stjames 0.0.35__tar.gz → 0.0.37__tar.gz

{stjames-0.0.35/stjames.egg-info → stjames-0.0.37}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: stjames
-Version: 0.0.35
+Version: 0.0.37
 Summary: standardized JSON atom/molecule encoding scheme
 Author-email: Corin Wagen <corin@rowansci.com>
 Project-URL: Homepage, https://github.com/rowansci/stjames

{stjames-0.0.35 → stjames-0.0.37}/pyproject.toml

@@ -1,6 +1,6 @@
 [project]
 name = "stjames"
-version = "0.0.35"
+version = "0.0.37"
 description = "standardized JSON atom/molecule encoding scheme"
 readme = "README.md"
 requires-python = ">=3.8"
@@ -40,5 +40,8 @@ select = [
 ]
 ignore = ["E741"]
 
+[tool.ruff.lint.per-file-ignores]
+"__init__.py" = ["F401", "F403"]
+
 [tool.mypy]
 plugins = ["pydantic.mypy"]

{stjames-0.0.35 → stjames-0.0.37}/stjames/__init__.py

@@ -1,4 +1,4 @@
-# ruff: noqa
+# ruff: noqa: I001
 
 from .calculation import *
 from .molecule import *
@@ -19,3 +19,5 @@ from .correction import *
 from .solvent import *
 from .mode import *
 from .status import *
+from .constraint import *
+from .message import *

{stjames-0.0.35 → stjames-0.0.37}/stjames/calculation.py

@@ -1,6 +1,7 @@
 from typing import Optional
 
 from .base import Base, LowercaseStrEnum
+from .message import Message
 from .molecule import Molecule
 from .settings import Settings
 from .status import Status
@@ -25,6 +26,7 @@ class Calculation(Base):
     name: Optional[str] = None
     elapsed: Optional[float] = None
     logfile: Optional[str] = None
+    messages: list[Message] = []
 
     engine: Optional[str] = "peregrine"
 

stjames-0.0.37/stjames/constraint.py

@@ -0,0 +1,16 @@
+from .base import Base, LowercaseStrEnum
+
+
+class ConstraintType(LowercaseStrEnum):
+    """Different sorts of constraints."""
+
+    BOND = "bond"
+    ANGLE = "angle"
+    DIHEDRAL = "dihedral"
+
+
+class Constraint(Base):
+    """Represents a single constraint."""
+
+    constraint_type: ConstraintType
+    atoms: list[int]  # 1-indexed

stjames-0.0.37/stjames/message.py

@@ -0,0 +1,13 @@
+from .base import Base, LowercaseStrEnum
+
+
+class MessageType(LowercaseStrEnum):
+    ERROR = "error"
+    WARNING = "warning"
+    INFO = "info"
+
+
+class Message(Base):
+    type: MessageType
+    title: str
+    body: str

{stjames-0.0.35 → stjames-0.0.37}/stjames/opt_settings.py

@@ -1,21 +1,7 @@
 from pydantic import Field, PositiveFloat, PositiveInt
 
-from .base import Base, LowercaseStrEnum
-
-
-class ConstraintType(LowercaseStrEnum):
-    """Different sorts of constraints."""
-
-    BOND = "bond"
-    ANGLE = "angle"
-    DIHEDRAL = "dihedral"
-
-
-class Constraint(Base):
-    """Represents a single constraint."""
-
-    constraint_type: ConstraintType
-    atoms: list[int]  # 1-indexed
+from .base import Base
+from .constraint import Constraint
 
 
 class OptimizationSettings(Base):

{stjames-0.0.35 → stjames-0.0.37}/stjames/workflows/__init__.py

@@ -1,8 +1,7 @@
-# ruff: noqa
-
-from .pka import *
 from .conformer import *
-from .tautomer import *
+from .descriptors import *
+from .fukui import *
+from .pka import *
 from .redox_potential import *
 from .scan import *
-from .fukui import *
+from .tautomer import *

{stjames-0.0.35 → stjames-0.0.37}/stjames/workflows/conformer.py

@@ -1,6 +1,7 @@
 from typing import Any, Optional
 
 from ..base import Base
+from ..constraint import Constraint
 from ..method import Method
 from ..mode import Mode
 from ..solvent import Solvent
@@ -16,6 +17,8 @@ class ConformerSettings(Base):
     solvent: Optional[Solvent] = Solvent.WATER
     max_energy: float = 5
 
+    constraints: list[Constraint] = []
+
 
 class RdkitConformerSettings(ConformerSettings):
     num_initial_confs: int = 100
@@ -42,29 +45,35 @@ class ConformerWorkflow(Workflow):
     conformers: list[Conformer] = []
 
     def model_post_init(self, __context: Any) -> None:
-        self.settings = csearch_settings_by_mode(self.mode)
+        self.settings = csearch_settings_by_mode(self.mode, self.settings)
+
+
+def csearch_settings_by_mode(mode: Mode, old_settings: Optional[ConformerSettings]) -> ConformerSettings:
+    if mode == Mode.MANUAL:
+        assert old_settings is not None
+        return old_settings
 
+    settings: ConformerSettings
 
-def csearch_settings_by_mode(mode: Mode) -> ConformerSettings:
     if mode == Mode.METICULOUS:
-        return CrestConformerSettings(
+        settings = CrestConformerSettings(
             gfn=2,
-            flags="--ewin 15",
+            flags="--ewin 15 --noreftopo",
             max_energy=10,
             num_confs_considered=500,
             num_confs_taken=150,
         )
 
     elif mode == Mode.CAREFUL:
-        return CrestConformerSettings(
+        settings = CrestConformerSettings(
             gfn="ff",
-            flags="--quick --ewin 10",
+            flags="--quick --ewin 10 --noreftopo",
             num_confs_considered=150,
             num_confs_taken=50,
         )
 
     elif mode == Mode.RAPID or Mode.AUTO:
-        return RdkitConformerSettings(
+        settings = RdkitConformerSettings(
             num_initial_confs=300,
             max_mmff_energy=15,
             num_confs_considered=100,
@@ -72,7 +81,7 @@ def csearch_settings_by_mode(mode: Mode) -> ConformerSettings:
         )
 
     elif mode == Mode.RECKLESS:
-        return RdkitConformerSettings(
+        settings = RdkitConformerSettings(
             num_initial_confs=200,
             max_mmff_energy=10,
             num_confs_considered=50,
@@ -82,3 +91,10 @@ def csearch_settings_by_mode(mode: Mode) -> ConformerSettings:
 
     else:
         raise ValueError(f"invalid mode ``{mode.value}`` for conformer settings")
+
+    if old_settings is not None:
+        settings.final_method = old_settings.final_method
+        settings.solvent = old_settings.solvent
+        settings.constraints = old_settings.constraints
+
+    return settings

stjames-0.0.37/stjames/workflows/descriptors.py

@@ -0,0 +1,10 @@
+from .workflow import Workflow
+
+Descriptors = dict[str, dict[str, float] | tuple[float | None, ...] | float]
+
+
+class DescriptorsWorkflow(Workflow):
+    # uuid of optimization
+    optimization: str | None = None
+
+    descriptors: Descriptors | None = None

{stjames-0.0.35 → stjames-0.0.37}/stjames/workflows/workflow.py

@@ -1,4 +1,5 @@
 from ..base import Base
+from ..message import Message
 from ..molecule import Molecule
 
 
@@ -6,6 +7,7 @@ class Workflow(Base):
     """All workflows should have these properties."""
 
     initial_molecule: Molecule
+    messages: list[Message] = []
 
 
 class DBCalculation(Base):

{stjames-0.0.35 → stjames-0.0.37/stjames.egg-info}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: stjames
-Version: 0.0.35
+Version: 0.0.37
 Summary: standardized JSON atom/molecule encoding scheme
 Author-email: Corin Wagen <corin@rowansci.com>
 Project-URL: Homepage, https://github.com/rowansci/stjames

{stjames-0.0.35 → stjames-0.0.37}/stjames.egg-info/SOURCES.txt

@@ -6,10 +6,12 @@ stjames/_deprecated_solvent_settings.py
 stjames/base.py
 stjames/basis_set.py
 stjames/calculation.py
+stjames/constraint.py
 stjames/correction.py
 stjames/diis_settings.py
 stjames/grid_settings.py
 stjames/int_settings.py
+stjames/message.py
 stjames/method.py
 stjames/mode.py
 stjames/molecule.py
@@ -28,6 +30,7 @@ stjames.egg-info/requires.txt
 stjames.egg-info/top_level.txt
 stjames/workflows/__init__.py
 stjames/workflows/conformer.py
+stjames/workflows/descriptors.py
 stjames/workflows/fukui.py
 stjames/workflows/pka.py
 stjames/workflows/redox_potential.py