stjames 0.0.89__py3-none-any.whl → 0.0.91__py3-none-any.whl

stjames/engine.py

@@ -0,0 +1,16 @@
+from .base import LowercaseStrEnum
+
+
+class Mode(LowercaseStrEnum):
+    AIMNET2 = "aimnet2"
+    MACE = "mace"
+    OCP24 = "ocp24"
+    OMOL25 = "omol25"
+    ORB = "orb"
+    TBLITE = "tblite"
+    XTB = "xtb"
+    TERRACHEM = "terrachem"
+    PYSCF = "pyscf"
+    PSI4 = "psi4"
+    OPENFF = "openff"
+    EGRET = "egret"

stjames/method.py

@@ -37,7 +37,6 @@ class Method(LowercaseStrEnum):
     OCP24_L = "ocp24_l"
     OMOL25_CONSERVING_S = "omol25_conserving_s"
     UMA_M_OMOL = "uma_m_omol"
-    ORB_V2 = "orb_v2"
     ORB_V3_CONSERVATIVE_INF_OMAT = "orb_v3_conservative_inf_omat"
 
     GFN_FF = "gfn_ff"
@@ -51,12 +50,53 @@ class Method(LowercaseStrEnum):
 
     OFF_SAGE_2_2_1 = "off_sage_2_2_1"
 
-    RM1 = "rm1"
-
     EGRET_1 = "egret_1"
     EGRET_1E = "egret_1e"
     EGRET_1T = "egret_1t"
 
+    def default_engine(self, *, is_periodic: bool = False) -> str:
+        """
+        Return the canonical engine name for this quantum-chemistry method.
+
+        :param bool is_periodic:
+            If ``True`` **and** the method is in the XTB family, return
+            ``"tblite"`` (periodic-capable backend) instead of ``"xtb"``.
+        :returns: Lower-case engine identifier (e.g. ``"psi4"``, ``"mace"``).
+
+        **Examples**
+
+        .. code-block:: python
+
+           Method.MACE_MP_0B2_L.default_engine()
+           # 'mace'
+
+           Method.GFN2_XTB.default_engine()
+           # 'xtb'
+
+           Method.GFN2_XTB.default_engine(is_periodic=True)
+           # 'tblite'
+        """
+        match self:
+            case Method.AIMNET2_WB97MD3:
+                return "aimnet2"
+            case Method.MACE_MP_0B2_L:
+                return "mace"
+            case Method.OCP24_S | Method.OCP24_L:
+                return "ocp24"
+            case Method.OMOL25_CONSERVING_S | Method.UMA_M_OMOL:
+                return "omol25"
+            case Method.ORB_V3_CONSERVATIVE_INF_OMAT:
+                return "orb"
+            case _ if self in XTB_METHODS:
+                return "tblite" if is_periodic else "xtb"
+            case Method.OFF_SAGE_2_2_1:
+                return "openff"
+            case Method.EGRET_1 | Method.EGRET_1E | Method.EGRET_1T:
+                return "egret"
+            case _:
+                # All remaining methods (HF, DFT, composite, etc.) fall back to Psi4
+                return "psi4"
+
 
 PrepackagedNNPMethod = Literal[
     Method.AIMNET2_WB97MD3,
@@ -64,7 +104,6 @@ PrepackagedNNPMethod = Literal[
     Method.OCP24_L,
     Method.OMOL25_CONSERVING_S,
     Method.UMA_M_OMOL,
-    Method.RM1,
     Method.ORB_V3_CONSERVATIVE_INF_OMAT,
     Method.EGRET_1,
     Method.EGRET_1E,
@@ -77,15 +116,14 @@ PREPACKAGED_NNP_METHODS = [
     Method.OCP24_L,
     Method.OMOL25_CONSERVING_S,
     Method.UMA_M_OMOL,
-    Method.RM1,
     Method.ORB_V3_CONSERVATIVE_INF_OMAT,
     Method.EGRET_1,
     Method.EGRET_1E,
     Method.EGRET_1T,
 ]
 
-CorrectableNNPMethod = Literal[Method.MACE_MP_0B2_L, Method.ORB_V2]
-CORRECTABLE_NNP_METHODS = [Method.MACE_MP_0B2_L, Method.ORB_V2]
+CorrectableNNPMethod = Literal[Method.MACE_MP_0B2_L]
+CORRECTABLE_NNP_METHODS = [Method.MACE_MP_0B2_L]
 
 NNPMethod = PrepackagedNNPMethod | CorrectableNNPMethod
 NNP_METHODS = [*PREPACKAGED_NNP_METHODS, *CORRECTABLE_NNP_METHODS]

stjames/workflows/ion_mobility.py

@@ -13,10 +13,13 @@ class IonMobilityWorkflow(MoleculeWorkflow):
     :param mode: Mode for workflow (currently unused)
 
     New:
+    :param protonate: automatically protonate the molecule
+    :param temperature: the temperature, in Kelvin
     :param do_csearch: whether to perform a conformational search
     :param do_optimization: whether to perform an optimization
 
     Results:
+    :param conformers: the UUIDs of the conformers
     :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
@@ -24,8 +27,11 @@ class IonMobilityWorkflow(MoleculeWorkflow):
     :param average_ccs_stdev: the uncertainty in the same
     """
 
+    protonate: bool = False
+    temperature: float = 300
     do_csearch: bool = True
     do_optimization: bool = True
+
     conformers: list[UUID] = []
 
     conformer_ccs: list[float] = []

{stjames-0.0.89.dist-info → stjames-0.0.91.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: stjames
-Version: 0.0.89
+Version: 0.0.91
 Summary: standardized JSON atom/molecule encoding scheme
 Author-email: Corin Wagen <corin@rowansci.com>
 Project-URL: Homepage, https://github.com/rowansci/stjames

{stjames-0.0.89.dist-info → stjames-0.0.91.dist-info}/RECORD

@@ -8,10 +8,11 @@ stjames/compute_settings.py,sha256=wuYE6W4WqP3oFHwAeEp7XQ0oMz_MNLucWgrsuJ4kEFQ,2
 stjames/constraint.py,sha256=B6oV0rYjmAWr8gpi5f03gRy_uuqjUURVDVwoez5Cfbg,2442
 stjames/correction.py,sha256=ZVErCcj4TPyZeKrdvXVjHa0tFynsCaoy96QZUVxWFM8,413
 stjames/diis_settings.py,sha256=4m1EQQWBlpHhMnWopix8qOqJv7QCluvdnV9jSKJDFtE,552
+stjames/engine.py,sha256=wVItZQSIeR3ap6EZG3kOw0xCZztZm-6KKFrX84ZyFsE,313
 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=aPFUhfUtJ_befRHO1Aa_c4ofEQAPZlQUvHWLaCv32Z4,2945
+stjames/method.py,sha256=mwCDlLmUlBWjVGDdlTIPODu-V_QtmQ_1L3N6xf4nVv0,4373
 stjames/mode.py,sha256=xw46Cc7f3eTS8i35qECi-8DocAlANhayK3w4akD4HBU,496
 stjames/molecule.py,sha256=l4S6prH1xflnZtbwidSF2THsiHaSJtRiy1rmUbH366Q,20631
 stjames/opt_settings.py,sha256=LEwGXUEKq5TfU5rr60Z4QQBhCqiw1Ch5w0M_lXawWo8,642
@@ -48,7 +49,7 @@ stjames/workflows/docking.py,sha256=GCW_-JeEZcMXKZ9EQFOxWUYRo0jsbzwIv10aSz8KuaQ,
 stjames/workflows/electronic_properties.py,sha256=GT3-NC7w-dbcOJ-3AzJ7LgzH6frTbiH2Iyb9BCa-SvY,4112
 stjames/workflows/fukui.py,sha256=T6TDg-lcE-sfTDVpa3KFBenLe7PGUO2QrQ2jNuw_iiU,1756
 stjames/workflows/hydrogen_bond_basicity.py,sha256=q9eXty68ZyCmrB6G_8bfeOT8Ui_IQquRPu6z-3rNreQ,1589
-stjames/workflows/ion_mobility.py,sha256=e6XSidrud5qSkrAcjzOzgHaf-G09JoP09V76myjdyjc,1097
+stjames/workflows/ion_mobility.py,sha256=HbO_222pjiG4YeJ70kYtQJvXQJieDSMAU5y26vIx1vI,1316
 stjames/workflows/irc.py,sha256=ZP7icylW8rgo_Uh7h3bmyumn0ru1IyF-61nP5Jnmq3M,3402
 stjames/workflows/macropka.py,sha256=KRIyk4gsSYL3eqyzCDndStGLwjWSo60cgCAzvAoD1Nk,3754
 stjames/workflows/molecular_dynamics.py,sha256=kxugE73Ntzpj-xpJSoQ1EwGzXXdvi_NTyeP4913EVwE,3173
@@ -62,8 +63,8 @@ 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=OE05pt2ZOd8TzTOlBngXCVg9wv_553ZR60VNRPlq0f8,1953
-stjames-0.0.89.dist-info/licenses/LICENSE,sha256=i7ehYBS-6gGmbTcgU4mgk28pyOx2kScJ0kcx8n7bWLM,1084
-stjames-0.0.89.dist-info/METADATA,sha256=qK-0cUePnvLM9_nDO4QkwixCJz7WfJhX4pC9iYe2dd8,1724
-stjames-0.0.89.dist-info/WHEEL,sha256=_zCd3N1l69ArxyTb8rzEoP9TpbYXkqRFSNOD5OuxnTs,91
-stjames-0.0.89.dist-info/top_level.txt,sha256=FYCwxl6quhYOAgG-mnPQcCK8vsVM7B8rIUrO-WrQ_PI,8
-stjames-0.0.89.dist-info/RECORD,,
+stjames-0.0.91.dist-info/licenses/LICENSE,sha256=i7ehYBS-6gGmbTcgU4mgk28pyOx2kScJ0kcx8n7bWLM,1084
+stjames-0.0.91.dist-info/METADATA,sha256=gUeuoa8dXyp9cjlUtCGQBGN8EUuZZciu17n_95tTVFk,1724
+stjames-0.0.91.dist-info/WHEEL,sha256=_zCd3N1l69ArxyTb8rzEoP9TpbYXkqRFSNOD5OuxnTs,91
+stjames-0.0.91.dist-info/top_level.txt,sha256=FYCwxl6quhYOAgG-mnPQcCK8vsVM7B8rIUrO-WrQ_PI,8
+stjames-0.0.91.dist-info/RECORD,,