sapiopycommons 2024.10.31a349__py3-none-any.whl → 2024.11.7a354__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.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
     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/flowcyto/flow_cyto.py

@@ -0,0 +1,77 @@
+from __future__ import annotations
+
+from weakref import WeakValueDictionary
+
+from sapiopylib.rest.User import SapioUser
+from databind.json import dumps
+
+from sapiopycommons.flowcyto.flowcyto_data import FlowJoWorkspaceInputJson, UploadFCSInputJson, \
+    ComputeFlowStatisticsInputJson
+
+
+class FlowCytoManager:
+    """
+    This manager includes flow cytometry analysis tools that would require FlowCyto license to use.
+    """
+    _user: SapioUser
+
+    __instances: WeakValueDictionary[SapioUser, FlowCytoManager] = WeakValueDictionary()
+    __initialized: bool
+
+    def __new__(cls, user: SapioUser):
+        """
+        Observes singleton pattern per record model manager object.
+
+        :param user: The user that will make the webservice request to the application.
+        """
+        obj = cls.__instances.get(user)
+        if not obj:
+            obj = object.__new__(cls)
+            obj.__initialized = False
+            cls.__instances[user] = obj
+        return obj
+
+    def __init__(self, user: SapioUser):
+        if self.__initialized:
+            return
+        self._user = user
+        self.__initialized = True
+
+    def create_flowjo_workspace(self, workspace_input: FlowJoWorkspaceInputJson) -> int:
+        """
+        Create FlowJo Workspace and return the workspace record ID of workspace root record,
+        after successful creation.
+        :param workspace_input: the request data payload.
+        :return: The new workspace record ID.
+        """
+        payload = dumps(workspace_input, FlowJoWorkspaceInputJson)
+        response = self._user.plugin_post("flowcyto/workspace", payload=payload, is_payload_plain_text=True)
+        self._user.raise_for_status(response)
+        return int(response.json())
+
+    def upload_fcs_for_sample(self, upload_input: UploadFCSInputJson) -> int:
+        """
+        Upload FCS file as root of the sample FCS.
+        :param upload_input: The request data payload
+        :return: The root FCS file uploaded under sample.
+        """
+        payload = dumps(upload_input, UploadFCSInputJson)
+        response = self._user.plugin_post("flowcyto/fcs", payload=payload, is_payload_plain_text=True)
+        self._user.raise_for_status(response)
+        return int(response.json())
+
+    def compute_statistics(self, stat_compute_input: ComputeFlowStatisticsInputJson) -> list[int]:
+        """
+        Requests to compute flow cytometry statistics.
+        The children are of type FCSStatistic.
+        If the FCS files have not been evaluated yet,
+        then the lazy evaluation will be performed immediately prior to computing statistics, which can take longer.
+        If any new statistics are computed as children of FCS, they will be returned in the result record id list.
+        Note: if input has multiple FCS files, the client should try to get parent FCS file from each record to figure out which one is for which FCS.
+        :param stat_compute_input:
+        :return:
+        """
+        payload = dumps(stat_compute_input, ComputeFlowStatisticsInputJson)
+        response = self._user.plugin_post("flowcyto/statistics", payload=payload, is_payload_plain_text=True)
+        self._user.raise_for_status(response)
+        return list(response.json())

sapiopycommons/flowcyto/flowcyto_data.py

@@ -0,0 +1,75 @@
+import base64
+from enum import Enum
+
+from databind.core.dataclasses import dataclass
+
+
+class ChannelStatisticType(Enum):
+    """
+    All supported channel statistics type.
+    """
+    MEAN = "(Mean) MFI"
+    MEDIAN = "(Median) MFI"
+    STD_EV = "Std. Dev."
+    COEFFICIENT_OF_VARIATION = "CV"
+
+    display_name: str
+
+    def __init__(self, display_name: str):
+        self.display_name = display_name
+
+
+@dataclass
+class ChannelStatisticsParameterJSON:
+    channelNameList: list[str]
+    statisticsType: ChannelStatisticType
+
+    def __init__(self, channel_name_list: list[str], stat_type: ChannelStatisticType):
+        self.channelNameList = channel_name_list
+        self.statisticsType = stat_type
+
+
+@dataclass
+class ComputeFlowStatisticsInputJson:
+    fcsFileRecordIdList: list[int]
+    statisticsParameterList: list[ChannelStatisticsParameterJSON]
+
+    def __init__(self, fcs_file_record_id_list: list[int], statistics_parameter_list: list[ChannelStatisticsParameterJSON]):
+        self.fcsFileRecordIdList = fcs_file_record_id_list
+        self.statisticsParameterList = statistics_parameter_list
+
+
+@dataclass
+class FlowJoWorkspaceInputJson:
+    filePath: str
+    base64Data: str
+
+    def __init__(self, filePath: str, file_data: bytes):
+        self.filePath = filePath
+        self.base64Data = base64.b64encode(file_data).decode('utf-8')
+
+
+@dataclass
+class UploadFCSInputJson:
+    """
+    Request to upload new FCS file
+    Attributes:
+        filePath: The file name of the FCS file to be uploaded. For FlowJo workspace, this is important to match the file in group (via file names).
+        attachmentDataType: the attachment data type that contains already-uploaded FCS data.
+        attachmentRecordId: the attachment record ID that contains already-uploaded FCS data.
+        associatedRecordDataType: the "parent" association for the FCS. Can either be a workspace or a sample record.
+        associatedRecordId: the "parent" association for the FCS. Can either be a workspace or a sample record.
+    """
+    filePath: str
+    attachmentDataType: str
+    attachmentRecordId: int
+    associatedRecordDataType: str
+    associatedRecordId: int
+
+    def __init__(self, associated_record_data_type: str, associated_record_id: int,
+                 file_path: str, attachment_data_type: str, attachment_record_id: int):
+        self.filePath = file_path
+        self.attachmentDataType = attachment_data_type
+        self.attachmentRecordId = attachment_record_id
+        self.associatedRecordDataType = associated_record_data_type
+        self.associatedRecordId = associated_record_id

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-2024.10.31a349.dist-info → sapiopycommons-2024.11.7a354.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.3
 Name: sapiopycommons
-Version: 2024.10.31a349
+Version: 2024.11.7a354
 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-2024.10.31a349.dist-info → sapiopycommons-2024.11.7a354.dist-info}/RECORD

@@ -2,8 +2,8 @@ sapiopycommons/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 sapiopycommons/callbacks/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 sapiopycommons/callbacks/callback_util.py,sha256=nb6cXK8yFq96gtG0Z2NiK-qdNaRh88bavUH-ZoBjh18,67953
 sapiopycommons/callbacks/field_builder.py,sha256=8n0jcbMgtMUHjie4C1-IkpAuHz4zBxbZtWpr4y0kABU,36868
-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=SQKnqdZnhYj_6HGtEZmE_1DormonRR1-nBAQ__z4gms,11485
 sapiopycommons/chem/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 sapiopycommons/customreport/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 sapiopycommons/customreport/column_builder.py,sha256=0RO53e9rKPZ07C--KcepN6_tpRw_FxF3O9vdG0ilKG8,3014
@@ -25,6 +25,8 @@ sapiopycommons/files/file_data_handler.py,sha256=SCsjODMJIPEBSsahzXUeOM7CfSCmYwP
 sapiopycommons/files/file_util.py,sha256=wbL3rxcFc-t2mXaPWWkoFWYGopvTcQts9Wf-L5GkhT8,29498
 sapiopycommons/files/file_validator.py,sha256=4OvY98ueJWPJdpndwnKv2nqVvLP9S2W7Il_dM0Y0ojo,28709
 sapiopycommons/files/file_writer.py,sha256=96Xl8TTT46Krxe_J8rmmlEMtel4nzZB961f5Yqtl1-I,17616
+sapiopycommons/flowcyto/flow_cyto.py,sha256=YlkKJR_zEHYRuNW0bnTqlTyZeXs0lOaeSCfG2fnfD7E,3227
+sapiopycommons/flowcyto/flowcyto_data.py,sha256=mYKFuLbtpJ-EsQxLGtu4tNHVlygTxKixgJxJqD68F58,2596
 sapiopycommons/general/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 sapiopycommons/general/accession_service.py,sha256=HYgyOsH_UaoRnoury-c2yTW8SeG4OtjLemdpCzoV4R8,13484
 sapiopycommons/general/aliases.py,sha256=tdDBNWSGx6s39eHJ3n2kscc4xxW3ZYaUfDftct6FmJE,12910
@@ -36,7 +38,7 @@ sapiopycommons/general/sapio_links.py,sha256=o9Z-8y2rz6AI0Cy6tq58ElPge9RBnisGc9N
 sapiopycommons/general/storage_util.py,sha256=ovmK_jN7v09BoX07XxwShpBUC5WYQOM7dbKV_VeLXJU,8892
 sapiopycommons/general/time_util.py,sha256=jUAWmQLNcLHZa4UYB4ht_I3d6uoi63VxYdo7T80Ydw0,7458
 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/custom_workflow_handler.py,sha256=0Si5RQ1YFmqmcZWV8jNDKTffix2iZnQJ6b97fn31pbc,23859
 sapiopycommons/processtracking/endpoints.py,sha256=w5bziI2xC7450M95rCF8JpRwkoni1kEDibyAux9B12Q,10848
@@ -51,7 +53,7 @@ sapiopycommons/webhook/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3
 sapiopycommons/webhook/webhook_context.py,sha256=D793uLsb1691SalaPnBUk3rOSxn_hYLhdvkaIxjNXss,1909
 sapiopycommons/webhook/webhook_handlers.py,sha256=JTquLBln49L1pJ9txJ4oc4Hpzy9kYtMKs0m4SLaFx78,18363
 sapiopycommons/webhook/webservice_handlers.py,sha256=1J56zFI0pWl5MHoNTznvcZumITXgAHJMluj8-2BqYEw,3315
-sapiopycommons-2024.10.31a349.dist-info/METADATA,sha256=1yXjlgfQmY1pFMmsMGgstHmji3QgQZIh20HuYKXA3Hc,3177
-sapiopycommons-2024.10.31a349.dist-info/WHEEL,sha256=1yFddiXMmvYK7QYTqtRNtX66WJ0Mz8PYEiEUoOUUxRY,87
-sapiopycommons-2024.10.31a349.dist-info/licenses/LICENSE,sha256=HyVuytGSiAUQ6ErWBHTqt1iSGHhLmlC8fO7jTCuR8dU,16725
-sapiopycommons-2024.10.31a349.dist-info/RECORD,,
+sapiopycommons-2024.11.7a354.dist-info/METADATA,sha256=n4E46KTnsKNHfAy2cPXalibDb5jALEdZVfaveMktPfc,3176
+sapiopycommons-2024.11.7a354.dist-info/WHEEL,sha256=1yFddiXMmvYK7QYTqtRNtX66WJ0Mz8PYEiEUoOUUxRY,87
+sapiopycommons-2024.11.7a354.dist-info/licenses/LICENSE,sha256=HyVuytGSiAUQ6ErWBHTqt1iSGHhLmlC8fO7jTCuR8dU,16725
+sapiopycommons-2024.11.7a354.dist-info/RECORD,,