stjames 0.0.63__py3-none-any.whl → 0.0.65__py3-none-any.whl

stjames/atomium_stjames/mmcif.py

@@ -516,7 +516,7 @@ def add_atom_to_polymer(atom: dict[str, Any], aniso: dict[int, Any], model: dict
         try:
             model["polymer"][mol_id]["residues"][res_id] = {
                 "name": name,
-                "full_name": names.get(name),
+                "full_name": names.get(name).upper() if names.get(name) is not None else None,  # type: ignore [union-attr]
                 "atoms": {int(atom["id"]): atom_dict_to_atom_dict(atom, aniso)},
                 "number": len(model["polymer"][mol_id]["residues"]) + 1,
             }
@@ -530,7 +530,7 @@ def add_atom_to_polymer(atom: dict[str, Any], aniso: dict[int, Any], model: dict
                         "name": name,
                         "atoms": {int(atom["id"]): atom_dict_to_atom_dict(atom, aniso)},
                         "number": 1,
-                        "full_name": names.get(name),
+                        "full_name": names.get(name).upper() if names.get(name) is not None else None,  # type: ignore [union-attr]
                     }
                 },
             }
@@ -547,6 +547,8 @@ def add_atom_to_non_polymer(atom: dict[str, Any], aniso: dict[int, Any], model:
     :param names: lookup dictionary for full name information
     """
     mol_id = make_residue_id(atom)
+    if mol_type == "non-polymer":
+        mol_type = "non_polymer"
 
     try:
         model[mol_type][mol_id]["atoms"][int(atom["id"])] = atom_dict_to_atom_dict(atom, aniso)
@@ -554,7 +556,7 @@ def add_atom_to_non_polymer(atom: dict[str, Any], aniso: dict[int, Any], model:
         name = atom["auth_comp_id"]
         model[mol_type][mol_id] = {
             "name": name,
-            "full_name": names.get(name),
+            "full_name": names.get(name).upper() if names.get(name) is not None and names.get(name).lower() != "water" else None,  # type: ignore [union-attr]
             "internal_id": atom["label_asym_id"],
             "polymer": atom["auth_asym_id"],
             "atoms": {int(atom["id"]): atom_dict_to_atom_dict(atom, aniso)},
@@ -644,7 +646,7 @@ def atom_dict_to_atom_dict(d: dict[str, Any], aniso_dict: dict[int, Any]) -> dic
         "bvalue": d.get("B_iso_or_equiv"),
         "charge": d.get(charge, 0) if d.get(charge) != "?" else 0,
         "alt_loc": d.get("label_alt_id") if d.get("label_alt_id") != "." else None,
-        "anisotropy": aniso_dict.get(int(d["id"]), [0, 0, 0, 0, 0, 0]),
+        "anisotropy": aniso_dict.get(int(d["id"]), None),
         "is_hetatm": d.get("group_PDB", "ATOM") == "HETATM",
     }
 

stjames/molecule.py

@@ -34,6 +34,7 @@ class VibrationalMode(Base):
     reduced_mass: Annotated[float, AfterValidator(round_float(3))]  # amu
     force_constant: Annotated[float, AfterValidator(round_float(3))]  # mDyne/Å
     displacements: Annotated[Vector3DPerAtom, AfterValidator(round_vector3d_per_atom(6))]  # Å
+    ir_intensity: Annotated[Optional[float], AfterValidator(round_optional_float(3))] = None  # km/mol
 
 
 class Molecule(Base):
@@ -68,6 +69,7 @@ class Molecule(Base):
     thermal_free_energy_corr: Annotated[Optional[float], AfterValidator(round_optional_float(6))] = None
 
     smiles: Optional[str] = None
+    calculation_index: int | None = None
 
     def __len__(self) -> int:
         return len(self.atoms)

stjames/pdb.py

@@ -204,6 +204,12 @@ def fetch_pdb(code: str) -> PDB:
     return PDB.model_validate(astj.fetch(code, data_dict=True))
 
 
+def fetch_pdb_from_mmcif(code: str) -> PDB:
+    """Fetch a pdb from the Protein Data Bank."""
+    code += ".cif"
+    return PDB.model_validate(astj.fetch(code, data_dict=True))
+
+
 def pdb_from_pdb_filestring(pdb: str) -> PDB:
     """Read a PDB from a string."""
     return PDB.model_validate(pdb_dict_to_data_dict(pdb_string_to_pdb_dict(pdb)))

stjames/workflows/__init__.py

@@ -12,6 +12,7 @@ from .docking import *
 from .electronic_properties import *
 from .fukui import *
 from .hydrogen_bond_basicity import *
+from .ion_mobility import *
 from .irc import *
 from .molecular_dynamics import *
 from .multistage_opt import *
@@ -34,6 +35,7 @@ WORKFLOW_NAME = Literal[
     "electronic_properties",
     "fukui",
     "hydrogen_bond_basicity",
+    "ion_mobility",
     "irc",
     "molecular_dynamics",
     "multistage_opt",
@@ -56,6 +58,7 @@ WORKFLOW_MAPPING: dict[WORKFLOW_NAME, Workflow] = {
     "electronic_properties": ElectronicPropertiesWorkflow,  # type: ignore [dict-item]
     "fukui": FukuiIndexWorkflow,  # type: ignore [dict-item]
     "hydrogen_bond_basicity": HydrogenBondBasicityWorkflow,  # type: ignore [dict-item]
+    "ion_mobility": IonMobilityWorkflow,  # type: ignore [dict-item]
     "irc": IRCWorkflow,  # type: ignore [dict-item]
     "molecular_dynamics": MolecularDynamicsWorkflow,  # type: ignore [dict-item]
     "multistage_opt": MultiStageOptWorkflow,  # type: ignore [dict-item]

stjames/workflows/admet.py

@@ -1,18 +1,39 @@
 """ADME-Tox property prediction workflow."""
 
-from .workflow import MoleculeWorkflow
+import warnings
+from typing import Self
 
+from pydantic import model_validator
 
-class ADMETWorkflow(MoleculeWorkflow):
+from ..molecule import Molecule
+from .workflow import MoleculeWorkflow, SMILESWorkflow
+
+
+class ADMETWorkflow(SMILESWorkflow, MoleculeWorkflow):
     """
     A workflow for predicting ADME-Tox properties.
 
     Inherited:
-    :param initial_molecule: Molecule of interest
+    :param initial_smiles: SMILES string of molecule (mutually exclusive with initial_molecule)
+    :param initial_molecule: Molecule of interest (deprecated)
     :param mode: Mode for workflow (currently unused)
 
     New:
     :param properties: predicted properties
     """
 
+    initial_smiles: str = ""
+    initial_molecule: Molecule | None = None  # type: ignore [assignment]  # Deprecated
     properties: dict[str, float | int] | None = None
+
+    @model_validator(mode="after")
+    def validate_mol_input(self) -> Self:
+        """Ensure that only one of initial_molecule or initial_smiles is set."""
+
+        if not (bool(self.initial_smiles) ^ bool(self.initial_molecule)):
+            raise ValueError("Can only set one of initial_molecule should and initial_smiles")
+
+        if self.initial_molecule is not None:
+            warnings.warn(DeprecationWarning("initial_molecule is deprecated. Use initial_smiles instead."))
+
+        return self

stjames/workflows/ion_mobility.py

@@ -0,0 +1,36 @@
+"""Ion mobility workflow."""
+
+from ..types import UUID
+from .workflow import MoleculeWorkflow
+
+
+class IonMobilityWorkflow(MoleculeWorkflow):
+    """
+    Workflow for calculating hydrogen bond basicity.
+
+    Inherited:
+    :param initial_molecule: Molecule of interest
+    :param mode: Mode for workflow (currently unused)
+
+    New:
+    :param do_csearch: whether to perform a conformational search
+    :param do_optimization: whether to perform an optimization
+
+    Results:
+    :param conformer_ccs: the collision cross section (Å**2) per conformer
+    :param conformer_ccs_stdev: the uncertainty in the same
+    :param conformer_weights: the Boltzmann weights at RT
+    :param average_ccs: the Boltzmann-weighted CCS for the ensemble
+    :param average_ccs_stdev: the uncertainty in the same
+    """
+
+    do_csearch: bool = True
+    do_optimization: bool = True
+    conformers: list[UUID] = []
+
+    conformer_ccs: list[float] = []
+    conformer_ccs_stdev: list[float] = []
+    boltzmann_weights: list[float] = []
+
+    average_ccs: float | None = None
+    average_ccs_stdev: float | None = None

stjames/workflows/macropka.py

@@ -0,0 +1,72 @@
+"""pKa workflow."""
+
+from typing import Annotated, Self
+
+from pydantic import AfterValidator, model_validator
+
+from ..base import Base, round_float
+from ..types import round_list
+from .workflow import SMILESWorkflow
+
+
+class MacropKaMicrostate(Base):
+    """
+    A microstate for pKa calculations.
+
+    :param smiles: SMILES string for this conformer
+    :param energy: free energy of this conformer
+    :param charge: the total charge
+    """
+
+    smiles: str
+    energy: Annotated[float, AfterValidator(round_float(3))]  # free energy
+    charge: int
+
+
+class MacropKaValue(Base):
+    """
+    Represents a change in pKa.
+
+    :param initial_charge: the charge of the initial state
+    :param final_charge: the charge of the final state
+    :param pKa: the pKa for the transition
+    """
+
+    initial_charge: int
+    final_charge: int
+    pKa: Annotated[float, AfterValidator(round_float(3))]
+
+
+class MacropKaWorkflow(SMILESWorkflow):
+    """
+    Workflow for calculating pKa.
+
+    Inherited:
+    :param initial_smiles:
+
+    New:
+    :param temperature: the temperature, in K
+    :param min_pH: for precomputed microstate weights
+    :param max_pH: for precomputed microstate weights
+
+    Results:
+    :param microstates: microstates
+    :param pKa_values: macroscopic pKa values
+    :param microstate_weights_by_pH: precompute the % of different microstates
+    """
+
+    temperature: Annotated[float, AfterValidator(round_float(3))] = 298.0
+    min_pH: Annotated[float, AfterValidator(round_float(3))] = 0.0
+    max_pH: Annotated[float, AfterValidator(round_float(3))] = 14.0
+
+    microstates: list[MacropKaMicrostate] = []
+    pKa_values: list[MacropKaValue] = []
+    microstate_weights_by_pH: dict[float, Annotated[list[float], AfterValidator(round_list(6))]] = {}
+
+    @model_validator(mode="after")
+    def check_weights(self) -> Self:
+        for weights in self.microstate_weights_by_pH.values():
+            if len(weights) != len(self.microstates):
+                raise ValueError("Length of microstate weights doesn't match!")
+
+        return self

stjames/workflows/scan.py

@@ -4,7 +4,7 @@ from typing import Annotated
 
 import numpy as np
 from numpy.typing import NDArray
-from pydantic import AfterValidator
+from pydantic import AfterValidator, field_validator
 
 from ..base import Base, round_optional_float
 from ..molecule import Molecule
@@ -62,15 +62,33 @@ class ScanWorkflow(MoleculeWorkflow):
     :param mode: Mode for workflow (currently unused)
 
     New:
-    :param scan_settings: information about what coordinate to scan
+    :param scan_settings: what coordinate(s) to scan; if more than one, all will be performed simultaneously and should have the same number of steps
+    :param scan_settings_2d: what additional coordinate(s) to scan; makes a grid with `scan_settings`
+    :param wavefront propagation: whether to use wavefront propagation (10.1063/5.0009232) for more expensive but smoother scans
     :param calc_settings: settings for the calculation
     :param calc_engine: engine to use for the calculation
     :param scan_points: points along the scan
     """
 
-    scan_settings: ScanSettings
+    scan_settings: ScanSettings | list[ScanSettings]
+    scan_settings_2d: ScanSettings | list[ScanSettings] = []
     calc_settings: Settings
     calc_engine: str
 
+    wavefront_propagation: bool = True
+
     # UUIDs of scan points
     scan_points: list[UUID | None] = []
+
+    @field_validator("scan_settings", "scan_settings_2d", mode="after")
+    @classmethod
+    def validate_scan_settings(cls, val: ScanSettings | list[ScanSettings]) -> list[ScanSettings]:
+        """Ensure that scan_settings is a list, and that every list item has the same number of steps."""
+        if isinstance(val, ScanSettings):
+            val = [val]
+
+        for ss in val:
+            if ss.num != val[0].num:
+                raise ValueError("Concerted scan settings must have same number of steps!")
+
+        return val

{stjames-0.0.63.dist-info → stjames-0.0.65.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.2
 Name: stjames
-Version: 0.0.63
+Version: 0.0.65
 Summary: standardized JSON atom/molecule encoding scheme
 Author-email: Corin Wagen <corin@rowansci.com>
 Project-URL: Homepage, https://github.com/rowansci/stjames

{stjames-0.0.63.dist-info → stjames-0.0.65.dist-info}/RECORD

@@ -13,9 +13,9 @@ stjames/int_settings.py,sha256=5HXp8opt5ZyY1UpmfaK7NVloWVLM5jkG0elEEqpVLUo,896
 stjames/message.py,sha256=Rq6QqmHZKecWxYH8fVyXmuoCCPZv8YinvgykSeorXSU,216
 stjames/method.py,sha256=5hBHk2xQLpxZ52LwJ9FHWaqQMdFKnsbQEOxaVe6O4Go,2321
 stjames/mode.py,sha256=xw46Cc7f3eTS8i35qECi-8DocAlANhayK3w4akD4HBU,496
-stjames/molecule.py,sha256=UjJu5nA6IeV8rcO-Tnu3xBiNt2reUm9_3DLLCyxJF0M,14227
+stjames/molecule.py,sha256=R0BalcXdvyhuyffoH11Nml_49qiVl4mD0dcGcLqfQYM,14371
 stjames/opt_settings.py,sha256=gxXGtjy9l-Q5Wen9eO6T6HHRCuS8rfOofdVQIJj0JcI,550
-stjames/pdb.py,sha256=-i0H029NEX-pcyCqdVyq7D62ZDvmUPWK7l83WdoDmpk,25759
+stjames/pdb.py,sha256=YxJgheU37H74cAPjRcYS16Z_-fZo2Yel9V_trluYq9Q,25938
 stjames/periodic_cell.py,sha256=eV_mArsY_MPEFSrFEsTC-CyCc6V8ITAXdk7yhjjNI7M,1080
 stjames/py.typed,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 stjames/scf_settings.py,sha256=WotVgVrayQ_8PUHP39zVtG7iLT9PV41lpzruttFACP8,2356
@@ -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=llbJ65p2B-aZN31-E_ODVDmrVeBoSw9y_Mg5XjyQvTA,26755
+stjames/atomium_stjames/mmcif.py,sha256=B5t_gxvMTG8OblXUWF0dnKgOHhn-8bufOv_a7ccbiqU,27081
 stjames/atomium_stjames/pdb.py,sha256=C2mEcBDDrnoXD9ZCMIH2uJpjiWPJy6ktXq8IFZsrQKM,22482
 stjames/atomium_stjames/utilities.py,sha256=-YtM7sRMvMk0wWrC3svWUWH4CGI0NtY77nXsg9tjHfc,4964
 stjames/data/__init__.py,sha256=O59Ksp7AIqwOELCWymfCx7YeBzwNOGCMlGQi7tNLqiE,24
@@ -37,8 +37,8 @@ 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=5KX0IcuYElj8K3qE2c-XY8dL-vPdG87US7ErfZlyK88,2293
-stjames/workflows/admet.py,sha256=m8yGWe-UeYK5F7TOeNsQMPTzdWL-aaRSTQsyO7SVa6k,421
+stjames/workflows/__init__.py,sha256=sHKzK6ZtVt8TkaX3JoIrg46SVK9rDi_elA7qCIAqBpE,2410
+stjames/workflows/admet.py,sha256=h8ph6oeRCxU3-_jqRRWPg3RZcheu9JzCHiWqSC9VYKY,1296
 stjames/workflows/basic_calculation.py,sha256=ZX3KwhfyyCTjc2ougQIL4If7gtwZP9WjqpL45mBquW0,573
 stjames/workflows/bde.py,sha256=hdTjwma5L9SrU5F5r6dB1ruB_B6buBUtZHf2sanNW2k,9802
 stjames/workflows/conformer.py,sha256=18aO6ngMBeGAmQkBdLGCCHr398RIYr1v2hD2IT1u4cc,3005
@@ -48,18 +48,20 @@ stjames/workflows/docking.py,sha256=GCW_-JeEZcMXKZ9EQFOxWUYRo0jsbzwIv10aSz8KuaQ,
 stjames/workflows/electronic_properties.py,sha256=GT3-NC7w-dbcOJ-3AzJ7LgzH6frTbiH2Iyb9BCa-SvY,4112
 stjames/workflows/fukui.py,sha256=e7CF7Mp2Dt1JTipQx-Sz_37W1urL-iRpjXY-9ItSvhM,1268
 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=d3jUKZIUU7ifcMCB6KuTEpP91Pl9sQA0WAmjnODbp6g,2058
 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/redox_potential.py,sha256=7S18t9Y3eynSnA3lZbRlvLfdbgeBopdiigLzt1zxg5c,3871
-stjames/workflows/scan.py,sha256=vGS1wWMpMSogb63DEED6U6oHsLgV0D2hXVQg2UWWJgs,1913
+stjames/workflows/scan.py,sha256=Lph2VhsxJMpzY-wtmUV7U1TOS7mIwjgkLniaipGDo8I,2899
 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-0.0.63.dist-info/LICENSE,sha256=i7ehYBS-6gGmbTcgU4mgk28pyOx2kScJ0kcx8n7bWLM,1084
-stjames-0.0.63.dist-info/METADATA,sha256=PlYrd27UJROPiSqNv6i1XqW-Kbvpk9h5Tcw3PDMqOnc,1672
-stjames-0.0.63.dist-info/WHEEL,sha256=jB7zZ3N9hIM9adW7qlTAyycLYW9npaWKLRzaoVcLKcM,91
-stjames-0.0.63.dist-info/top_level.txt,sha256=FYCwxl6quhYOAgG-mnPQcCK8vsVM7B8rIUrO-WrQ_PI,8
-stjames-0.0.63.dist-info/RECORD,,
+stjames-0.0.65.dist-info/LICENSE,sha256=i7ehYBS-6gGmbTcgU4mgk28pyOx2kScJ0kcx8n7bWLM,1084
+stjames-0.0.65.dist-info/METADATA,sha256=OQsAzZU4ZxSwkHhpyaHaiI-3SvcHB5VS_nDKKlv-3FM,1672
+stjames-0.0.65.dist-info/WHEEL,sha256=beeZ86-EfXScwlR_HKu4SllMC9wUEj_8Z_4FJ3egI2w,91
+stjames-0.0.65.dist-info/top_level.txt,sha256=FYCwxl6quhYOAgG-mnPQcCK8vsVM7B8rIUrO-WrQ_PI,8
+stjames-0.0.65.dist-info/RECORD,,

{stjames-0.0.63.dist-info → stjames-0.0.65.dist-info}/WHEEL

@@ -1,5 +1,5 @@
 Wheel-Version: 1.0
-Generator: setuptools (75.8.2)
+Generator: setuptools (76.1.0)
 Root-Is-Purelib: true
 Tag: py3-none-any