merge salt, solvent remover in single fn

datamol/__init__.py

@@ -83,9 +83,7 @@
     "clear_atom_map_number": "datamol.mol",
     "set_atom_positions": "datamol.mol",
     "get_atom_positions": "datamol.mol",
-    "remove_salts": "datamol.mol",
-    "remove_solvents": "datamol.mol",
-    "remove_stereochemistry": "datamol.mol",
+    "remove_salts_solvents": "datamol.mol",
     # cluster
     "cluster_mols": "datamol.cluster",
     "pick_diverse": "datamol.cluster",
@@ -275,9 +273,7 @@ def __dir__():
     from .mol import clear_atom_map_number
     from .mol import set_atom_positions
     from .mol import get_atom_positions
-    from .mol import remove_stereochemistry
-    from .mol import remove_salts
-    from .mol import remove_solvents
+    from .mol import remove_salts_solvents
 
     from .cluster import cluster_mols
     from .cluster import pick_diverse

datamol/data/salts.smi → datamol/data/salts_solvents.smi

@@ -1,3 +1,7 @@
+//////////////////////////////////// PART 1  /////////////////////////////////////////////
+// Salts data from Rdkit
+// https://github.com/rdkit/rdkit/blob/master/Data/Salts.txt
+
 // $Id: Salts.txt 198 2006-12-15 18:06:48Z landrgr1 $
 // Created by Greg Landrum, December 2006
 //  Definitions from Thomas Zoller
@@ -26,8 +30,7 @@
 [S](=O)(=O)(O)O
 [CH3][S](=O)(=O)(O)
 c1cc([CH3])ccc1[S](=O)(=O)(O)	p-Toluene sulfonate
-// Salts data from Rdkit
-// https://github.com/rdkit/rdkit/blob/master/Data/Salts.txt
+
 // organics
 [CH3]C(=O)O	  Acetic acid
 FC(F)(F)C(=O)O	  TFA
@@ -64,7 +67,7 @@ C1CCCCC1[NH]C1CCCCC1	  Dicylcohexylammonium
 // THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
 // (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
 // OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
-//
+///////////////////////////// PART 2  /////////////////////////////////////////////
 // Salt data from Chembl structure pipeline
 // Version: 2022.09
 // https://github.com/chembl/ChEMBL_Structure_Pipeline/tree/master/chembl_structure_pipeline/data
@@ -230,4 +233,17 @@ CC(=O)OS(=O)(=O)O	Acetylsulfate
 [Be]	Beryllium
 [Ra]	Radium
 C(=O)C(O)C(O)C(O)C(O)C(=O)O	Glucuronate open form
-CC(O)CN(C)C	Dimepranol
+CC(O)CN(C)C	Dimepranol
+
+// Solvent data from Chembl structure pipeline
+// Version: 2019
+// https://github.com/chembl/ChEMBL_Structure_Pipeline/tree/master/chembl_structure_pipeline/data
+[OH2]	WATER
+ClCCl	DICHLOROMETHANE
+ClC(Cl)Cl	TRICHLOROMETHANE
+CCOC(=O)C	ETHYL ACETATE
+CO	METHANOL
+CC(C)O	PROPAN-2-OL
+CC(=O)C	ACETONE
+CS(=O)C	DMSO
+CCO	ETHANOL

datamol/mol.py

@@ -10,7 +10,6 @@
 import random
 import itertools
 import hashlib
-import importlib_resources
 
 from loguru import logger
 
@@ -28,7 +27,6 @@
 from rdkit.Chem.MolStandardize import rdMolStandardize
 from rdkit.Chem.MolStandardize import canonicalize_tautomer_smiles
 from rdkit.Chem.SaltRemover import SaltRemover
-from rdkit.Chem.rdmolops import RemoveStereochemistry
 
 import datamol
 from . import _sanifix4
@@ -48,10 +46,8 @@
 AROMATIC_BOND = Chem.rdchem.BondType.AROMATIC
 DATIVE_BOND = Chem.rdchem.BondType.DATIVE
 UNSPECIFIED_BOND = Chem.rdchem.BondType.UNSPECIFIED
-SALT_PATH = str(importlib_resources.files("datamol").joinpath("data/salts.smi"))
-SALT_REMOVER = SaltRemover(defnFilename=SALT_PATH)
-SOLVENT_PATH = str(importlib_resources.files("datamol").joinpath("data/solvents.smi"))
-SOLVENT_REMOVER = SaltRemover(defnFilename=SOLVENT_PATH)
+SALT_SOLVENT_PATH = datamol.data.open_datamol_data_file("salts_solvents.smi").name
+SALT_SOLVENT_REMOVER = SaltRemover(defnFilename=SALT_SOLVENT_PATH)
 
 
 def copy_mol(mol: Mol) -> Mol:
@@ -1386,40 +1382,15 @@ def get_atom_positions(
     return positions
 
 
-def remove_salts(mol: Mol, remover: Optional[SaltRemover] = SALT_REMOVER) -> Mol:
-    """Remove all salts from the molecule
+def remove_salts_solvents(mol: Mol) -> Mol:
+    """Remove all salts and solvents from the molecule.
 
     Args:
         mol: A molecule.
-        remover: A object that defines salts to be removed.
 
     See Also:
         <rdkit.Chem.SaltRemover.SaltRemover>
+        "datamol/data/salts_solvents.smi"
     """
-    return remover.StripMol(mol)
-
-
-def remove_solvents(mol: Mol, remover: Optional = SOLVENT_REMOVER) -> Mol:
-    """Remove all solvents from the molecule.
-
-    Args:
-        mol: A molecule.
-        remover: A object that defines solvents to be removed.
-
-    """
-    return remover.StripMol(mol)
-
-
-def remove_stereochemistry(mol: Mol) -> Mol:
-    """Removes all stereochemistry info from the molecule.
-
-    Args:
-        mol: A molecule.
-
-    See Also:
-        <rdkit.Chem.rdmolops.RemoveStereochemistry>
-
-    """
-    mol_copy = datamol.copy_mol(mol)
-    RemoveStereochemistry(mol_copy)
-    return mol_copy
+    mol_copy = copy_mol(mol)
+    return SALT_SOLVENT_REMOVER.StripMol(mol_copy)

tests/test_mol.py

@@ -910,13 +910,13 @@ def test_remove_salt():
     mol = dm.to_mol(smiles)
 
     # case of success
-    mol_no_salt = dm.remove_salts(mol)
+    mol_no_salt = dm.remove_salts_solvents(mol)
     assert mol_no_salt.GetNumAtoms() == mol.GetNumAtoms() - 3
 
     # case salt-like atoms in the molecule are unchanged
     smiles = "CN(Br)Cl"
     mol = dm.to_mol(smiles)
-    mol_no_salt = dm.remove_salts(mol)
+    mol_no_salt = dm.remove_salts_solvents(mol)
     assert mol_no_salt.GetNumAtoms() == mol.GetNumAtoms()
 
 
@@ -925,26 +925,11 @@ def test_remove_solvent():
     mol = dm.to_mol(smiles)
 
     # case of success
-    mol_no_salt = dm.remove_solvents(mol)
-    assert mol_no_salt.GetNumAtoms() == mol.GetNumAtoms() - 4
+    mol_no_solvent = dm.remove_salts_solvents(mol)
+    assert mol_no_solvent.GetNumAtoms() == mol.GetNumAtoms() - 4
 
     # case solvent-like atoms in the molecule are unchanged
     smiles = "CCOc1ccccc1C(=O)O"
     mol = dm.to_mol(smiles)
-    mol_no_salt = dm.remove_solvents(mol)
+    mol_no_salt = dm.remove_salts_solvents(mol)
     assert mol_no_salt.GetNumAtoms() == mol.GetNumAtoms()
-
-
-def test_remove_stereochemistry():
-    smiles = "CC1=CC(=O)[C@@H](CC1)C(C)C"
-    mol = dm.to_mol(smiles)
-
-    # case where removes the stereochemistry information from molecule
-    mol_no_stereo = dm.remove_stereochemistry(mol)
-    assert dm.same_mol(mol, mol_no_stereo) == False
-
-    # case where there is no stereochemistry information to be removed
-    smiles = "CC1=CC(=O)C(CC1)C(C)C"
-    mol = dm.to_mol(smiles)
-    mol_no_stereo = dm.remove_stereochemistry(mol)
-    assert dm.same_mol(mol, mol_no_stereo) == True