sapiopycommons 2024.9.5a324__tar.gz → 2024.9.6a326__tar.gz

{sapiopycommons-2024.9.5a324 → sapiopycommons-2024.9.6a326}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.3
 Name: sapiopycommons
-Version: 2024.9.5a324
+Version: 2024.9.6a326
 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-2024.9.5a324 → sapiopycommons-2024.9.6a326}/pyproject.toml

@@ -4,7 +4,7 @@ build-backend = "hatchling.build"
 
 [project]
 name = "sapiopycommons"
-version='2024.09.05a324'
+version='2024.09.06a326'
 authors = [
     { name="Jonathan Steck", email="jsteck@sapiosciences.com" },
     { name="Yechen Qiao", email="yqiao@sapiosciences.com" },

{sapiopycommons-2024.9.5a324 → sapiopycommons-2024.9.6a326}/src/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-2024.9.5a324 → sapiopycommons-2024.9.6a326}/src/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-2024.9.5a324 → sapiopycommons-2024.9.6a326}/src/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-2024.9.5a324 → sapiopycommons-2024.9.6a326}/src/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-2024.9.6a326/tests/chem_test_curation_queue.py

@@ -0,0 +1,31 @@
+import unittest
+
+from sapiopycommons.multimodal.multimodal import MultiModalManager
+from sapiopycommons.multimodal.multimodal_data import *
+from data_type_models import *
+
+from sapiopylib.rest.DataMgmtService import DataMgmtServer
+from sapiopylib.rest.User import SapioUser
+
+user = SapioUser(url="https://linux-vm:8443/webservice/api", verify_ssl_cert=False,
+                 guid="ae4e92e1-34c6-4336-8d80-7f6804d3e51c",
+                 username="yqiao_api", password="Password1!")
+
+multi_modal_manager = MultiModalManager(user)
+
+
+class ChemCurationTest(unittest.TestCase):
+    def test_curation_reg(self):
+        with open("curation_queue_test.sdf", "rb") as f:
+            file_data: bytes = f.read()
+            loader_result = multi_modal_manager.load_compounds(
+                CompoundLoadRequestPojo(ChemicalReagentPartModel.DATA_TYPE_NAME, ChemLoadType.SDF_FILE,
+                                        file_data=file_data))
+            compound_list = loader_result.compoundList
+            for compound in compound_list:
+                self.assertTrue(compound.originalMol.CXSMILESHash)
+                self.assertTrue(compound.originalMol.registrationHash)
+            multi_modal_manager.register_compounds(ChemRegisterRequestPojo(
+                ChemicalReagentPartModel.DATA_TYPE_NAME, compound_list))
+            # User manually log in and resolve the curation queue.
+            print("Loaded! Now play with curation queue inside Sapio!")

sapiopycommons-2024.9.6a326/tests/curation_queue_test.sdf

@@ -0,0 +1,168 @@
+
+  -INDIGO-07302413292D
+
+  0  0  0  0  0  0  0  0  0  0  0 V3000
+M  V30 BEGIN CTAB
+M  V30 COUNTS 12 13 0 0 0
+M  V30 BEGIN ATOM
+M  V30 1 C 19.7652 6.17863 0.0 0
+M  V30 2 C 19.4069 5.24519 0.0 0
+M  V30 3 C 18.4082 5.29746 0.0 0
+M  V30 4 C 18.1494 6.26337 0.0 0
+M  V30 5 C 18.9881 6.80795 0.0 0
+M  V30 6 C 19.9516 4.40647 0.0 0
+M  V30 7 C 20.9461 4.30193 0.0 0
+M  V30 8 C 21.154 3.32371 0.0 0 CFG=1
+M  V30 9 C 20.2879 2.82375 0.0 0
+M  V30 10 C 19.5449 3.49292 0.0 0 CFG=1
+M  V30 11 I 18.5667 3.28501 0.0 0
+M  V30 12 C 22.0676 2.91705 0.0 0
+M  V30 END ATOM
+M  V30 BEGIN BOND
+M  V30 1 1 1 2
+M  V30 2 1 2 3
+M  V30 3 1 3 4
+M  V30 4 1 4 5
+M  V30 5 1 5 1
+M  V30 6 1 2 6
+M  V30 7 1 6 7
+M  V30 8 1 7 8
+M  V30 9 1 8 9
+M  V30 10 1 9 10
+M  V30 11 1 10 6
+M  V30 12 1 10 11 CFG=1
+M  V30 13 1 8 12 CFG=3
+M  V30 END BOND
+M  V30 BEGIN COLLECTION
+M  V30 MDLV30/STEREL1 ATOMS=(1 8)
+M  V30 MDLV30/STEABS ATOMS=(1 10)
+M  V30 END COLLECTION
+M  V30 END CTAB
+M  END
+$$$$
+
+  -INDIGO-07302413312D
+
+  0  0  0  0  0  0  0  0  0  0  0 V3000
+M  V30 BEGIN CTAB
+M  V30 COUNTS 12 13 0 0 0
+M  V30 BEGIN ATOM
+M  V30 1 C 16.3152 -4.32137 0.0 0
+M  V30 2 C 15.9569 -5.25482 0.0 0
+M  V30 3 C 14.9582 -5.20255 0.0 0
+M  V30 4 C 14.6994 -4.23663 0.0 0
+M  V30 5 C 15.5381 -3.69205 0.0 0
+M  V30 6 C 16.5016 -6.09353 0.0 0
+M  V30 7 C 17.4961 -6.19807 0.0 0
+M  V30 8 C 17.704 -7.17629 0.0 0 CFG=2
+M  V30 9 C 16.8379 -7.67626 0.0 0
+M  V30 10 C 16.0949 -7.00708 0.0 0 CFG=1
+M  V30 11 I 15.1167 -7.21499 0.0 0
+M  V30 12 C 18.6176 -7.58295 0.0 0
+M  V30 END ATOM
+M  V30 BEGIN BOND
+M  V30 1 1 1 2
+M  V30 2 1 2 3
+M  V30 3 1 3 4
+M  V30 4 1 4 5
+M  V30 5 1 5 1
+M  V30 6 1 2 6
+M  V30 7 1 6 7
+M  V30 8 1 7 8
+M  V30 9 1 8 9
+M  V30 10 1 9 10
+M  V30 11 1 10 6
+M  V30 12 1 10 11 CFG=1
+M  V30 13 1 8 12 CFG=1
+M  V30 END BOND
+M  V30 BEGIN COLLECTION
+M  V30 MDLV30/STEREL1 ATOMS=(1 8)
+M  V30 MDLV30/STEABS ATOMS=(1 10)
+M  V30 END COLLECTION
+M  V30 END CTAB
+M  END
+$$$$
+
+  -INDIGO-07302413322D
+
+  0  0  0  0  0  0  0  0  0  0  0 V3000
+M  V30 BEGIN CTAB
+M  V30 COUNTS 12 13 0 0 0
+M  V30 BEGIN ATOM
+M  V30 1 C 19.7652 -4.32136 0.0 0
+M  V30 2 C 19.4068 -5.25486 0.0 0
+M  V30 3 C 18.4082 -5.20257 0.0 0
+M  V30 4 C 18.1494 -4.23667 0.0 0
+M  V30 5 C 18.9881 -3.69209 0.0 0
+M  V30 6 C 19.9515 -6.09354 0.0 0
+M  V30 7 C 20.9461 -6.19803 0.0 0
+M  V30 8 C 21.154 -7.17622 0.0 0 CFG=1
+M  V30 9 C 20.288 -7.67621 0.0 0
+M  V30 10 C 19.5448 -7.00704 0.0 0 CFG=1
+M  V30 11 I 18.5666 -7.21491 0.0 0
+M  V30 12 C 22.0676 -7.58291 0.0 0
+M  V30 END ATOM
+M  V30 BEGIN BOND
+M  V30 1 1 1 2
+M  V30 2 1 2 3
+M  V30 3 1 3 4
+M  V30 4 1 4 5
+M  V30 5 1 5 1
+M  V30 6 1 2 6
+M  V30 7 1 6 7
+M  V30 8 1 7 8
+M  V30 9 1 8 9
+M  V30 10 1 9 10
+M  V30 11 1 10 6
+M  V30 12 1 10 11 CFG=1
+M  V30 13 1 8 12 CFG=3
+M  V30 END BOND
+M  V30 BEGIN COLLECTION
+M  V30 MDLV30/STERAC1 ATOMS=(1 8)
+M  V30 MDLV30/STEABS ATOMS=(1 10)
+M  V30 END COLLECTION
+M  V30 END CTAB
+M  END
+$$$$
+
+  -INDIGO-07302413322D
+
+  0  0  0  0  0  0  0  0  0  0  0 V3000
+M  V30 BEGIN CTAB
+M  V30 COUNTS 12 13 0 0 0
+M  V30 BEGIN ATOM
+M  V30 1 C 16.3152 -4.32137 0.0 0
+M  V30 2 C 15.9569 -5.25481 0.0 0
+M  V30 3 C 14.9582 -5.20255 0.0 0
+M  V30 4 C 14.6994 -4.23663 0.0 0
+M  V30 5 C 15.5381 -3.69205 0.0 0
+M  V30 6 C 16.5016 -6.09353 0.0 0
+M  V30 7 C 17.4961 -6.19806 0.0 0
+M  V30 8 C 17.704 -7.17629 0.0 0 CFG=2
+M  V30 9 C 16.8379 -7.67626 0.0 0
+M  V30 10 C 16.0949 -7.00708 0.0 0 CFG=1
+M  V30 11 I 15.1167 -7.21499 0.0 0
+M  V30 12 C 18.6176 -7.58295 0.0 0
+M  V30 END ATOM
+M  V30 BEGIN BOND
+M  V30 1 1 1 2
+M  V30 2 1 2 3
+M  V30 3 1 3 4
+M  V30 4 1 4 5
+M  V30 5 1 5 1
+M  V30 6 1 2 6
+M  V30 7 1 6 7
+M  V30 8 1 7 8
+M  V30 9 1 8 9
+M  V30 10 1 9 10
+M  V30 11 1 10 6
+M  V30 12 1 10 11 CFG=1
+M  V30 13 1 8 12 CFG=1
+M  V30 END BOND
+M  V30 BEGIN COLLECTION
+M  V30 MDLV30/STERAC1 ATOMS=(1 8)
+M  V30 MDLV30/STEABS ATOMS=(1 10)
+M  V30 END COLLECTION
+M  V30 END CTAB
+M  END
+$$$$