rdworks 0.40.2__py3-none-any.whl → 0.42.1__py3-none-any.whl

rdworks/__init__.py

@@ -1,4 +1,4 @@
-__version__ = '0.40.2'
+__version__ = '0.42.1'
 
 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.
@@ -59,6 +64,8 @@ class Conf:
             return
 
         if isinstance(molecule, str): # 3-D MolBLock string
+            if compressed:
+                molecule = decompress_string(molecule)
             try:
                 self.rdmol = Chem.MolFromMolBlock(molecule, 
                                                   sanitize=False, 
@@ -446,7 +453,7 @@ class Conf:
                 }
         
         if simplify:
-            frag, frag_ijkl = create_torsion_fragment(ref_conf.rdmol, indices)
+            (frag, frag_ijkl, frag_created, wbo_filtered) = create_torsion_fragment(ref_conf.rdmol, indices)
             frag_conf = Conf(frag)
             for angle in np.arange(-180.0, 180.0, interval): 
                 # Iterated numpy.ndarray does not contain the last 180: -180., ..., (180).

rdworks/torsion.py

@@ -426,7 +426,7 @@ def create_fragment_on_bonds(rdmol: Chem.Mol, bonds: dict, cap: bool = True) ->
 
 def create_torsion_fragment(rdmol: Chem.Mol, 
                             torsion_indices: tuple,
-                            wbo_tolerance: float = 0.03) -> tuple[Chem.Mol, list[int]]:
+                            wbo_tolerance: float = 0.03) -> tuple[Chem.Mol, list[int], bool, bool]:
     """Create a close surrogate fragment that captures the PES of the intended torsion.
     
     Fragmentation aims to preserve the local chemical environment around the targeted torsion
@@ -443,7 +443,10 @@ def create_torsion_fragment(rdmol: Chem.Mol,
         torsion_indices (tuple): (i, j, k, l, atoms to be rotated, atoms to be fixed)
 
     Returns:
-        Chem.Mol: simplified fragment molecule.
+        (Chem.Mol: fragment molecule, 
+        list[int]: fragment indices, 
+        bool: True if fragmented, 
+        bool: True if WBO filtering is used)
 
     References:
         https://pubs.acs.org/doi/10.1021/acs.jcim.2c01153
@@ -455,8 +458,10 @@ def create_torsion_fragment(rdmol: Chem.Mol,
     
     if not candidates:
         # no fragmentation
-        return rdmol, torsion_indices
-    
+        return (rdmol, torsion_indices, False, False)
+
+    # fragmented
+    WBO_filtered = False
     if GFN2xTB().version() is not None:
         # filter candidate(s) by Wiberg bond order (WBO) if xTB is available
         jk = tuple(sorted([j, k]))
@@ -472,11 +477,12 @@ def create_torsion_fragment(rdmol: Chem.Mol,
             frag_jk = tuple(sorted(frag_jk))
             if abs(fragment.wbo[frag_jk] - parent.wbo[jk]) < wbo_tolerance:
                 wbo_passed_candidates[bond_idx] = (p, q)
-        frag_multi_breaks = create_fragment_on_bonds(rdmol, wbo_passed_candidates) 
+        frag_multi_breaks = create_fragment_on_bonds(rdmol, wbo_passed_candidates)
+        WBO_filtered = True
     else:
         # skip WBO filtering
         frag_multi_breaks = create_fragment_on_bonds(rdmol, candidates)
 
-    frag_ijkl = get_fragment_idx(rdmol, (i, j, k, l), frag_multi_breaks)
+    frag_indices = get_fragment_idx(rdmol, (i, j, k, l), frag_multi_breaks)
     
-    return frag_multi_breaks, frag_ijkl
+    return (frag_multi_breaks, frag_indices, True, WBO_filtered)

{rdworks-0.40.2.dist-info → rdworks-0.42.1.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: rdworks
-Version: 0.40.2
+Version: 0.42.1
 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>

{rdworks-0.40.2.dist-info → rdworks-0.42.1.dist-info}/RECORD

@@ -1,5 +1,5 @@
-rdworks/__init__.py,sha256=C-rebVhw25NuMe3T71a03rlj7CC6K9gaxU1VOhqIEfY,1368
-rdworks/conf.py,sha256=3qDEWq4cKnMd423Tx4jt88KIP11OLRG7Ab-w5755OZw,31031
+rdworks/__init__.py,sha256=7OkViRiczFQfW5O29ls7ozHiJrbVoYudKHxplgQ8Wmo,1368
+rdworks/conf.py,sha256=wSAffrHMbZW55gh8Dahz4ZkusUN_DlD_ieiVHFKVdXY,31348
 rdworks/descriptor.py,sha256=34T_dQ6g8v3u-ym8TLKbQtxIIV5TEo-d3pdedq3o-cg,2106
 rdworks/display.py,sha256=JR0gR26UpH-JCxVOaqXZCUj2MiGZSrx9Me87FncspVI,13469
 rdworks/ionized.py,sha256=5oIjMRpkX792RIpEEE2Ir96icfFaN_h21mSihhfQPAw,6713
@@ -14,7 +14,7 @@ rdworks/std.py,sha256=qOVS_lGogueLKh4rsbrsYIMR0c7z_xh6BqLEzD4X9sE,7938
 rdworks/stereoisomers.py,sha256=g8hhPI-mbYX-MzbF1uAqo5fDZOCNiKYjxI-kLBGdGgg,4980
 rdworks/tautomers.py,sha256=gtZHZJ-aJbryhBdljHbfjx7xhVW3u_OzdYPtwPail54,610
 rdworks/testdata.py,sha256=TmbNPA-ju6nTBt_Yts4EJUFmL9Cd6DCVXrDF42QLlHw,1732
-rdworks/torsion.py,sha256=qTRJWsxSktqprL8pUHWEOoV2dKEgoMozh3BB0eGNlZ8,18571
+rdworks/torsion.py,sha256=7xlOUYXmBSkjPuNxGXNF-F3G9XWO2ER15xGOY0ejpcc,18801
 rdworks/units.py,sha256=nljKPHcr6IWoAp0CkL7y1gSNDd6a07NeVfxXwSMuHQM,365
 rdworks/utils.py,sha256=d2Sio8WTlGPsmBOHIYDCMWg_7X4rTWjJQAqzd7ywo2A,14191
 rdworks/xml.py,sha256=aaMhwVRGvt1VzasaKDnkYnZ4kp2cIgvGb1CsmMgwQ_c,10704
@@ -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-0.40.2.dist-info/licenses/LICENSE,sha256=UOkJSBqYyQUvtCp7a-vdCANeEcLE2dnTie_eB1By5SY,1074
-rdworks-0.40.2.dist-info/METADATA,sha256=isXahzjh1NSTZQFuGPaUpRAI4Ef6dSEaXgHU56j-o7s,1967
-rdworks-0.40.2.dist-info/WHEEL,sha256=_zCd3N1l69ArxyTb8rzEoP9TpbYXkqRFSNOD5OuxnTs,91
-rdworks-0.40.2.dist-info/top_level.txt,sha256=05C98HbvBK2axUBogC_hAT_CdpOeQYGnQ6vRAgawr8s,8
-rdworks-0.40.2.dist-info/RECORD,,
+rdworks-0.42.1.dist-info/licenses/LICENSE,sha256=UOkJSBqYyQUvtCp7a-vdCANeEcLE2dnTie_eB1By5SY,1074
+rdworks-0.42.1.dist-info/METADATA,sha256=Fsnm3LWrztWcME2P9Ej-GreKrd5ltyt2PJOLOQ8e1AU,1967
+rdworks-0.42.1.dist-info/WHEEL,sha256=_zCd3N1l69ArxyTb8rzEoP9TpbYXkqRFSNOD5OuxnTs,91
+rdworks-0.42.1.dist-info/top_level.txt,sha256=05C98HbvBK2axUBogC_hAT_CdpOeQYGnQ6vRAgawr8s,8
+rdworks-0.42.1.dist-info/RECORD,,