sapiopycommons 2024.11.7a354__py3-none-any.whl → 2024.11.8a359__py3-none-any.whl

sapiopycommons/chem/IndigoMolecules.py

@@ -6,10 +6,8 @@ indigo = Indigo()
 renderer = IndigoRenderer(indigo)
 indigo.setOption("render-output-format", "svg")
 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

@@ -1,6 +1,5 @@
 # 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
@@ -21,25 +20,6 @@ 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
@@ -106,6 +86,7 @@ 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.
@@ -115,7 +96,7 @@ def mol_to_sapio_partial_pojo(mol: Mol):
     Chem.SanitizeMol(mol)
     mol.UpdatePropertyCache()
     smiles = Chem.MolToSmiles(mol)
-    molBlock = Chem.MolToMolBlock(mol, forceV3000=True)
+    molBlock = Chem.MolToMolBlock(mol)
     img = mol_to_img(mol)
     molecule = dict()
     molecule["smiles"] = smiles
@@ -124,52 +105,23 @@ def mol_to_sapio_partial_pojo(mol: Mol):
     return molecule
 
 
-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,
+def mol_to_sapio_substance(mol: Mol, include_stereoisomers: bool = False,
                            normalize: bool = False, remove_salt: bool = False, make_images: bool = False,
-                           salt_def: str | None = None, canonical_tautomer: bool = True,
-                           enhanced_stereo: bool = False, remove_atom_map: bool = True):
+                           salt_def: str | None = None, canonical_tautomer: 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)
@@ -205,7 +157,7 @@ def mol_to_sapio_substance(mol: Mol, include_stereoisomers=False,
     exactMass = Descriptors.ExactMolWt(mol)
     molFormula = rdMolDescriptors.CalcMolFormula(mol)
     charge = Chem.GetFormalCharge(mol)
-    molBlock = Chem.MolToMolBlock(mol, forceV3000=True)
+    molBlock = Chem.MolToMolBlock(mol)
 
     molecule["cLogP"] = cLogP
     molecule["tpsa"] = tpsa
@@ -229,38 +181,27 @@ def mol_to_sapio_substance(mol: Mol, include_stereoisomers=False,
     # We need to test the INCHI can be loaded back to indigo.
     indigo_mol = indigo.loadMolecule(molBlock)
     indigo_mol.aromatize()
-    if enhanced_stereo:
-        # Remove enhanced stereo layer when generating InChI as the stereo hash is generated separately for reg.
-        mol_copy: Mol = Chem.Mol(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
+    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=False, enhanced_stereo: bool = False,
+def mol_to_sapio_compound(mol: Mol, include_stereoisomers: bool = False,
                           salt_def: str | None = None, resolve_canonical: bool = True,
-                          make_images: bool = False, canonical_tautomer: bool = True,
-                          remove_atom_map: bool = True):
+                          make_images: bool = False, canonical_tautomer: bool = True):
     ret = dict()
-    ret['originalMol'] = mol_to_sapio_substance(mol, include_stereoisomers=False,
+    ret['originalMol'] = mol_to_sapio_substance(mol, include_stereoisomers,
                                                 normalize=False, remove_salt=False, make_images=make_images,
-                                                canonical_tautomer=canonical_tautomer,
-                                                enhanced_stereo=enhanced_stereo, remove_atom_map=remove_atom_map)
+                                                canonical_tautomer=canonical_tautomer)
     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,
-                                                     enhanced_stereo=enhanced_stereo, remove_atom_map=remove_atom_map)
+                                                     salt_def=salt_def, canonical_tautomer=canonical_tautomer)
     return ret

sapiopycommons/datatype/attachment_util.py

@@ -1,9 +1,10 @@
 import io
 
-from sapiopylib.rest.DataMgmtService import DataMgmtServer
+from sapiopylib.rest.User import SapioUser
+from sapiopylib.rest.pojo.webhook.WebhookContext import SapioWebhookContext
 from sapiopylib.rest.utils.recordmodel.RecordModelWrapper import WrappedType
 
-from sapiopycommons.general.aliases import AliasUtil, SapioRecord, UserIdentifier
+from sapiopycommons.general.aliases import AliasUtil, SapioRecord
 from sapiopycommons.general.exceptions import SapioException
 from sapiopycommons.recordmodel.record_handler import RecordHandler
 
@@ -11,32 +12,31 @@ from sapiopycommons.recordmodel.record_handler import RecordHandler
 # FR-46064 - Initial port of PyWebhookUtils to sapiopycommons.
 class AttachmentUtil:
     @staticmethod
-    def get_attachment_bytes(context: UserIdentifier, attachment: SapioRecord) -> bytes:
+    def get_attachment_bytes(context: SapioWebhookContext, attachment: SapioRecord) -> bytes:
         """
         Get the data bytes for the given attachment record. Makes a webservice call to retrieve the data.
 
-        :param context: The current webhook context or a user object to send requests from.
+        :param context: The current webhook context.
         :param attachment: The attachment record.
         :return: The bytes for the attachment's file data.
         """
         attachment = AliasUtil.to_data_record(attachment)
-        dr_man = DataMgmtServer.get_data_record_manager(AliasUtil.to_sapio_user(context))
         with io.BytesIO() as data_sink:
             def consume_data(chunk: bytes):
                 data_sink.write(chunk)
-            dr_man.get_attachment_data(attachment, consume_data)
+            context.data_record_manager.get_attachment_data(attachment, consume_data)
             data_sink.flush()
             data_sink.seek(0)
             file_bytes = data_sink.read()
         return file_bytes
 
     @staticmethod
-    def set_attachment_bytes(context: UserIdentifier, attachment: SapioRecord,
+    def set_attachment_bytes(context: SapioWebhookContext, attachment: SapioRecord,
                              file_name: str, file_bytes: bytes) -> None:
         """
         Set the attachment data for a given attachment record. Makes a webservice call to set the data.
 
-        :param context: The current webhook context or a user object to send requests from.
+        :param context: The current webhook context.
         :param attachment: The attachment record. Must be an existing data record that is an attachment type.
         :param file_name: The name of the attachment.
         :param file_bytes: The bytes of the attachment data.
@@ -45,12 +45,11 @@ class AttachmentUtil:
             raise SapioException("Provided record cannot have its attachment data set, as it does not exist in the "
                                  "system yet.")
         attachment = AliasUtil.to_data_record(attachment)
-        dr_man = DataMgmtServer.get_data_record_manager(AliasUtil.to_sapio_user(context))
         with io.BytesIO(file_bytes) as stream:
-            dr_man.set_attachment_data(attachment, file_name, stream)
+            context.data_record_manager.set_attachment_data(attachment, file_name, stream)
 
     @staticmethod
-    def create_attachment(context: UserIdentifier, file_name: str, file_bytes: bytes,
+    def create_attachment(context: SapioWebhookContext | SapioUser, file_name: str, file_bytes: bytes,
                           wrapper_type: type[WrappedType]) -> WrappedType:
         """
         Create an attachment data type and initialize its attachment bytes at the same time.