stjames 0.0.39__py3-none-any.whl → 0.0.40__py3-none-any.whl

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Files changed (9) hide show
  1. stjames/molecule.py +3 -0
  2. stjames/settings.py +1 -1
  3. stjames/solvent.py +1 -0
  4. stjames/workflows/conformer.py +1 -0
  5. {stjames-0.0.39.dist-info → stjames-0.0.40.dist-info}/METADATA +1 -1
  6. {stjames-0.0.39.dist-info → stjames-0.0.40.dist-info}/RECORD +9 -9
  7. {stjames-0.0.39.dist-info → stjames-0.0.40.dist-info}/LICENSE +0 -0
  8. {stjames-0.0.39.dist-info → stjames-0.0.40.dist-info}/WHEEL +0 -0
  9. {stjames-0.0.39.dist-info → stjames-0.0.40.dist-info}/top_level.txt +0 -0
stjames/molecule.py CHANGED
@@ -46,6 +46,9 @@ class Molecule(Base):
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  thermal_enthalpy_corr: Optional[float] = None
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  thermal_free_energy_corr: Optional[float] = None
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+ def __len__(self) -> int:
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+ return len(self.atoms)
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+
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  @property
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  def coordinates(self) -> list[list[float]]:
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  return [a.position for a in self.atoms]
stjames/settings.py CHANGED
@@ -105,7 +105,7 @@ class Settings(Base):
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  @classmethod
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  def remove_empty_string(cls, v: list[T]) -> list[T]:
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  """Remove empty string values."""
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- return [c for c in v if c]
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+ return [c for c in v if c] if v is not None else v
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  def _assign_settings_by_mode(settings: Settings) -> None:
stjames/solvent.py CHANGED
@@ -35,6 +35,7 @@ class SolventModel(LowercaseStrEnum):
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  CPCM = "cpcm"
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  ALPB = "alpb"
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  COSMO = "cosmo"
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+ CPCMX = "cpcmx"
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  class SolventSettings(Base):
stjames/workflows/conformer.py CHANGED
@@ -13,6 +13,7 @@ class ConformerSettings(Base):
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  num_confs_taken: int = 50
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  rmsd_cutoff: float = 0.1
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+ transition_state: bool = False
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  final_method: Method = Method.AIMNET2_WB97MD3
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  solvent: Optional[Solvent] = Solvent.WATER
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  max_energy: float = 5
{stjames-0.0.39.dist-info → stjames-0.0.40.dist-info}/METADATA RENAMED
@@ -1,6 +1,6 @@
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  Metadata-Version: 2.1
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  Name: stjames
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- Version: 0.0.39
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+ Version: 0.0.40
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  Summary: standardized JSON atom/molecule encoding scheme
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  Author-email: Corin Wagen <corin@rowansci.com>
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  Project-URL: Homepage, https://github.com/rowansci/stjames
{stjames-0.0.39.dist-info → stjames-0.0.40.dist-info}/RECORD RENAMED
@@ -11,17 +11,17 @@ stjames/int_settings.py,sha256=5HXp8opt5ZyY1UpmfaK7NVloWVLM5jkG0elEEqpVLUo,896
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  stjames/message.py,sha256=Rq6QqmHZKecWxYH8fVyXmuoCCPZv8YinvgykSeorXSU,216
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  stjames/method.py,sha256=iThn9tkkM0x0uX95o3Tcz3QQtad47UYGDL76hW3ySaM,787
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  stjames/mode.py,sha256=xw46Cc7f3eTS8i35qECi-8DocAlANhayK3w4akD4HBU,496
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- stjames/molecule.py,sha256=jCOvFYbEXmUbQpWaWPj5ssaZYTSQN2P7aQ6baOZBFKU,2970
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+ stjames/molecule.py,sha256=G78Bm88r8w-4cx_AOUyxLrn_gIt-TdeoYeBoiociqX8,3032
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  stjames/opt_settings.py,sha256=5nTGih8KZ3x_yGfPL7pdGdsuOpCIfuJUrKoSK5YSDJg,458
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  stjames/py.typed,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
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  stjames/scf_settings.py,sha256=xMMCQ0hVB4nNFSiWesNQZUa_aLsozSZGYWweAPPDGBg,2356
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- stjames/settings.py,sha256=d5hgkHzupa9BT3ILi18TscLhnO3J7MaOz3RLtc-Q6Us,8636
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- stjames/solvent.py,sha256=bGh10jZmfHQACZEAid7zYPyf6tx4G1ql3GgINHswy7Y,1120
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+ stjames/settings.py,sha256=mn9TY2y2Juqou-bfIkXFWM_pbs_90-MgYYzAnWXCwVQ,8660
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+ stjames/solvent.py,sha256=0Kb2O3kTXMbcTH2br9bg7vtgG-Q7uRzhcMKSdUktVNo,1140
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  stjames/status.py,sha256=wTKNcNxStoEHrxxgr_zTyN90NITa3rxMQZzOgrCifEw,332
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  stjames/task.py,sha256=TTl-iTdvDNCZTdPsyS6bYmxzY0ez9PgYlL62fztayXQ,307
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  stjames/thermochem_settings.py,sha256=ZTLz31v8Ltutde5Nfm0vH5YahWjcfFWfr_R856KffxE,517
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  stjames/workflows/__init__.py,sha256=sy9J04mCJpyVGcG4DecCi6pncwbZVvybI7sJKzavjgo,167
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- stjames/workflows/conformer.py,sha256=10mMhXhFoCUsOvSBp06Q16WufD66YiWCBuBcJEZr9vg,2697
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+ stjames/workflows/conformer.py,sha256=YYwL3l7OaVeea4N9-ihghwa_ieKY6hia9LNbiTraMb0,2732
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  stjames/workflows/descriptors.py,sha256=Jqx_4u_ZhdFJrT-ITU6zlFY0n8llh6zhzIhM38e8NCs,255
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  stjames/workflows/fukui.py,sha256=FAabgLi_ig6Zp_jiTkuveP0wAObwv68liuumr85rb0g,366
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  stjames/workflows/pka.py,sha256=zpR90Yv2L-D56o2mGArM8027DWpnFFnay31UR9Xh5Nc,774
@@ -29,8 +29,8 @@ stjames/workflows/redox_potential.py,sha256=iPkFt1Dj1sUywS9pLSEBVpCjHZcEwUESluY0
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  stjames/workflows/scan.py,sha256=d1ca1uk1nxdzlSwqMLZ0W1_DHyrQMnHJmvPfziCS0SA,773
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  stjames/workflows/tautomer.py,sha256=kZSCHo2Q7LzqtQjF_WyyxjECkndG49T9QOM12hsUkx8,421
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  stjames/workflows/workflow.py,sha256=6hFe5PZejJu6bZ3yTkoJ9-xQMBn_-8tUsbk4FUZxog0,367
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- stjames-0.0.39.dist-info/LICENSE,sha256=i7ehYBS-6gGmbTcgU4mgk28pyOx2kScJ0kcx8n7bWLM,1084
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- stjames-0.0.39.dist-info/METADATA,sha256=I5myRzxjdcbV2yKvOX3QiCw3o_w3Y2c5j2b3ehFZGvE,1626
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- stjames-0.0.39.dist-info/WHEEL,sha256=Z4pYXqR_rTB7OWNDYFOm1qRk0RX6GFP2o8LgvP453Hk,91
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- stjames-0.0.39.dist-info/top_level.txt,sha256=FYCwxl6quhYOAgG-mnPQcCK8vsVM7B8rIUrO-WrQ_PI,8
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- stjames-0.0.39.dist-info/RECORD,,
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+ stjames-0.0.40.dist-info/LICENSE,sha256=i7ehYBS-6gGmbTcgU4mgk28pyOx2kScJ0kcx8n7bWLM,1084
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+ stjames-0.0.40.dist-info/METADATA,sha256=GeuHmCFTQwu5cq521KVGYIdQBKmyOuBwonQ19a3ShO0,1626
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+ stjames-0.0.40.dist-info/WHEEL,sha256=Z4pYXqR_rTB7OWNDYFOm1qRk0RX6GFP2o8LgvP453Hk,91
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+ stjames-0.0.40.dist-info/top_level.txt,sha256=FYCwxl6quhYOAgG-mnPQcCK8vsVM7B8rIUrO-WrQ_PI,8
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+ stjames-0.0.40.dist-info/RECORD,,