rdworks 0.36.4__tar.gz → 0.38.1__tar.gz

{rdworks-0.36.4 → rdworks-0.38.1}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: rdworks
-Version: 0.36.4
+Version: 0.38.1
 Summary: Frequently used 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-0.36.4 → rdworks-0.38.1}/src/rdworks/__init__.py

@@ -1,4 +1,4 @@
-__version__ = '0.36.4'
+__version__ = '0.38.1'
 
 from rdworks.conf    import Conf
 from rdworks.mol     import Mol

{rdworks-0.36.4 → rdworks-0.38.1}/src/rdworks/conf.py

@@ -3,6 +3,7 @@ import copy
 import json
 import numpy as np
 import ase
+import itertools
 
 from collections.abc import Callable
 from typing import Self
@@ -15,6 +16,8 @@ from rdkit.Chem import rdMolTransforms, AllChem, rdMolAlign, rdmolops
 from rdkit.Chem.Draw import rdMolDraw2D
 from PIL import Image
 
+from rdworks.std import clean_2d
+from rdworks.torsion import get_torsion_atoms, create_torsion_fragment
 from rdworks.units import ev2kcalpermol, pm2angstrom
 from rdworks.utils import recursive_round
 from rdworks.xtb.wrapper import GFN2xTB
@@ -387,7 +390,124 @@ class Conf:
                 raise RuntimeError("ASE calculator error")
 
 
-    def torsion_angle(self, i:int, j:int, k:int, l:int) -> float:
+    def torsion_atoms(self, strict: bool = True) -> dict[int, tuple]:
+        """Determine torsion/dihedral angle atoms (i-j-k-l) and rotating group for each rotatable bond (j-k).
+
+        Args:
+            strict (bool): whether to exclude amide/imide/ester/acid bonds.
+
+        Returns:
+            {torsion_key: (i, j, k, l), ...,}
+        """
+        return {i: d[:4] for i, d in enumerate(get_torsion_atoms(self.rdmol, strict))}
+    
+
+    def torsion_energies(self,
+                         calculator: str | Callable,
+                         torsion_key: int | None = None,
+                         simplify: bool = True, 
+                         fmax: float = 0.05,
+                         interval: float = 20.0,
+                         use_converged_only: bool = True,
+                         **kwargs,
+                         ) -> Self:
+        """Calculates potential energy profiles for each torsion angle using ASE optimizer.
+
+        It uses the first conformer as a reference.
+
+        Args:
+            calculator (str | Callable): 'MMFF', 'UFF', or ASE calculator.
+            torsion_key (int | None): key to the torsion indices to calculate. Defaults to None (all).
+            simplify (bool, optional): whether to use fragment surrogate. Defaults to True.
+            fmax (float, optional): fmax of ASE optimizer. Defaults to 0.05.
+            interval (float, optional): interval of torsion angles in degree. Defaults to 15.0.
+            use_converged_only (bool, optional): whether to use only converged data. Defaults to True.
+
+        Returns:
+            Self: modified self.
+        """
+
+        if torsion_key is None:
+            torsion_atoms_indices = self.torsion_atoms()
+            # {0: (5, 4, 3, 1)}
+        else:
+            torsion_atoms_indices = {torsion_key: self.torsion_atoms()[torsion_key]}
+
+        ref_conf = self.copy()
+
+        data = {}
+
+        if simplify:
+            for tk, indices in torsion_atoms_indices.items():
+                frag, frag_ijkl = create_torsion_fragment(ref_conf.rdmol, indices)
+                frag_conf = Conf(frag)
+                data[tk] = {'indices': indices, 'angle':[], 'init':[], 'last':[], 'Converged':[]}
+                for angle in np.arange(-180.0, 180.0, interval): 
+                    # Iterated numpy.ndarray does not contain the last 180: -180., ..., (180).
+                    conf = frag_conf.copy()
+                    conf.props.update({'torsion_key': tk, 'angle': float(angle)})
+                    conf.set_torsion(*frag_ijkl, angle) # atoms bonded to `l` move.
+                    conf = conf.optimize(calculator, fmax, **kwargs)
+                    # conf.optimize() updates coordinates and conf.props: 
+                    #   `angle`, `E_tot_init(kcal/mol)`, `E_tot(kcal/mol)`, `Converged`.
+                    tk = conf.props['torsion_key']
+                    data[tk]['angle'].append(conf.props['angle'])
+                    data[tk]['init'].append(conf.props['E_tot_init(kcal/mol)'])
+                    data[tk]['last'].append(conf.props['E_tot(kcal/mol)'])
+                    data[tk]['Converged'].append(conf.props['Converged'])
+                    frag_cleaned, _ = clean_2d(frag, reset_isotope=True, remove_H=True)
+                    # to serialize the molecule
+                    data[tk]['frag'] = Chem.MolToMolBlock(frag_cleaned)
+                    data[tk]['frag_indices'] = frag_ijkl
+
+        else:
+            # mol.confs will be populated with torsion conformers. 
+            # It is designed for a batch optimization in the future.
+            torsion_angle_confs = []
+            for tk, indices in torsion_atoms_indices.items():
+                data[tk] = {'indices': indices, 'angle':[], 'init':[], 'last':[], 'Converged':[]}
+                for angle in np.arange(-180.0, 180.0, interval): 
+                    # Iterated numpy.ndarray does not contain the last 180: -180., ..., (180).
+                    x = ref_conf.copy()
+                    x.props.update({'torsion_key': tk, 'angle': float(angle)})
+                    x.set_torsion(*indices, angle) # atoms bonded to `l` move.
+                    torsion_angle_confs.append(x)
+
+            # Calculate relaxation energies
+            for conf in torsion_angle_confs:
+                conf = conf.optimize(calculator, fmax, **kwargs)
+                # conf.optimize() updates coordinates and conf.props: 
+                #   `angle`, `E_tot_init(kcal/mol)`, `E_tot(kcal/mol)`, `Converged`.
+                tk = conf.props['torsion_key']
+                data[tk]['angle'].append(conf.props['angle'])
+                data[tk]['init'].append(conf.props['E_tot_init(kcal/mol)'])
+                data[tk]['last'].append(conf.props['E_tot(kcal/mol)'])
+                data[tk]['Converged'].append(conf.props['Converged'])
+        
+        # Post-processing
+        torsion_energy_profiles = {}
+        for tk, dictdata in data.items():
+            if use_converged_only:
+                dictdata['angle'] = list(itertools.compress(dictdata['angle'], dictdata['Converged']))
+                dictdata['init'] = list(itertools.compress(dictdata['init'], dictdata['Converged']))
+                dictdata['last'] = list(itertools.compress(dictdata['last'], dictdata['Converged']))
+            relax = np.array(dictdata['init']) - np.median(dictdata['last'])
+            E_rel = relax - np.min(relax)
+            torsion_energy_profiles[tk] = {
+                'indices' : dictdata['indices'],
+                'angle' : np.round(np.array(dictdata['angle']), 1).tolist(), # np.ndarray -> list for serialization
+                'E_rel(kcal/mol)': np.round(E_rel, 2).tolist(), # np.ndarray -> list for serialization
+                'frag' : dictdata.get('frag', None),
+                'frag_indices' : dictdata.get('frag_indices', None),
+                }
+
+        self.props['torsion'] = torsion_energy_profiles
+        self.props['torsion_calculator'] = str(calculator)
+
+        return self
+    
+
+    def torsion_angle(self, i: int, j: int, k: int, l: int) -> float:
         """Get dihedral angle (i-j-k-l) in degrees.
 
         Args:
@@ -419,8 +539,10 @@ class Conf:
             return json.dumps(self.props)
     
 
-    def serialize(self, decimals:int=3) -> str:
-        """Serialize information necessary to rebuild.
+    def serialize(self, decimals: int = 3) -> str:
+        """Serialize information necessary to rebuild a Conf object.
+        Args:
+            decimals (int, optional): number of decimal places for float data type. Defaults to 3.
 
         Returns:
             str: serialized string for json.loads()
@@ -435,14 +557,18 @@ class Conf:
         return serialized
 
 
-    def deserialize(self, serialized:str) -> Self:
-        """De-serialize information and rebuild.
+    def deserialize(self, serialized: str) -> Self:
+        """De-serialize information and rebuild a Conf object.
+        
+        Example:
+            serialized = conf1.serialize()
+            conf2 = Conf().deserialize(serialized)
 
         Args:
-            serialized (str): _description_
+            serialized (str): serialized string.
 
         Returns:
-            Self: _description_
+            Self: modified self.
         """
         data = json.loads(serialized)
 

{rdworks-0.36.4 → rdworks-0.38.1}/src/rdworks/mol.py

@@ -33,7 +33,7 @@ from rdkit.ML.Cluster import Butina
 from PIL import Image
 
 from rdworks.conf import Conf
-from rdworks.std import desalt_smiles, standardize, clean_2d
+from rdworks.std import generate_inchi_key, desalt_smiles, standardize, clean_2d
 from rdworks.xml import list_predefined_xml, get_predefined_xml, parse_xml
 from rdworks.scaffold import rigid_fragment_indices
 from rdworks.descriptor import rd_descriptor, rd_descriptor_f
@@ -141,8 +141,7 @@ class Mol:
             self.name = 'untitled'
 
         self.rdmol.SetProp('_Name', self.name) # _Name can't be None
-        self.InChI = Chem.MolToInchi(self.rdmol)
-        self.InChIKey = inchi.InchiToInchiKey(self.InChI)
+        self.InChIKey = generate_inchi_key(self.rdmol)
         self.props.update({
             'aka' : [], # <-- to be set by MolLibr.unique()
             'atoms' : self.rdmol.GetNumAtoms(), # hydrogens not excluded?
@@ -942,18 +941,6 @@ class Mol:
         return [atom.GetAtomicNum() for atom in self.rdmol.GetAtoms()]
     
 
-    def torsion_atoms(self, strict: bool = True) -> dict[int, tuple]:
-        """Determine torsion/dihedral angle atoms (i-j-k-l) and rotating group for each rotatable bond (j-k).
-
-        Args:
-            strict (bool): whether to exclude amide/imide/ester/acid bonds.
-
-        Returns:
-            {torsion_key: (i, j, k, l), ...,}
-        """
-        return {i: d[:4] for i, d in enumerate(get_torsion_atoms(self.rdmol, strict))}
-
-
     def compute(self, **kwargs) -> Self:
         """Change settings for parallel computing.
 
@@ -972,6 +959,18 @@ class Mol:
         return self
     
 
+    def torsion_atoms(self, strict: bool = True) -> dict[int, tuple]:
+        """Determine torsion/dihedral angle atoms (i-j-k-l) and rotating group for each rotatable bond (j-k).
+
+        Args:
+            strict (bool): whether to exclude amide/imide/ester/acid bonds.
+
+        Returns:
+            {torsion_key: (i, j, k, l), ...,}
+        """
+        return {i: d[:4] for i, d in enumerate(get_torsion_atoms(self.rdmol, strict))}
+    
+
     def torsion_energies(self,
                          calculator: str | Callable,
                          torsion_key: int | None = None,
@@ -997,87 +996,16 @@ class Mol:
             Self: modified self.
         """
         assert self.count() > 0, "torsion_energies() requires at least one conformer"
-
-        self = self.compute(**kwargs)
-
-        if torsion_key is None:
-            torsion_atoms_indices = self.torsion_atoms()
-            # {0: (5, 4, 3, 1)}
-        else:
-            torsion_atoms_indices = {torsion_key: self.torsion_atoms()[torsion_key]}
-
         ref_conf = self.confs[0].copy()
-
-        data = {}
-
-        if simplify:
-            for tk, indices in torsion_atoms_indices.items():
-                frag, frag_ijkl = create_torsion_fragment(ref_conf.rdmol, indices)
-                frag_conf = Conf(frag)
-                data[tk] = {'indices': indices, 'angle':[], 'init':[], 'last':[], 'Converged':[]}
-                for angle in np.arange(-180.0, 180.0, interval): 
-                    # Iterated numpy.ndarray does not contain the last 180: -180., ..., (180).
-                    conf = frag_conf.copy()
-                    conf.props.update({'torsion_key': tk, 'angle': float(angle)})
-                    conf.set_torsion(*frag_ijkl, angle) # atoms bonded to `l` move.
-                    conf = conf.optimize(calculator, fmax, **kwargs)
-                    # conf.optimize() updates coordinates and conf.props: 
-                    #   `angle`, `E_tot_init(kcal/mol)`, `E_tot(kcal/mol)`, `Converged`.
-                    tk = conf.props['torsion_key']
-                    data[tk]['angle'].append(conf.props['angle'])
-                    data[tk]['init'].append(conf.props['E_tot_init(kcal/mol)'])
-                    data[tk]['last'].append(conf.props['E_tot(kcal/mol)'])
-                    data[tk]['Converged'].append(conf.props['Converged'])
-                    frag_cleaned, _ = clean_2d(frag, reset_isotope=True, remove_H=True)
-                    rdDepictor.Compute2DCoords(frag_cleaned)
-                    # to serialize the molecule
-                    data[tk]['frag'] = Chem.MolToMolBlock(frag_cleaned)
-                    data[tk]['frag_indices'] = frag_ijkl
-
-        else:
-            # mol.confs will be populated with torsion conformers. 
-            # It is designed for a batch optimization in the future.
-            mol = self.copy()
-            mol.confs = []
-            for tk, indices in torsion_atoms_indices.items():
-                data[tk] = {'indices': indices, 'angle':[], 'init':[], 'last':[], 'Converged':[]}
-                for angle in np.arange(-180.0, 180.0, interval): 
-                    # Iterated numpy.ndarray does not contain the last 180: -180., ..., (180).
-                    x = ref_conf.copy()
-                    x.props.update({'torsion_key': tk, 'angle': float(angle)})
-                    x.set_torsion(*indices, angle) # atoms bonded to `l` move.
-                    mol.confs.append(x)
-
-            # Calculate relaxation energies
-            for conf in mol.confs:
-                conf = conf.optimize(calculator, fmax, **kwargs)
-                # conf.optimize() updates coordinates and conf.props: 
-                #   `angle`, `E_tot_init(kcal/mol)`, `E_tot(kcal/mol)`, `Converged`.
-                tk = conf.props['torsion_key']
-                data[tk]['angle'].append(conf.props['angle'])
-                data[tk]['init'].append(conf.props['E_tot_init(kcal/mol)'])
-                data[tk]['last'].append(conf.props['E_tot(kcal/mol)'])
-                data[tk]['Converged'].append(conf.props['Converged'])
-        
-        # Post-processing
-        torsion_energy_profiles = {}
-        for tk, dictdata in data.items():
-            if use_converged_only:
-                dictdata['angle'] = list(itertools.compress(dictdata['angle'], dictdata['Converged']))
-                dictdata['init'] = list(itertools.compress(dictdata['init'], dictdata['Converged']))
-                dictdata['last'] = list(itertools.compress(dictdata['last'], dictdata['Converged']))
-            relax = np.array(dictdata['init']) - np.median(dictdata['last'])
-            E_rel = relax - np.min(relax)
-            torsion_energy_profiles[tk] = {
-                'indices' : dictdata['indices'],
-                'angle' : np.round(np.array(dictdata['angle']), 1).tolist(), # np.ndarray -> list for serialization
-                'E_rel(kcal/mol)': np.round(E_rel, 2).tolist(), # np.ndarray -> list for serialization
-                'frag' : dictdata.get('frag', None),
-                'frag_indices' : dictdata.get('frag_indices', None),
-                }
-
-        self.props['torsion'] = torsion_energy_profiles
-        self.props['torsion_calculator'] = str(calculator)
+        ref_conf = ref_conf.torsion_energies(calculator, 
+                                             torsion_key, 
+                                             simplify, 
+                                             fmax, 
+                                             interval, 
+                                             use_converged_only, 
+                                             **kwargs)
+        for k in ['torsion', 'torsion_calculator']:
+            self.props[k] = ref_conf.props[k]
 
         return self
 
@@ -1629,7 +1557,15 @@ class Mol:
         return json.dumps(props)
 
 
-    def serialize(self, decimals: int = 2) -> str:       
+    def serialize(self, decimals: int = 2) -> str:
+        """Serialize information necessary to rebuild a Mol object.
+
+        Args:
+            decimals (int, optional): number of decimal places for float data type. Defaults to 2.
+
+        Returns:
+            str: serialized string for json.loads()
+        """
         serialized = json.dumps({
             'name'  : self.name,
             'smiles': self.smiles,
@@ -1641,10 +1577,14 @@ class Mol:
 
     
     def deserialize(self, serialized: str) -> Self:
-        """Updates self with the serialized string input.
+        """De-serialize the information and build a new Mol object.
+
+        Example:
+            serialized = mol1.serialize()
+            mol2 = Mol().deserialize(serialized)
 
         Args:
-            serialized (str): input
+            serialized (str): serialized string.
 
         Returns:
             Self: modified self.
@@ -1655,8 +1595,7 @@ class Mol:
         self.smiles = data['smiles'] # isomeric SMILES, no H
         self.rdmol = Chem.MolFromSmiles(data['smiles']) # for 2D depiction
         self.rdmol.SetProp('_Name', self.name)
-        self.InChI = Chem.MolToInchi(self.rdmol)
-        self.InChIKey = inchi.InchiToInchiKey(self.InChI)
+        self.InChIKey = generate_inchi_key(self.rdmol)
         self.props = data['props']
         self.confs = [Conf().deserialize(_) for _ in data['confs']] # for 3D conformers (iterable)
         

{rdworks-0.36.4 → rdworks-0.38.1}/src/rdworks/std.py

@@ -1,10 +1,32 @@
 import operator
 
 from rdkit import Chem
-from rdkit.Chem import rdDepictor
+from rdkit.Chem import rdDepictor, inchi
 from rdkit.Chem.MolStandardize import rdMolStandardize
 
 
+def generate_inchi_key(rdmol: Chem.Mol) -> str:
+    """Generate InChIKey.
+
+    Note:
+        - An InChIKey is a 27-character string consisting of three parts: 
+            - 14 characters: Derived from the connectivity layer of the InChI.
+            - Hyphen (-): Separates the first two blocks.
+            - 9 characters: Derived from the remaining InChI layers.
+            - A hyphen (-): Separates the second and third blocks.
+            - A final checksum character: Ensures the integrity of the key.
+
+    Args:
+        rdmol (Chem.Mol): input molecule
+
+    Returns:
+        str: 27-character InChIKey
+    """
+    InChI = Chem.MolToInchi(rdmol)
+    InChIKey = inchi.InchiToInchiKey(InChI)
+    
+    return InChIKey
+
 
 def desalt_smiles(smiles: str) -> tuple[str, Chem.Mol]:
     """Remove salt(s) from SMILES.
@@ -180,4 +202,6 @@ def clean_2d(rdmol: Chem.Mol,
     if remove_H:
         mol = Chem.RemoveHs(mol)
 
+    rdDepictor.Compute2DCoords(mol)
+
     return (mol, conformers)

{rdworks-0.36.4 → rdworks-0.38.1}/src/rdworks.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: rdworks
-Version: 0.36.4
+Version: 0.38.1
 Summary: Frequently used 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-0.36.4 → rdworks-0.38.1}/tests/test_basics.py

@@ -475,12 +475,42 @@ def test_torsion_fragment():
     frag, frag_ijkl = create_torsion_fragment(mol.confs[0].rdmol, ta[6])
     assert frag_ijkl == (5, 6, 7, 12)
 
-
     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])
+    # expects no fragmentation
+    assert frag == mol2.confs[0].rdmol
+    assert frag_ijkl == ta2[0]
+
+
+def test_torsion_fragment_from_conf():
+    from rdworks.torsion import create_torsion_fragment
+    mol = Mol(molecule="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",
+              name="atorvastatin").make_confs(n=1)
+    ref_conf = mol.confs[0]
+    ta = ref_conf.torsion_atoms()
+    assert len(ta) == 12
+    # {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])
+    assert frag_ijkl == (5, 6, 7, 12)
+
+    ref_conf = ref_conf.torsion_energies(calculator='MMFF94', torsion_key=6, interval=15)
+
+    mol2 = Mol(molecule='CC(=O)Nc1ccc(O)cc1', name='acetaminophen.3').make_confs(n=1)
+    ref_conf2 = mol2.confs[0]
+    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])
+    # expects no fragmentation
+    assert frag == ref_conf2.rdmol
+    assert frag_ijkl == ta2[0]
+
+    ref_conf2 = ref_conf2.torsion_energies(calculator='MMFF94', interval=15)
 
 
 def test_torsion_energies():
@@ -488,7 +518,8 @@ def test_torsion_energies():
     with open(workdir / 'test_torsion_energies.html', 'w') as f:
         for mol in libr[:1]:
             mol = mol.make_confs().drop_confs(similar=True, similar_rmsd=0.3).sort_confs().rename()
-            mol = mol.optimize_confs(calculator='MMFF94').torsion_energies(calculator='MMFF94', interval=15)
+            mol = mol.optimize_confs(calculator='MMFF94').torsion_energies(calculator='MMFF94', 
+                                                                           interval=15)
             f.write(mol.to_html())
             print(mol.dumps('torsion', decimals=2))