sapiopycommons 2024.9.4a323__py3-none-any.whl → 2024.9.6a325__py3-none-any.whl

sapiopycommons/chem/IndigoMolecules.py

@@ -9,6 +9,7 @@ indigo.setOption("ignore-stereochemistry-errors", True)
 indigo.setOption("render-stereo-style", "ext")
 indigo.setOption("aromaticity-model", "generic")
 indigo.setOption("render-coloring", True)
+indigo.setOption("molfile-saving-mode", "3000")
 indigo_inchi = IndigoInchi(indigo);
 
 

sapiopycommons/chem/Molecules.py

@@ -1,5 +1,6 @@
 # Author Yechen Qiao
 # Common Molecule Utilities for Molecule Transfers with Sapio
+from typing import cast
 
 from rdkit import Chem
 from rdkit.Chem import Crippen, MolToInchi
@@ -20,6 +21,25 @@ tautomer_params.tautomerReassignStereo = False
 tautomer_params.tautomerRemoveIsotopicHs = True
 enumerator = rdMolStandardize.TautomerEnumerator(tautomer_params)
 
+
+def get_enhanced_stereo_reg_hash(mol: Mol, enhanced_stereo: bool) -> str:
+    """
+    Get the Registration Hash for the molecule by the current registration configuration.
+    When we are running if we are canonicalization of tautomers or cleaning up any other way, do they first before calling.
+    :param mol: The molecule to obtain hash for.
+    :param canonical_tautomer: Whether the registry system canonicalize the tautomers.
+    :param enhanced_stereo: Whether we are computing enhanced stereo at all.
+    :return: The enhanced stereo hash.
+    """
+    if enhanced_stereo:
+        from rdkit.Chem.RegistrationHash import GetMolLayers, GetMolHash, HashScheme
+        layers = GetMolLayers(mol, enable_tautomer_hash_v2=True)
+        hash_scheme: HashScheme = HashScheme.TAUTOMER_INSENSITIVE_LAYERS
+        return GetMolHash(layers, hash_scheme=hash_scheme)
+    else:
+        return ""
+
+
 def neutralize_atoms(mol) -> Mol:
     """
     Neutralize atoms per https://baoilleach.blogspot.com/2019/12/no-charge-simple-approach-to.html
@@ -86,7 +106,6 @@ def mol_to_img(mol_str: str) -> str:
     return renderer.renderToString(mol)
 
 
-
 def mol_to_sapio_partial_pojo(mol: Mol):
     """
     Get the minimum information about molecule to Sapio, just its SMILES, V3000, and image data.
@@ -96,7 +115,7 @@ def mol_to_sapio_partial_pojo(mol: Mol):
     Chem.SanitizeMol(mol)
     mol.UpdatePropertyCache()
     smiles = Chem.MolToSmiles(mol)
-    molBlock = Chem.MolToMolBlock(mol)
+    molBlock = Chem.MolToMolBlock(mol, forceV3000=True)
     img = mol_to_img(mol)
     molecule = dict()
     molecule["smiles"] = smiles
@@ -105,23 +124,52 @@ def mol_to_sapio_partial_pojo(mol: Mol):
     return molecule
 
 
-def mol_to_sapio_substance(mol: Mol, include_stereoisomers: bool = False,
+def get_cxs_smiles_hash(mol: Mol, enhanced_stereo: bool) -> str:
+    """
+    Return the SHA1 CXS Smiles hash for the canonical, isomeric CXS SMILES of the molecule.
+    """
+    if not enhanced_stereo:
+        return ""
+    import hashlib
+    return hashlib.sha1(Chem.MolToCXSmiles(mol, canonical=True, isomericSmiles=True).encode()).hexdigest()
+
+
+def get_has_or_group(mol: Mol, enhanced_stereo: bool) -> bool:
+    """
+    Return true if and only if: enhanced stereochemistry is enabled and there is at least one OR group in mol.
+    """
+    if not enhanced_stereo:
+        return False
+    from rdkit.Chem import StereoGroup_vect, STEREO_OR
+    stereo_groups: StereoGroup_vect = mol.GetStereoGroups()
+    for stereo_group in stereo_groups:
+        if stereo_group.GetGroupType() == STEREO_OR:
+            return True
+    return False
+
+
+def mol_to_sapio_substance(mol: Mol, include_stereoisomers=False,
                            normalize: bool = False, remove_salt: bool = False, make_images: bool = False,
-                           salt_def: str | None = None, canonical_tautomer: bool = True):
+                           salt_def: str | None = None, canonical_tautomer: bool = True,
+                           enhanced_stereo: bool = False, remove_atom_map: bool = True):
     """
     Convert a molecule in RDKit to a molecule POJO in Sapio.
 
     :param mol: The molecule in RDKit.
-    :param include_stereoisomers: If true, will compute all stereoisomer permutations of this molecule.
     :param normalize If true, will normalize the functional groups and return normalized result.
     :param remove_salt If true, we will remove salts iteratively from the molecule before returning their data.
     We will also populate desaltedList with molecules we deleted.
+    :param make_images Whether to make images as part of the result without having another script to resolve it.
     :param salt_def: if not none, specifies custom salt to be used during the desalt process.
     :param canonical_tautomer: if True, we will attempt to compute canonical tautomer for the molecule. Slow!
     This is needed for a registry. Note it stops after enumeration of 1000.
+    :param enhanced_stereo: If enabled, enhanced stereo hash will be produced.
+    :param remove_atom_map: When set, clear all atom AAM maps that were set had it been merged into some reactions earlier.
     :return: The molecule POJO for Sapio.
     """
     molecule = dict()
+    if remove_atom_map:
+        [a.SetAtomMapNum(0) for a in mol.GetAtoms()]
     Chem.SanitizeMol(mol)
     mol.UpdatePropertyCache()
     Chem.GetSymmSSSR(mol)
@@ -157,7 +205,7 @@ def mol_to_sapio_substance(mol: Mol, include_stereoisomers: bool = False,
     exactMass = Descriptors.ExactMolWt(mol)
     molFormula = rdMolDescriptors.CalcMolFormula(mol)
     charge = Chem.GetFormalCharge(mol)
-    molBlock = Chem.MolToMolBlock(mol)
+    molBlock = Chem.MolToMolBlock(mol, forceV3000=True)
 
     molecule["cLogP"] = cLogP
     molecule["tpsa"] = tpsa
@@ -181,28 +229,38 @@ def mol_to_sapio_substance(mol: Mol, include_stereoisomers: bool = False,
     # We need to test the INCHI can be loaded back to indigo.
     indigo_mol = indigo.loadMolecule(molBlock)
     indigo_mol.aromatize()
-    indigo_inchi.resetOptions()
-    indigo_inchi_str = indigo_inchi.getInchi(indigo_mol)
-    molecule["inchi"] = indigo_inchi_str
-    indigo_inchi_key_str = indigo_inchi.getInchiKey(indigo_inchi_str)
-    molecule["inchiKey"] = indigo_inchi_key_str
+    if enhanced_stereo:
+        # Remove enhanced stereo layer when generating InChI as the stereo hash is generated separately for reg.
+        mol_copy: Mol = Chem.MolFromMolBlock(Chem.MolToMolBlock(mol))
+        Chem.CanonicalizeEnhancedStereo(mol_copy)
+        molecule["inchi"] = Chem.MolToInchi(mol_copy)
+        molecule["inchiKey"] = Chem.MolToInchiKey(mol_copy)
+    else:
+        indigo_inchi.resetOptions()
+        indigo_inchi_str = indigo_inchi.getInchi(indigo_mol)
+        molecule["inchi"] = indigo_inchi_str
+        indigo_inchi_key_str = indigo_inchi.getInchiKey(indigo_inchi_str)
+        molecule["inchiKey"] = indigo_inchi_key_str
     molecule["smiles"] = indigo_mol.smiles()
+    molecule["reg_hash"] = get_enhanced_stereo_reg_hash(mol, enhanced_stereo=enhanced_stereo)
+    molecule["cxsmiles_hash"] = get_cxs_smiles_hash(mol, enhanced_stereo=enhanced_stereo)
+    molecule["has_or_group"] = get_has_or_group(mol, enhanced_stereo=enhanced_stereo)
 
-    if include_stereoisomers and has_chiral_centers(mol):
-        stereoisomers = find_all_possible_stereoisomers(mol, only_unassigned=False, try_embedding=False, unique=True)
-        molecule["stereoisomers"] = [mol_to_sapio_partial_pojo(x) for x in stereoisomers]
     return molecule
 
 
-def mol_to_sapio_compound(mol: Mol, include_stereoisomers: bool = False,
+def mol_to_sapio_compound(mol: Mol, include_stereoisomers=False, enhanced_stereo: bool = False,
                           salt_def: str | None = None, resolve_canonical: bool = True,
-                          make_images: bool = False, canonical_tautomer: bool = True):
+                          make_images: bool = False, canonical_tautomer: bool = True,
+                          remove_atom_map: bool = True):
     ret = dict()
-    ret['originalMol'] = mol_to_sapio_substance(mol, include_stereoisomers,
+    ret['originalMol'] = mol_to_sapio_substance(mol, include_stereoisomers=False,
                                                 normalize=False, remove_salt=False, make_images=make_images,
-                                                canonical_tautomer=canonical_tautomer)
+                                                canonical_tautomer=canonical_tautomer,
+                                                enhanced_stereo=enhanced_stereo, remove_atom_map=remove_atom_map)
     if resolve_canonical:
         ret['canonicalMol'] = mol_to_sapio_substance(mol, include_stereoisomers=False,
                                                      normalize=True, remove_salt=True, make_images=make_images,
-                                                     salt_def=salt_def, canonical_tautomer=canonical_tautomer)
+                                                     salt_def=salt_def, canonical_tautomer=canonical_tautomer,
+                                                     enhanced_stereo=enhanced_stereo, remove_atom_map=remove_atom_map)
     return ret

sapiopycommons/general/aliases.py

@@ -14,7 +14,7 @@ from sapiopycommons.general.exceptions import SapioException
 
 FieldValue = int | float | str | bool | None
 """Allowable values for fields in the system."""
-RecordModel = PyRecordModel | WrappedRecordModel | WrappedType
+RecordModel = PyRecordModel | WrappedRecordModel
 """Different forms that a record model could take."""
 SapioRecord = DataRecord | RecordModel
 """A record could be provided as either a DataRecord, PyRecordModel, or WrappedRecordModel (WrappedType)."""

sapiopycommons/general/custom_report_util.py

@@ -243,7 +243,8 @@ class CustomReportUtil:
             else:
                 encountered_names.append(field_name)
 
-        filters: dict[str, Iterable[FieldValue]] = AliasUtil.to_data_field_names_dict(filters)
+        if filters:
+            filters: dict[str, Iterable[FieldValue]] = AliasUtil.to_data_field_names_dict(filters)
 
         ret: list[dict[str, FieldValue]] = []
         for row in rows:

sapiopycommons/multimodal/multimodal_data.py

@@ -38,6 +38,9 @@ class PyMolecule:
     normError: str | None
     desaltError: str | None
     desaltedList: list[str] | None
+    registrationHash: str | None
+    hasOrGroup: bool
+    CXSMILESHash: str | None
 
 
 @dataclass
@@ -100,9 +103,9 @@ class PyMoleculeLoaderResult:
         compoundList: the compounds successfully loaded.
         errorList: an error record is added here for each one we failed to load in Sapio.
     """
-    compoundByStr: dict[str, PyCompound]
-    compoundList: list[PyCompound]
-    errorList: list[ChemLoadingError]
+    compoundByStr: dict[str, PyCompound] | None
+    compoundList: list[PyCompound] | None
+    errorList: list[ChemLoadingError] | None
 
 
 @dataclass

{sapiopycommons-2024.9.4a323.dist-info → sapiopycommons-2024.9.6a325.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.3
 Name: sapiopycommons
-Version: 2024.9.4a323
+Version: 2024.9.6a325
 Summary: Official Sapio Python API Utilities Package
 Project-URL: Homepage, https://github.com/sapiosciences
 Author-email: Jonathan Steck <jsteck@sapiosciences.com>, Yechen Qiao <yqiao@sapiosciences.com>

{sapiopycommons-2024.9.4a323.dist-info → sapiopycommons-2024.9.6a325.dist-info}/RECORD

@@ -1,8 +1,8 @@
 sapiopycommons/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 sapiopycommons/callbacks/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 sapiopycommons/callbacks/callback_util.py,sha256=7gUyJ-i3Owdy9bdQSOYKX_AgNRaT0PTbdhulA59tNys,63616
-sapiopycommons/chem/IndigoMolecules.py,sha256=QqFDi9CKERj6sn_ZwVcS2xZq4imlkaTeCrpq1iNcEJA,1992
-sapiopycommons/chem/Molecules.py,sha256=t80IsQBPJ9mwE8ZxnWomAGrZDhdsOuPvLaTPb_N6jGU,8639
+sapiopycommons/chem/IndigoMolecules.py,sha256=3f-aig3AJkKJhRmhlQ0cI-5G8oeaQk_3foJTDZCvoko,2040
+sapiopycommons/chem/Molecules.py,sha256=0B_SsXB2swg2DiP50p0tcNOVO1ajlxumSI42YyDiSHI,11517
 sapiopycommons/chem/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 sapiopycommons/customreport/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 sapiopycommons/customreport/column_builder.py,sha256=sS_wZYOR72rs3syTNjwCVP4h8M8N0b0burkTxFQItVU,3019
@@ -24,16 +24,16 @@ sapiopycommons/files/file_validator.py,sha256=4OvY98ueJWPJdpndwnKv2nqVvLP9S2W7Il
 sapiopycommons/files/file_writer.py,sha256=96Xl8TTT46Krxe_J8rmmlEMtel4nzZB961f5Yqtl1-I,17616
 sapiopycommons/general/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 sapiopycommons/general/accession_service.py,sha256=HYgyOsH_UaoRnoury-c2yTW8SeG4OtjLemdpCzoV4R8,13484
-sapiopycommons/general/aliases.py,sha256=l15Z_Q7BRntUVbDT0Jnin2hww4RTzNRqnFRzH3knpII,10423
+sapiopycommons/general/aliases.py,sha256=Gih9shHsj765q4HimfFTTI7wWDPAtXjoqCgHisyIQZY,10409
 sapiopycommons/general/audit_log.py,sha256=tJi4uU4qRY2WWcK4ItkjRvoCHCwwiU9LwCNv4lP5-QQ,8713
-sapiopycommons/general/custom_report_util.py,sha256=6Vr3itz5Bav9yBIlblnWMMSc0Mc-HPeVfnpymdLf6fU,15629
+sapiopycommons/general/custom_report_util.py,sha256=BGu9Ki0wn3m4Nk-LKM6inDSfe8ULUSG9d-HJJNOTtGc,15653
 sapiopycommons/general/exceptions.py,sha256=DOlLKnpCatxQF-lVCToa8ryJgusWLvip6N_1ALN00QE,1679
 sapiopycommons/general/popup_util.py,sha256=L-4qpTemSZdlD6_6oEsDYIzLOCiZgDK6wC6DqUwzOYA,31925
 sapiopycommons/general/sapio_links.py,sha256=o9Z-8y2rz6AI0Cy6tq58ElPge9RBnisGc9NyccbaJxs,2610
 sapiopycommons/general/storage_util.py,sha256=ovmK_jN7v09BoX07XxwShpBUC5WYQOM7dbKV_VeLXJU,8892
 sapiopycommons/general/time_util.py,sha256=sXThADCRAQDWYDD9C5CdhcKYIt3qOaVNyZfGBR7HW9A,8701
 sapiopycommons/multimodal/multimodal.py,sha256=A1QsC8QTPmgZyPr7KtMbPRedn2Ie4WIErodUvQ9otgU,6724
-sapiopycommons/multimodal/multimodal_data.py,sha256=p_caXW0vrURkzDHHspUptEI7lVFpZUrmyF7foz2fAvA,14983
+sapiopycommons/multimodal/multimodal_data.py,sha256=t-0uY4cVgm88uXaSOL4ZeB6zmdHufowXuLFlMk61wFg,15087
 sapiopycommons/processtracking/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 sapiopycommons/processtracking/endpoints.py,sha256=w5bziI2xC7450M95rCF8JpRwkoni1kEDibyAux9B12Q,10848
 sapiopycommons/recordmodel/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
@@ -44,7 +44,7 @@ sapiopycommons/rules/on_save_rule_handler.py,sha256=Rkqvph20RbNq6m-RF4fbvCP-YfD2
 sapiopycommons/webhook/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 sapiopycommons/webhook/webhook_handlers.py,sha256=jwc4xu-wwl8haS5k1dENZ1UIYK9GQk74TAo3CGxMW9U,16583
 sapiopycommons/webhook/webservice_handlers.py,sha256=1J56zFI0pWl5MHoNTznvcZumITXgAHJMluj8-2BqYEw,3315
-sapiopycommons-2024.9.4a323.dist-info/METADATA,sha256=bM7wn8uKO7Ek13P7T1t8hXt7Y7h5WFN07g0xmKbew1U,3175
-sapiopycommons-2024.9.4a323.dist-info/WHEEL,sha256=1yFddiXMmvYK7QYTqtRNtX66WJ0Mz8PYEiEUoOUUxRY,87
-sapiopycommons-2024.9.4a323.dist-info/licenses/LICENSE,sha256=HyVuytGSiAUQ6ErWBHTqt1iSGHhLmlC8fO7jTCuR8dU,16725
-sapiopycommons-2024.9.4a323.dist-info/RECORD,,
+sapiopycommons-2024.9.6a325.dist-info/METADATA,sha256=NwL6x_WCcT82lr4t5YN-C5eIWyXrW7rKNEL2_GE9s9Y,3175
+sapiopycommons-2024.9.6a325.dist-info/WHEEL,sha256=1yFddiXMmvYK7QYTqtRNtX66WJ0Mz8PYEiEUoOUUxRY,87
+sapiopycommons-2024.9.6a325.dist-info/licenses/LICENSE,sha256=HyVuytGSiAUQ6ErWBHTqt1iSGHhLmlC8fO7jTCuR8dU,16725
+sapiopycommons-2024.9.6a325.dist-info/RECORD,,