stjames 0.0.70__py3-none-any.whl → 0.0.71__py3-none-any.whl

stjames/atomium_stjames/mmcif.py

@@ -425,7 +425,7 @@ def update_models_list(mmcif_dict: dict[str, Any], data_dict: dict[str, Any]) ->
 
     data_dict["models"] = []
     types = {e["id"]: e["type"] for e in mmcif_dict.get("entity", {})}
-    names = {e["id"]: e["name"] for e in mmcif_dict.get("chem_comp", {}) if e["mon_nstd_flag"] != "y"}
+    names = {e["id"]: e["name"] for e in mmcif_dict.get("chem_comp", {}) if e.get("mon_nstd_flag", "n") != "y"}
     entities = {m["id"]: m["entity_id"] for m in mmcif_dict.get("struct_asym", [])}
 
     # sequences = make_sequences(mmcif_dict)

stjames/workflows/__init__.py

@@ -18,6 +18,7 @@ from .macropka import *
 from .molecular_dynamics import *
 from .multistage_opt import *
 from .pka import *
+from .protein_cofolding import *
 from .redox_potential import *
 from .scan import *
 from .solubility import *
@@ -42,6 +43,7 @@ WORKFLOW_NAME = Literal[
     "molecular_dynamics",
     "multistage_opt",
     "pka",
+    "protein_cofolding",
     "redox_potential",
     "scan",
     "solubility",
@@ -70,5 +72,6 @@ WORKFLOW_MAPPING: dict[WORKFLOW_NAME, Workflow] = {
     "scan": ScanWorkflow,  # type: ignore [dict-item]
     "solubility": SolubilityWorkflow,  # type: ignore [dict-item]
     "spin_states": SpinStatesWorkflow,  # type: ignore [dict-item]
+    "protein_cofolding": ProteinCofoldingWorkflow,  # type: ignore [dict-item]
     "tautomers": TautomerWorkflow,  # type: ignore [dict-item]
 }

stjames/workflows/macropka.py

@@ -45,24 +45,35 @@ class MacropKaWorkflow(SMILESWorkflow):
     :param initial_smiles:
 
     New:
-    :param temperature: the temperature, in K
-    :param min_pH: for precomputed microstate weights
-    :param max_pH: for precomputed microstate weights
+    :param min_pH: for precomputed microstate weights, logD, etc
+    :param max_pH: for precomputed microstate weights, logD, etc
+    :param max_charge: max charge to consider for microstates
+    :param min_charge: min charge to consider for microstates
+    :param compute_aqueous_solubility: whether or not to compute aqueous solubility
+    :param compute_solvation_energy: whether to run a csearch + compute the solvation energy (for Kpuu)
 
     Results:
     :param microstates: microstates
     :param pKa_values: macroscopic pKa values
-    :param microstate_weights_by_pH: precompute the % of different microstates
+    :param isoelectric_point: the isoelectric point (in pH units)
+    :param solvation_energy: the solvation energy, in kcal/mol
+    :param microstate_weights_by_pH: the % of different microstates by pH
+    :param logD_by_pH: the distribution constant (water/octanol) by pH
+    :param aqueous_solubility_by_pH: the log(S)/L of the compound in water, by pH
     """
 
     min_pH: Annotated[float, AfterValidator(round_float(3))] = 0.0
     max_pH: Annotated[float, AfterValidator(round_float(3))] = 14.0
-
     max_charge: int = 2
     min_charge: int = -2
+    compute_aqueous_solubility: bool = False
+    compute_solvation_energy: bool = True
 
     microstates: list[MacropKaMicrostate] = []
     pKa_values: list[MacropKaValue] = []
+    isoelectric_point: Annotated[Optional[float], AfterValidator(round_float(3))] = None
+    solvation_energy: Annotated[Optional[float], AfterValidator(round_float(3))] = None
+
     microstate_weights_by_pH: list[
         tuple[
             Annotated[float, AfterValidator(round_float(3))],
@@ -70,8 +81,6 @@ class MacropKaWorkflow(SMILESWorkflow):
         ]
     ] = []
 
-    isoelectric_point: Annotated[Optional[float], AfterValidator(round_float(3))] = None
-
     logD_by_pH: list[
         tuple[
             Annotated[float, AfterValidator(round_float(3))],

stjames/workflows/protein_cofolding.py

@@ -0,0 +1,31 @@
+"""Protein Cofolding Workflow."""
+
+from pydantic import BaseModel
+
+from ..types import UUID
+from .workflow import FASTAWorkflow
+
+
+class CofoldingScores(BaseModel):
+    confidence_score: float
+    ptm: float  # predicted template modelling score
+    iptm: float  # interface predicted template modelling score
+
+
+class ProteinCofoldingWorkflow(FASTAWorkflow):
+    """
+    A workflow for predicting structures. Especially protein structures.
+
+    Inherited:
+    :param initial_fasta: fasta string of interest
+
+    New:
+    :param use_msa_server: whether to use the MSA server
+    :param use_templates_server: whether to use the templates server
+    :param predicted_structure_uuid: UUID of the predicted structure
+    """
+
+    use_msa_server: bool = False
+    use_templates_server: bool = False
+    predicted_structure_uuid: UUID | None = None
+    scores: CofoldingScores | None = None

stjames/workflows/workflow.py

@@ -22,6 +22,19 @@ class Workflow(Base):
         return repr(self)
 
 
+class FASTAWorkflow(Workflow):
+    """
+    Base class for Workflows that operate on a fasta string.
+
+    :param initial_fasta: fasta string of interest
+    """
+
+    initial_fasta: str
+
+    def __repr__(self) -> str:
+        return f"<{type(self).__name__} {self.initial_fasta}>"
+
+
 class SMILESWorkflow(Workflow):
     """
     Base class for Workflows that operate on a single SMILES string.

{stjames-0.0.70.dist-info → stjames-0.0.71.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: stjames
-Version: 0.0.70
+Version: 0.0.71
 Summary: standardized JSON atom/molecule encoding scheme
 Author-email: Corin Wagen <corin@rowansci.com>
 Project-URL: Homepage, https://github.com/rowansci/stjames

{stjames-0.0.70.dist-info → stjames-0.0.71.dist-info}/RECORD

@@ -27,7 +27,7 @@ stjames/thermochem_settings.py,sha256=ZTLz31v8Ltutde5Nfm0vH5YahWjcfFWfr_R856Kffx
 stjames/types.py,sha256=rs2CdpkruIfU-PS98rjr9HAJNFGdZDB_zl-u3wa5rAs,4092
 stjames/atomium_stjames/__init__.py,sha256=gZkzC7i9D_fmWUTN55gtygITo3-qvJUda5CXLR0jyCQ,306
 stjames/atomium_stjames/data.py,sha256=-hzwBpTHq5JetsOVyopUJswKnKAkMtJ_XkONxjXVupU,5675
-stjames/atomium_stjames/mmcif.py,sha256=B5t_gxvMTG8OblXUWF0dnKgOHhn-8bufOv_a7ccbiqU,27081
+stjames/atomium_stjames/mmcif.py,sha256=em1fNt6577OaUjL7Pctru7aJp3ceZ9kEnj5w6BRWdVs,27090
 stjames/atomium_stjames/pdb.py,sha256=C2mEcBDDrnoXD9ZCMIH2uJpjiWPJy6ktXq8IFZsrQKM,22482
 stjames/atomium_stjames/utilities.py,sha256=-YtM7sRMvMk0wWrC3svWUWH4CGI0NtY77nXsg9tjHfc,4964
 stjames/data/__init__.py,sha256=O59Ksp7AIqwOELCWymfCx7YeBzwNOGCMlGQi7tNLqiE,24
@@ -37,7 +37,7 @@ stjames/data/isotopes.json,sha256=5ba8QnLrHD_Ypv2xekv2cIRwYrX3MQ19-1FOFtt0RuU,83
 stjames/data/nist_isotopes.json,sha256=d5DNk1dX0iB1waEYIRR6JMHuA7AuYwSBEgBvb4EKyhM,14300
 stjames/data/read_nist_isotopes.py,sha256=y10FNjW43QpC45qib7VHsIghEwT7GG5rsNwHdc9osRI,3309
 stjames/data/symbol_element.json,sha256=vl_buFusTqBd-muYQtMLtTDLy2OtBI6KkBeqkaWRQrg,1186
-stjames/workflows/__init__.py,sha256=X8uBwvmpaP38QQxYlvl9TbejEnnujpyWCLbxq0gRKao,2512
+stjames/workflows/__init__.py,sha256=rC4KfLzrOKr5FlS4uT3UW1s36-y32vp20VGCw0iHQp0,2649
 stjames/workflows/admet.py,sha256=h8ph6oeRCxU3-_jqRRWPg3RZcheu9JzCHiWqSC9VYKY,1296
 stjames/workflows/basic_calculation.py,sha256=ZX3KwhfyyCTjc2ougQIL4If7gtwZP9WjqpL45mBquW0,573
 stjames/workflows/bde.py,sha256=hdTjwma5L9SrU5F5r6dB1ruB_B6buBUtZHf2sanNW2k,9802
@@ -50,18 +50,19 @@ stjames/workflows/fukui.py,sha256=T6TDg-lcE-sfTDVpa3KFBenLe7PGUO2QrQ2jNuw_iiU,17
 stjames/workflows/hydrogen_bond_basicity.py,sha256=XDpHEluw6DQ9Zk5g2Je2a81HqIkqPglZ-6f2YZnd4Bc,1159
 stjames/workflows/ion_mobility.py,sha256=e6XSidrud5qSkrAcjzOzgHaf-G09JoP09V76myjdyjc,1097
 stjames/workflows/irc.py,sha256=ZP7icylW8rgo_Uh7h3bmyumn0ru1IyF-61nP5Jnmq3M,3402
-stjames/workflows/macropka.py,sha256=k7ebG4s-GoTG3ZKxq-OQ7gmzT8Yaq_Zd4pkL7pqL_pI,2827
+stjames/workflows/macropka.py,sha256=jFdo0log2ZDeqXYcLpGHq3L9zEUJLBgVQhzrwtKCM44,3566
 stjames/workflows/molecular_dynamics.py,sha256=kxugE73Ntzpj-xpJSoQ1EwGzXXdvi_NTyeP4913EVwE,3173
 stjames/workflows/multistage_opt.py,sha256=pPLAZDztHd37q8cxCUkdq8EzOFyrTzZJHNfDV5auiHs,13638
 stjames/workflows/pka.py,sha256=j3vBh2YM3nJzJ1XJKPsmYahRCeaU9n3P-G-u9_moaFw,2065
+stjames/workflows/protein_cofolding.py,sha256=woDdmyMYVhrmOyB55mxIP56Rpw6iElDoS5YiX5oyixY,883
 stjames/workflows/redox_potential.py,sha256=7S18t9Y3eynSnA3lZbRlvLfdbgeBopdiigLzt1zxg5c,3871
 stjames/workflows/scan.py,sha256=DXQBpa2t2PowAtOwmdgpxaSLq--fEShljzAGSb8Nf5U,2993
 stjames/workflows/solubility.py,sha256=kGfVyPPGDLRpf2j6dSY7woCkfsoXSbUzdSImA4mcMpw,1898
 stjames/workflows/spin_states.py,sha256=0degmE-frovgoXweshZyjfjqL7nkbaFoO9YoJhvQnaI,4748
 stjames/workflows/tautomer.py,sha256=7eYKziGPg8Km6lfowTzSkgJfJ4SHUPrAmnTf8Bi-SB0,1164
-stjames/workflows/workflow.py,sha256=sk2BUz59wdIkT_EyKOnMt5woNrjo3aHVK38cU8x8I7Q,1423
-stjames-0.0.70.dist-info/licenses/LICENSE,sha256=i7ehYBS-6gGmbTcgU4mgk28pyOx2kScJ0kcx8n7bWLM,1084
-stjames-0.0.70.dist-info/METADATA,sha256=MOZJAAQ9roamz5kJ2Y5_vzOmCU97hPvzi_4pG6KhVDM,1694
-stjames-0.0.70.dist-info/WHEEL,sha256=CmyFI0kx5cdEMTLiONQRbGQwjIoR1aIYB7eCAQ4KPJ0,91
-stjames-0.0.70.dist-info/top_level.txt,sha256=FYCwxl6quhYOAgG-mnPQcCK8vsVM7B8rIUrO-WrQ_PI,8
-stjames-0.0.70.dist-info/RECORD,,
+stjames/workflows/workflow.py,sha256=dmJbjI3Ng95zHEZd1Qkhhk5Eb1aF4W36Oy_GwZPJdBk,1704
+stjames-0.0.71.dist-info/licenses/LICENSE,sha256=i7ehYBS-6gGmbTcgU4mgk28pyOx2kScJ0kcx8n7bWLM,1084
+stjames-0.0.71.dist-info/METADATA,sha256=jFy2RQUS3wHe4vRo0w-OZskC6Yk3ctdMAhYhDrNPE-Q,1694
+stjames-0.0.71.dist-info/WHEEL,sha256=CmyFI0kx5cdEMTLiONQRbGQwjIoR1aIYB7eCAQ4KPJ0,91
+stjames-0.0.71.dist-info/top_level.txt,sha256=FYCwxl6quhYOAgG-mnPQcCK8vsVM7B8rIUrO-WrQ_PI,8
+stjames-0.0.71.dist-info/RECORD,,