stjames 0.0.68__py3-none-any.whl → 0.0.70__py3-none-any.whl

stjames/method.py

@@ -36,6 +36,7 @@ class Method(LowercaseStrEnum):
     OCP24_S = "ocp24_s"
     OCP24_L = "ocp24_l"
     ORB_V2 = "orb_v2"
+    ORB_V3_CONSERVATIVE_INF_OMAT = "orb_v3_conservative_inf_omat"
 
     GFN_FF = "gfn_ff"
     GFN0_XTB = "gfn0_xtb"
@@ -50,8 +51,8 @@ class Method(LowercaseStrEnum):
     RM1 = "rm1"
 
 
-PrepackagedNNPMethod = Literal[Method.AIMNET2_WB97MD3, Method.OCP24_S, Method.OCP24_L, Method.RM1]
-PREPACKAGED_NNP_METHODS = [Method.AIMNET2_WB97MD3, Method.OCP24_S, Method.OCP24_L, Method.RM1]
+PrepackagedNNPMethod = Literal[Method.AIMNET2_WB97MD3, Method.OCP24_S, Method.OCP24_L, Method.RM1, Method.ORB_V3_CONSERVATIVE_INF_OMAT]
+PREPACKAGED_NNP_METHODS = [Method.AIMNET2_WB97MD3, Method.OCP24_S, Method.OCP24_L, Method.RM1, Method.ORB_V3_CONSERVATIVE_INF_OMAT]
 
 CorrectableNNPMethod = Literal[Method.MACE_MP_0B2_L, Method.ORB_V2]
 CORRECTABLE_NNP_METHODS = [Method.MACE_MP_0B2_L, Method.ORB_V2]

stjames/opt_settings.py

@@ -9,6 +9,7 @@ from .constraint import Constraint
 class OptimizationSettings(Base):
     max_steps: PositiveInt = 250
     transition_state: bool = False
+    recalc_hess_every: int = 0  # Recalculate the hessian every `n` steps (or never with 0)
 
     # when are we converged? (Hartree and Hartree/Å)
     max_gradient_threshold: PositiveFloat = 7e-4

stjames/workflows/__init__.py

@@ -14,6 +14,7 @@ from .fukui import *
 from .hydrogen_bond_basicity import *
 from .ion_mobility import *
 from .irc import *
+from .macropka import *
 from .molecular_dynamics import *
 from .multistage_opt import *
 from .pka import *
@@ -37,6 +38,7 @@ WORKFLOW_NAME = Literal[
     "hydrogen_bond_basicity",
     "ion_mobility",
     "irc",
+    "macropka",
     "molecular_dynamics",
     "multistage_opt",
     "pka",
@@ -60,6 +62,7 @@ WORKFLOW_MAPPING: dict[WORKFLOW_NAME, Workflow] = {
     "hydrogen_bond_basicity": HydrogenBondBasicityWorkflow,  # type: ignore [dict-item]
     "ion_mobility": IonMobilityWorkflow,  # type: ignore [dict-item]
     "irc": IRCWorkflow,  # type: ignore [dict-item]
+    "macropka": MacropKaWorkflow,  # type: ignore [dict-item]
     "molecular_dynamics": MolecularDynamicsWorkflow,  # type: ignore [dict-item]
     "multistage_opt": MultiStageOptWorkflow,  # type: ignore [dict-item]
     "pka": pKaWorkflow,  # type: ignore [dict-item]

stjames/workflows/fukui.py

@@ -5,6 +5,7 @@ from typing import Annotated
 from pydantic import AfterValidator
 
 from ..base import round_optional_float
+from ..settings import Settings
 from ..types import UUID, FloatPerAtom, round_optional_float_per_atom
 from .workflow import MoleculeWorkflow
 
@@ -17,6 +18,12 @@ class FukuiIndexWorkflow(MoleculeWorkflow):
     :param initial_molecule: Molecule of interest
     :param mode: Mode for workflow (currently unused)
 
+    Settings:
+    :param opt_settings: if given, the settings for optimization. if none, no optimization will be conducted.
+    :param opt_engine: the engine for optimization
+    :param fukui_settings: the settings for Fukui index calculations.
+    :param fukui_engine: the engine for Fukui index calculations
+
     Results:
     :param optimization: UUID of optimization
     :param global_electrophilicity_index: global electrophilicity index
@@ -25,7 +32,12 @@ class FukuiIndexWorkflow(MoleculeWorkflow):
     :param fukui_zero: Fukui index for zero charges
     """
 
-    # UUID of optimization
+    opt_settings: Settings | None = None
+    opt_engine: str | None = None
+
+    fukui_settings: Settings = Settings(method="gfn1_xtb")
+    fukui_engine: str | None = None
+
     optimization: UUID | None = None
 
     global_electrophilicity_index: Annotated[float | None, AfterValidator(round_optional_float(6))] = None

stjames/workflows/macropka.py

@@ -1,6 +1,6 @@
 """pKa workflow."""
 
-from typing import Annotated, Self
+from typing import Annotated, Optional, Self
 
 from pydantic import AfterValidator, model_validator
 
@@ -55,18 +55,48 @@ class MacropKaWorkflow(SMILESWorkflow):
     :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
 
+    max_charge: int = 2
+    min_charge: int = -2
+
     microstates: list[MacropKaMicrostate] = []
     pKa_values: list[MacropKaValue] = []
-    microstate_weights_by_pH: dict[float, Annotated[list[float], AfterValidator(round_list(6))]] = {}
+    microstate_weights_by_pH: list[
+        tuple[
+            Annotated[float, AfterValidator(round_float(3))],
+            Annotated[list[float], AfterValidator(round_list(6))],
+        ]
+    ] = []
+
+    isoelectric_point: Annotated[Optional[float], AfterValidator(round_float(3))] = None
+
+    logD_by_pH: list[
+        tuple[
+            Annotated[float, AfterValidator(round_float(3))],
+            Annotated[float, AfterValidator(round_float(3))],
+        ]
+    ] = []
+
+    aqueous_solubility_by_pH: list[
+        tuple[
+            Annotated[float, AfterValidator(round_float(3))],
+            Annotated[float, AfterValidator(round_float(3))],
+        ]
+    ] = []
 
     @model_validator(mode="after")
     def check_weights(self) -> Self:
-        for weights in self.microstate_weights_by_pH.values():
+        for _, weights in self.microstate_weights_by_pH:
             if len(weights) != len(self.microstates):
                 raise ValueError("Length of microstate weights doesn't match!")
 
         return self
+
+    @model_validator(mode="after")
+    def check_minmax_charges(self) -> Self:
+        if self.min_charge >= self.max_charge:
+            raise ValueError("Incoherent min/max charge specification")
+
+        return self

{stjames-0.0.68.dist-info → stjames-0.0.70.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: stjames
-Version: 0.0.68
+Version: 0.0.70
 Summary: standardized JSON atom/molecule encoding scheme
 Author-email: Corin Wagen <corin@rowansci.com>
 Project-URL: Homepage, https://github.com/rowansci/stjames

{stjames-0.0.68.dist-info → stjames-0.0.70.dist-info}/RECORD

@@ -11,10 +11,10 @@ stjames/diis_settings.py,sha256=4m1EQQWBlpHhMnWopix8qOqJv7QCluvdnV9jSKJDFtE,552
 stjames/grid_settings.py,sha256=WrSNGc-8_f87YBZYt9Hh7RbhM4MweADoVzwBMcSqcsE,640
 stjames/int_settings.py,sha256=5HXp8opt5ZyY1UpmfaK7NVloWVLM5jkG0elEEqpVLUo,896
 stjames/message.py,sha256=Rq6QqmHZKecWxYH8fVyXmuoCCPZv8YinvgykSeorXSU,216
-stjames/method.py,sha256=5hBHk2xQLpxZ52LwJ9FHWaqQMdFKnsbQEOxaVe6O4Go,2321
+stjames/method.py,sha256=4X2OdeOQCj0Ihtthl9mx6Q26RrZljYhvRUVz-huf0s8,2461
 stjames/mode.py,sha256=xw46Cc7f3eTS8i35qECi-8DocAlANhayK3w4akD4HBU,496
 stjames/molecule.py,sha256=4dakMkn-_I5bSWsijLLY0tn5NkBEuZhmtYDj-MDSJE0,17987
-stjames/opt_settings.py,sha256=gxXGtjy9l-Q5Wen9eO6T6HHRCuS8rfOofdVQIJj0JcI,550
+stjames/opt_settings.py,sha256=LEwGXUEKq5TfU5rr60Z4QQBhCqiw1Ch5w0M_lXawWo8,642
 stjames/pdb.py,sha256=_pIdJCMhIzS4t2HWQa_susDWjZEl0oLn4Njb1QoKvKw,26460
 stjames/periodic_cell.py,sha256=eV_mArsY_MPEFSrFEsTC-CyCc6V8ITAXdk7yhjjNI7M,1080
 stjames/py.typed,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
@@ -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=sHKzK6ZtVt8TkaX3JoIrg46SVK9rDi_elA7qCIAqBpE,2410
+stjames/workflows/__init__.py,sha256=X8uBwvmpaP38QQxYlvl9TbejEnnujpyWCLbxq0gRKao,2512
 stjames/workflows/admet.py,sha256=h8ph6oeRCxU3-_jqRRWPg3RZcheu9JzCHiWqSC9VYKY,1296
 stjames/workflows/basic_calculation.py,sha256=ZX3KwhfyyCTjc2ougQIL4If7gtwZP9WjqpL45mBquW0,573
 stjames/workflows/bde.py,sha256=hdTjwma5L9SrU5F5r6dB1ruB_B6buBUtZHf2sanNW2k,9802
@@ -46,11 +46,11 @@ stjames/workflows/conformer_search.py,sha256=4yPEKIIedeaVvaAwgjwC1FxiHqM6n2zOF6c
 stjames/workflows/descriptors.py,sha256=T4tc7xdtBdxESGO86KR323jPQ2pgwxBqgV0khA6MEgQ,584
 stjames/workflows/docking.py,sha256=GCW_-JeEZcMXKZ9EQFOxWUYRo0jsbzwIv10aSz8KuaQ,3027
 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/fukui.py,sha256=T6TDg-lcE-sfTDVpa3KFBenLe7PGUO2QrQ2jNuw_iiU,1756
 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/macropka.py,sha256=k7ebG4s-GoTG3ZKxq-OQ7gmzT8Yaq_Zd4pkL7pqL_pI,2827
 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
@@ -60,8 +60,8 @@ stjames/workflows/solubility.py,sha256=kGfVyPPGDLRpf2j6dSY7woCkfsoXSbUzdSImA4mcM
 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-0.0.68.dist-info/licenses/LICENSE,sha256=i7ehYBS-6gGmbTcgU4mgk28pyOx2kScJ0kcx8n7bWLM,1084
-stjames-0.0.68.dist-info/METADATA,sha256=QvoqeoYNBF5Kb1_Ojvaj08H4S1ObPREu1-9ocQ_RTtI,1694
-stjames-0.0.68.dist-info/WHEEL,sha256=DK49LOLCYiurdXXOXwGJm6U4DkHkg4lcxjhqwRa0CP4,91
-stjames-0.0.68.dist-info/top_level.txt,sha256=FYCwxl6quhYOAgG-mnPQcCK8vsVM7B8rIUrO-WrQ_PI,8
-stjames-0.0.68.dist-info/RECORD,,
+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-0.0.68.dist-info → stjames-0.0.70.dist-info}/WHEEL

@@ -1,5 +1,5 @@
 Wheel-Version: 1.0
-Generator: setuptools (78.0.2)
+Generator: setuptools (78.1.0)
 Root-Is-Purelib: true
 Tag: py3-none-any