stjames 0.0.35__py3-none-any.whl → 0.0.36__py3-none-any.whl

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/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/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/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/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/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/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
@@ -49,7 +52,7 @@ def csearch_settings_by_mode(mode: Mode) -> ConformerSettings:
     if mode == Mode.METICULOUS:
         return CrestConformerSettings(
             gfn=2,
-            flags="--ewin 15",
+            flags="--ewin 15 --noreftopo",
             max_energy=10,
             num_confs_considered=500,
             num_confs_taken=150,
@@ -58,7 +61,7 @@ def csearch_settings_by_mode(mode: Mode) -> ConformerSettings:
     elif mode == Mode.CAREFUL:
         return CrestConformerSettings(
             gfn="ff",
-            flags="--quick --ewin 10",
+            flags="--quick --ewin 10 --noreftopo",
             num_confs_considered=150,
             num_confs_taken=50,
         )

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/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.dist-info → stjames-0.0.36.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: stjames
-Version: 0.0.35
+Version: 0.0.36
 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.dist-info → stjames-0.0.36.dist-info}/RECORD

@@ -1,16 +1,18 @@
-stjames/__init__.py,sha256=_gX08PEdPHoE6oyc0OF2gKPBfk9op0am75y1TDUo-MU,451
+stjames/__init__.py,sha256=RJ1b132RSXVbQfptduVM1ZSQrnSTsg0a-VfgBwQn9zo,506
 stjames/_deprecated_solvent_settings.py,sha256=gj5j9p3zakIwSTK5_ndqBXJx--IzjZNxZ75z-wipLOo,450
 stjames/base.py,sha256=GTISjYPBi4KCxAR9DPLf4mp6ZYuh2MwlNI0jZ1N41Io,1142
 stjames/basis_set.py,sha256=Fi6vJx-ni2aOozFYH2hrSlc9lL01XzPO4zO6onJliuE,1035
-stjames/calculation.py,sha256=6xnoKLn6tr1QaactTWsdu8Ciqdu8oa-hmB2y9RIrJTI,786
+stjames/calculation.py,sha256=0eCZ59lqmnI_QxEdMp7esrTeutNyO_pIFrZQf_FncSo,848
+stjames/constraint.py,sha256=gkp0y0yQPeii8jdBNllZ9JS8t0o2bkEVTFAkyhShmWk,329
 stjames/correction.py,sha256=_pNG3qSylfx0iyUxqwx9HPU0m032YwP6wSPCjbJrD94,358
 stjames/diis_settings.py,sha256=QHc7L-hktkbOWBYr29byTdqL8lWJzKJiY9XW8ha4Qzo,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=e7A3XH808JglgfCzISKyRKAxGDj7BQdcQQtgtTlgfNk,843
 stjames/mode.py,sha256=xw46Cc7f3eTS8i35qECi-8DocAlANhayK3w4akD4HBU,496
 stjames/molecule.py,sha256=t0jOmkTMgQE2ayBn9igjpY_4gPyqLPqZLlgtwd4uBOA,2910
-stjames/opt_settings.py,sha256=81vYDBEbqLGN_crI1GtAxiOoRa791WN0m2HfT5_A7pE,729
+stjames/opt_settings.py,sha256=5nTGih8KZ3x_yGfPL7pdGdsuOpCIfuJUrKoSK5YSDJg,458
 stjames/py.typed,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 stjames/scf_settings.py,sha256=xMMCQ0hVB4nNFSiWesNQZUa_aLsozSZGYWweAPPDGBg,2356
 stjames/settings.py,sha256=cUiAydIVes9iDEky4coOYQ2kF97AYaLClx5qjJmEpWY,8462
@@ -18,16 +20,17 @@ stjames/solvent.py,sha256=3ssY-vQCCa071srfJbwCYEKDpWos8Mgvmg_dTpAnbJw,1104
 stjames/status.py,sha256=wTKNcNxStoEHrxxgr_zTyN90NITa3rxMQZzOgrCifEw,332
 stjames/task.py,sha256=TTl-iTdvDNCZTdPsyS6bYmxzY0ez9PgYlL62fztayXQ,307
 stjames/thermochem_settings.py,sha256=ZTLz31v8Ltutde5Nfm0vH5YahWjcfFWfr_R856KffxE,517
-stjames/workflows/__init__.py,sha256=TibQzeD3X3YGq9TaAzPlBMxU7zskFoa8PwPUam4TcZY,154
-stjames/workflows/conformer.py,sha256=tqACquXy8wqIbxl3T-n4dfNNNkVdLos2dIG1u0CV8cc,2169
+stjames/workflows/__init__.py,sha256=sy9J04mCJpyVGcG4DecCi6pncwbZVvybI7sJKzavjgo,167
+stjames/workflows/conformer.py,sha256=TLux80MCgVH7RsJdElMtpWt5_hbWu7dyjg0zSim_lbA,2269
+stjames/workflows/descriptors.py,sha256=Jqx_4u_ZhdFJrT-ITU6zlFY0n8llh6zhzIhM38e8NCs,255
 stjames/workflows/fukui.py,sha256=FAabgLi_ig6Zp_jiTkuveP0wAObwv68liuumr85rb0g,366
 stjames/workflows/pka.py,sha256=zpR90Yv2L-D56o2mGArM8027DWpnFFnay31UR9Xh5Nc,774
 stjames/workflows/redox_potential.py,sha256=iPkFt1Dj1sUywS9pLSEBVpCjHZcEwUESluY0ggLii8A,1213
 stjames/workflows/scan.py,sha256=d1ca1uk1nxdzlSwqMLZ0W1_DHyrQMnHJmvPfziCS0SA,773
 stjames/workflows/tautomer.py,sha256=kZSCHo2Q7LzqtQjF_WyyxjECkndG49T9QOM12hsUkx8,421
-stjames/workflows/workflow.py,sha256=jzkHO8mdmoy9zW3iD457KAXYrCCkV2OHjg6T3896nCQ,304
-stjames-0.0.35.dist-info/LICENSE,sha256=i7ehYBS-6gGmbTcgU4mgk28pyOx2kScJ0kcx8n7bWLM,1084
-stjames-0.0.35.dist-info/METADATA,sha256=Hk0XDUPqTndq0PHE98rDpNPXWPdbunZa_nVGwAIK_84,1626
-stjames-0.0.35.dist-info/WHEEL,sha256=GJ7t_kWBFywbagK5eo9IoUwLW6oyOeTKmQ-9iHFVNxQ,92
-stjames-0.0.35.dist-info/top_level.txt,sha256=FYCwxl6quhYOAgG-mnPQcCK8vsVM7B8rIUrO-WrQ_PI,8
-stjames-0.0.35.dist-info/RECORD,,
+stjames/workflows/workflow.py,sha256=6hFe5PZejJu6bZ3yTkoJ9-xQMBn_-8tUsbk4FUZxog0,367
+stjames-0.0.36.dist-info/LICENSE,sha256=i7ehYBS-6gGmbTcgU4mgk28pyOx2kScJ0kcx8n7bWLM,1084
+stjames-0.0.36.dist-info/METADATA,sha256=qj3omHcwp2JrTGjc2UMR9NdGBjho6ItqsxoRvLgiR-U,1626
+stjames-0.0.36.dist-info/WHEEL,sha256=cpQTJ5IWu9CdaPViMhC9YzF8gZuS5-vlfoFihTBC86A,91
+stjames-0.0.36.dist-info/top_level.txt,sha256=FYCwxl6quhYOAgG-mnPQcCK8vsVM7B8rIUrO-WrQ_PI,8
+stjames-0.0.36.dist-info/RECORD,,

{stjames-0.0.35.dist-info → stjames-0.0.36.dist-info}/WHEEL

@@ -1,5 +1,5 @@
 Wheel-Version: 1.0
-Generator: bdist_wheel (0.43.0)
+Generator: setuptools (70.1.0)
 Root-Is-Purelib: true
 Tag: py3-none-any