rdworks 0.40.2__tar.gz → 0.42.1__tar.gz

{rdworks-0.40.2 → rdworks-0.42.1}/PKG-INFO

@@ -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 → rdworks-0.42.1}/src/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-0.40.2 → rdworks-0.42.1}/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.
@@ -59,6 +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-0.40.2 → rdworks-0.42.1}/src/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 → rdworks-0.42.1}/src/rdworks.egg-info/PKG-INFO

@@ -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 → rdworks-0.42.1}/tests/test_basics.py

@@ -472,17 +472,22 @@ def test_torsion_fragment():
     # {0: (0, 1, 3, 7),  1: (3, 4, 32, 33),  2: (4, 5, 26, 27),  3: (7, 6, 19, 20),
     # 4: (3, 7, 8, 9),  5: (7, 8, 9, 10),   6: (8, 9, 10, 18),   7: (18, 10, 11, 12),
     # 8: (10, 11, 12, 17),  9: (17, 12, 13, 14),   10: (12, 13, 14, 15),   11: (36, 35, 34, 32)}
-    frag, frag_ijkl = create_torsion_fragment(mol.confs[0].rdmol, ta[6])
+    (frag, frag_ijkl, frag_created, wbo_filtered) = create_torsion_fragment(mol.confs[0].rdmol, ta[6])
     assert frag_ijkl == (5, 6, 7, 12)
+    assert frag_created == True
+    assert wbo_filtered == True
 
     mol2 = Mol(molecule='CC(=O)Nc1ccc(O)cc1', name='acetaminophen.3').make_confs(n=1)
     ta2 = mol2.torsion_atoms()
     # {0: (5, 4, 3, 1)}
     assert len(ta2) == 1
-    frag, frag_ijkl = create_torsion_fragment(mol2.confs[0].rdmol, ta2[0])
+
+    (frag, frag_ijkl, frag_created, wbo_filtered) = create_torsion_fragment(mol2.confs[0].rdmol, ta2[0])
     # expects no fragmentation
     assert frag == mol2.confs[0].rdmol
     assert frag_ijkl == ta2[0]
+    assert frag_created == False
+    assert wbo_filtered == False
 
 
 def test_torsion_fragment_from_conf():
@@ -495,8 +500,10 @@ def test_torsion_fragment_from_conf():
     # {0: (0, 1, 3, 7),  1: (3, 4, 32, 33),  2: (4, 5, 26, 27),  3: (7, 6, 19, 20),
     # 4: (3, 7, 8, 9),  5: (7, 8, 9, 10),   6: (8, 9, 10, 18),   7: (18, 10, 11, 12),
     # 8: (10, 11, 12, 17),  9: (17, 12, 13, 14),   10: (12, 13, 14, 15),   11: (36, 35, 34, 32)}
-    frag, frag_ijkl = create_torsion_fragment(ref_conf.rdmol, ta[6])
+    frag, frag_ijkl, frag_created, wbo_filtered = create_torsion_fragment(ref_conf.rdmol, ta[6])
     assert frag_ijkl == (5, 6, 7, 12)
+    assert frag_created == True
+    assert wbo_filtered == True
 
     ref_conf = ref_conf.torsion_energies(calculator='MMFF94', torsion_key=6, interval=15)
 
@@ -505,10 +512,12 @@ def test_torsion_fragment_from_conf():
     ta2 = ref_conf2.torsion_atoms()
     # {0: (5, 4, 3, 1)}
     assert len(ta2) == 1
-    frag, frag_ijkl = create_torsion_fragment(ref_conf2.rdmol, ta2[0])
+    frag, frag_ijkl, frag_created, wbo_filtered = create_torsion_fragment(ref_conf2.rdmol, ta2[0])
     # expects no fragmentation
     assert frag == ref_conf2.rdmol
     assert frag_ijkl == ta2[0]
+    assert frag_created == False
+    assert wbo_filtered == False
 
     ref_conf2 = ref_conf2.torsion_energies(calculator='MMFF94', interval=15)
     ref_conf3 = ref_conf2.torsion_energies_one(calculator='MMFF94', indices=frag_ijkl)