworks
-Higher level wrapper using RDKit
+# Rdworks - routine tasks made easy
+
+Rdworks is designed to perform routine cheminformatics tasks easily. It is built on RDKit and other tools. 
+
+## Install
+
+```sh
+$ pip install rdworks
+```
+
+OR
+
+```sh
+$ pip install git+https://github.com/sunghunbae/rdworks.git
+```
+
+## Getting started
+
+```py
+from rdworks import Mol
+
+version = rdworks.__version__
+
+mol = Mol('CC(=O)Nc1ccc(O)cc1', 'acetaminophen')
+
+mol = mol.make_confs(n=5)
+mol.to_sdf('acetaminophen.sdf')
+
+torsion_dict = mol.torsion_atoms() 
+# torsion_dict = {0: (5,4,3,1)}
+
+mol = mol.torsion_energies(calculator='MMFF94', simplify=True)
+
+mol.plot_torsion_energies(0, figsize=(6,4))
+
+mol.to_png(300, 300, atom_index=True, highlight_atoms=torsion_dict.get(0))
+
+serialized = mol.serialize(compress=True)
+mol2 = Mol().deserialize(serialized, compress=True)
+
+mol3 = mol.copy()
+```

{rdworks-0.40.1 → rdworks-0.41.1}/tests/test_basics.py

@@ -42,8 +42,6 @@ drug_smiles = [
     "CC(=O)OC1=CC=CC=C1C(=O)O",
     "C1=CC(=C(C=C1F)F)C(CN2C=NC=N2)(CN3C=NC=N3)O",
     "CC(=O)NC[C@H]1CN(C(=O)O1)C2=CC(=C(C=C2)N3CCOCC3)F", # [19]
-    "CC(C)C1=C(C(=C(N1CC[C@H](C[C@H](CC(=O)O)O)O)C2=CC=C(C=C2)F)C3=CC=CC=C3)C(=O)NC4=CC=CC=C4",
-    "CC(=O)Nc1ccc(O)cc1",
     ]
 
 drug_names = [
@@ -51,7 +49,6 @@ drug_names = [
     "Granisetron", "Pergolide", "Molindone", "Rifampin", "Cefdinir",
     "Cimetidine", "Famotidine", "Atovaquone", "Chlorprothixene", "Clomipramine",
     "Methixene",  "Ethopropazine", "Aspirin", "Fluconazole", "Linezolid",
-    "Atorvastatin", "Acetaminophen"
     ]
 
 # Lahey, S.-L. J., Thien Phuc, T. N. & Rowley, C. N. 
@@ -553,4 +550,4 @@ def test_serialization():
     rebuilt = Mol().deserialize(serialized)
     assert rebuilt.count() == 10
     assert rebuilt.name == name
-    assert rebuilt == mol
+    assert rebuilt == mol

rdworks-0.40.1/README.md

@@ -1,2 +0,0 @@
-# rdworks
-Higher level wrapper using RDKit