rdworks 0.54.2__tar.gz → 0.55.1__tar.gz

{rdworks-0.54.2 → rdworks-0.55.1}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: rdworks
-Version: 0.54.2
+Version: 0.55.1
 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-0.54.2 → rdworks-0.55.1}/src/rdworks/__init__.py

@@ -1,16 +1,15 @@
-__version__ = '0.54.2'
+__version__ = '0.55.1'
 
 from rdworks.conf    import Conf
 from rdworks.mol     import Mol
 from rdworks.mollibr import MolLibr
 
-from rdworks.workflow import complete_stereoisomers, 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.complete import complete_stereoisomers, complete_tautomers
+from rdworks.ionized import IonizedStates
+
 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

rdworks-0.54.2/src/rdworks/workflow.py → rdworks-0.55.1/src/rdworks/complete.py

@@ -1,8 +1,5 @@
-
+from rdworks import Mol, MolLibr
 from rdworks.stereoisomers import enumerate_stereoisomers, enumerate_ring_bond_stereoisomers
-from rdworks.mol import Mol
-from rdworks.mollibr import MolLibr
-
 from rdkit import Chem
 from rdkit.Chem.MolStandardize import rdMolStandardize
 
@@ -26,6 +23,8 @@ def complete_stereoisomers(molecular_input: str | Chem.Mol | Mol,
     Returns:
         MolLibr: a library of complete stereoisomers.
     """
+    from rdworks import Mol, MolLibr
+    
     if isinstance(molecular_input, Mol):
         if name:
             mol = molecular_input.rename(name)

{rdworks-0.54.2 → rdworks-0.55.1}/src/rdworks/conf.py

@@ -546,9 +546,9 @@ class Conf:
                 conf = frag_conf.copy()
                 conf.set_torsion(*frag_ijkl, angle) # atoms bonded to `l` move.
                 conf = conf.optimize(calculator, fmax, **kwargs)
+                data['angle'].append(angle)
                 # conf.optimize() updates coordinates and conf.props: 
                 #   `E_tot_init(kcal/mol)`, `E_tot(kcal/mol)`, `Converged`.
-                data['angle'].append(angle)
                 data['init'].append(conf.props['E_tot_init(kcal/mol)'])
                 data['last'].append(conf.props['E_tot(kcal/mol)'])
                 data['Converged'].append(conf.props['Converged'])
@@ -562,9 +562,9 @@ class Conf:
                 conf = ref_conf.copy()
                 conf.set_torsion(*indices, angle) # atoms bonded to `l` move.
                 conf = conf.optimize(calculator, fmax, **kwargs)
+                data['angle'].append(angle)
                 # conf.optimize() updates coordinates and conf.props: 
                 #   `E_tot_init(kcal/mol)`, `E_tot(kcal/mol)`, `Converged`.
-                data['angle'].append(conf.props['angle'])
                 data['init'].append(conf.props['E_tot_init(kcal/mol)'])
                 data['last'].append(conf.props['E_tot(kcal/mol)'])
                 data['Converged'].append(conf.props['Converged'])

{rdworks-0.54.2 → rdworks-0.55.1}/src/rdworks/microstates.py

@@ -4,9 +4,16 @@ import itertools
 import logging
 
 from types import SimpleNamespace
+from pathlib import Path
 from rdworks import Conf, Mol
 from rdworks.xtb.wrapper import GFN2xTB
 
+from rdkit import Chem
+from rdkit.Chem import (
+    AllChem, RemoveHs, CanonSmiles, MolFromSmarts,
+    GetFormalCharge, RWMol, AddHs, SanitizeMol, 
+    MolToSmiles, MolFromSmiles,
+    )
 
 logger = logging.getLogger(__name__)
 

{rdworks-0.54.2 → rdworks-0.55.1}/src/rdworks.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: rdworks
-Version: 0.54.2
+Version: 0.55.1
 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-0.54.2 → rdworks-0.55.1}/src/rdworks.egg-info/SOURCES.txt

@@ -2,6 +2,7 @@ LICENSE
 README.md
 pyproject.toml
 src/rdworks/__init__.py
+src/rdworks/complete.py
 src/rdworks/conf.py
 src/rdworks/descriptor.py
 src/rdworks/display.py
@@ -10,7 +11,6 @@ src/rdworks/matchedseries.py
 src/rdworks/microstates.py
 src/rdworks/mol.py
 src/rdworks/mollibr.py
-src/rdworks/pka.py
 src/rdworks/readin.py
 src/rdworks/rgroup.py
 src/rdworks/scaffold.py
@@ -20,7 +20,6 @@ src/rdworks/testdata.py
 src/rdworks/torsion.py
 src/rdworks/units.py
 src/rdworks/utils.py
-src/rdworks/workflow.py
 src/rdworks/xml.py
 src/rdworks.egg-info/PKG-INFO
 src/rdworks.egg-info/SOURCES.txt

rdworks-0.54.2/src/rdworks/pka.py

@@ -1,38 +0,0 @@
-"""This module is an implementation in progress of the decision tree method for pKa prediction.
-
-Crippen, J. Chem. Inf. Model., Vol. 48, No. 10, 2008, 2042-2053.
-
-The SMARTS patterns and pKa values were taken from the supporting information of the paper.
-These "MOE SMARTS" were converted to generic SMARTS which relied on use of some recursive SMARTS patterns.  
-The first data row then describes nodes 1, and then the tree expands out based on decisions of SMARTS-matching:
-    if node 2 is yes to pattern [#8,#16,#34,#52,#84;H]C(=O) - giving pKa 3.68 and range 5.96
-    node 3 is no to the same pattern - giving pKa 7.21 and range 17.32
-Then nodes 4,5 are under 2 and 6,7 are under 3, etc, etc until the leaf nodes are reached
-"""
-
-
-import importlib.resources
-from collections import namedtuple
-from typing import Union
-
-from rdkit import Chem
-from rdkit.Chem import AllChem
-
-datadir = importlib.resources.files('rdworks.predefined')
-DecisionTreeNode = namedtuple('DecisionTree', ('node', 'parent', 'child', 'FP', 'SMARTS', 'YN', 'pKa', 'pKa_range'))
-decision_tree = []
-with open(datadir / "pKa_decision_tree.ext", "r") as f: 
-    for line in f:
-        if (not line) or line.startswith('#'):
-            continue
-        decision_tree.append(DecisionTreeNode(line.strip().split()))
-        
-
-def decision_tree_pKa(rdmol:Chem.Mol) -> Union[float, None]:
-    pKa = None
-    for _ in decision_tree:
-        patt = Chem.MolFromSmarts(_.SMARTS) # make an RDKit query molecule
-        match = rdmol.HasSubstructMatch(patt) # check if we have a match for our test molecule
-        # pKa = float(values[6])
-        # pKa_range = float(values[7])
-    return pKa