rdworks 0.40.1__py3-none-any.whl → 0.41.1__py3-none-any.whl

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/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.dist-info → rdworks-0.41.1.dist-info}/METADATA

@@ -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.dist-info → rdworks-0.41.1.dist-info}/RECORD

@@ -1,5 +1,5 @@
-rdworks/__init__.py,sha256=u0oNboUCvBT6mkw6z5qRQiMVr-aglMbFITjb7Ut-DEM,1368
-rdworks/conf.py,sha256=vMKVaHKvlPQ87CNfROodzwZ7l9h-tFCs8MGwon6_sJU,30823
+rdworks/__init__.py,sha256=peU479Cq6wwRIRlgq5oXG-OkjglPAzoBFl2m0syn3jg,1368
+rdworks/conf.py,sha256=y4fuAOSTOm8sMPxP6rKktKQY9b5SRJ5wjTshrwIyRrw,31318
 rdworks/descriptor.py,sha256=34T_dQ6g8v3u-ym8TLKbQtxIIV5TEo-d3pdedq3o-cg,2106
 rdworks/display.py,sha256=JR0gR26UpH-JCxVOaqXZCUj2MiGZSrx9Me87FncspVI,13469
 rdworks/ionized.py,sha256=5oIjMRpkX792RIpEEE2Ir96icfFaN_h21mSihhfQPAw,6713
@@ -66,8 +66,8 @@ rdworks/predefined/misc/reactive-part-3.xml,sha256=LgWHSEbRTVmgBoIO45xbTo1xQJs0X
 rdworks/predefined/misc/reactive.xml,sha256=syedoQ6VYUfRLnxy99ObuDniJ_a_WhrWAJbTKFfJ6VY,11248
 rdworks/xtb/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 rdworks/xtb/wrapper.py,sha256=I0nW89vlJZ5Za5pCjIpjsEOFbTm7HpeNGiPgssheWn8,11350
-rdworks-0.40.1.dist-info/licenses/LICENSE,sha256=UOkJSBqYyQUvtCp7a-vdCANeEcLE2dnTie_eB1By5SY,1074
-rdworks-0.40.1.dist-info/METADATA,sha256=ksYcRcoRSez6WZGRR-0mEMLWk0aO_A3fvK3QVHcHEpw,1183
-rdworks-0.40.1.dist-info/WHEEL,sha256=_zCd3N1l69ArxyTb8rzEoP9TpbYXkqRFSNOD5OuxnTs,91
-rdworks-0.40.1.dist-info/top_level.txt,sha256=05C98HbvBK2axUBogC_hAT_CdpOeQYGnQ6vRAgawr8s,8
-rdworks-0.40.1.dist-info/RECORD,,
+rdworks-0.41.1.dist-info/licenses/LICENSE,sha256=UOkJSBqYyQUvtCp7a-vdCANeEcLE2dnTie_eB1By5SY,1074
+rdworks-0.41.1.dist-info/METADATA,sha256=_t5_Rn30kucD0VBt08335lotOO7QtN0pyAwaJot7gac,1967
+rdworks-0.41.1.dist-info/WHEEL,sha256=_zCd3N1l69ArxyTb8rzEoP9TpbYXkqRFSNOD5OuxnTs,91
+rdworks-0.41.1.dist-info/top_level.txt,sha256=05C98HbvBK2axUBogC_hAT_CdpOeQYGnQ6vRAgawr8s,8
+rdworks-0.41.1.dist-info/RECORD,,