stjames 0.0.84__py3-none-any.whl → 0.0.87__py3-none-any.whl

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Files changed (7) hide show
  1. stjames/method.py +3 -2
  2. stjames/workflows/pose_analysis_md.py +1 -0
  3. {stjames-0.0.84.dist-info → stjames-0.0.87.dist-info}/METADATA +1 -1
  4. {stjames-0.0.84.dist-info → stjames-0.0.87.dist-info}/RECORD +7 -7
  5. {stjames-0.0.84.dist-info → stjames-0.0.87.dist-info}/WHEEL +0 -0
  6. {stjames-0.0.84.dist-info → stjames-0.0.87.dist-info}/licenses/LICENSE +0 -0
  7. {stjames-0.0.84.dist-info → stjames-0.0.87.dist-info}/top_level.txt +0 -0
stjames/method.py CHANGED
@@ -43,6 +43,7 @@ class Method(LowercaseStrEnum):
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  GFN0_XTB = "gfn0_xtb"
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  GFN1_XTB = "gfn1_xtb"
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  GFN2_XTB = "gfn2_xtb"
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+ G_XTB = "g_xtb"
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  # this was going to be removed, but Jonathon wrote such a nice basis set test... it's off the front end.
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  BP86 = "bp86"
@@ -86,8 +87,8 @@ CORRECTABLE_NNP_METHODS = [Method.MACE_MP_0B2_L, Method.ORB_V2]
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  NNPMethod = PrepackagedNNPMethod | CorrectableNNPMethod
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  NNP_METHODS = [*PREPACKAGED_NNP_METHODS, *CORRECTABLE_NNP_METHODS]
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- XTBMethod = Literal[Method.GFN_FF, Method.GFN0_XTB, Method.GFN1_XTB, Method.GFN2_XTB]
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- XTB_METHODS = [Method.GFN_FF, Method.GFN0_XTB, Method.GFN1_XTB, Method.GFN2_XTB]
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+ XTBMethod = Literal[Method.GFN_FF, Method.GFN0_XTB, Method.GFN1_XTB, Method.GFN2_XTB, Method.G_XTB]
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+ XTB_METHODS = [Method.GFN_FF, Method.GFN0_XTB, Method.GFN1_XTB, Method.GFN2_XTB, Method.G_XTB]
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  CompositeMethod = Literal[Method.HF3C, Method.B973C, Method.R2SCAN3C, Method.WB97X3C]
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  COMPOSITE_METHODS = [Method.HF3C, Method.B973C, Method.R2SCAN3C, Method.WB97X3C]
stjames/workflows/pose_analysis_md.py CHANGED
@@ -94,6 +94,7 @@ class PoseAnalysisMolecularDynamicsWorkflow(MoleculeWorkflow):
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  water_buffer: Annotated[PositiveFloat, AfterValidator(round_float(3))] = 6.0
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  minimized_protein_uuid: UUID | None = None
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+ bonds: list[tuple[int, int]] = []
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  trajectories: list[BindingPoseTrajectory] = []
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  @model_validator(mode="after")
{stjames-0.0.84.dist-info → stjames-0.0.87.dist-info}/METADATA RENAMED
@@ -1,6 +1,6 @@
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  Metadata-Version: 2.4
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  Name: stjames
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- Version: 0.0.84
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+ Version: 0.0.87
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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-0.0.84.dist-info → stjames-0.0.87.dist-info}/RECORD RENAMED
@@ -11,7 +11,7 @@ stjames/diis_settings.py,sha256=4m1EQQWBlpHhMnWopix8qOqJv7QCluvdnV9jSKJDFtE,552
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  stjames/grid_settings.py,sha256=WrSNGc-8_f87YBZYt9Hh7RbhM4MweADoVzwBMcSqcsE,640
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  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=k7WtNvD_0OyXWWDjukmVXFFYfIO-Wg4vY1W58o99-gQ,2821
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+ stjames/method.py,sha256=xurVdREwRfn_eR3P2dB5p1zUlksO2zwXksN5hvsdKhs,2869
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  stjames/mode.py,sha256=xw46Cc7f3eTS8i35qECi-8DocAlANhayK3w4akD4HBU,496
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  stjames/molecule.py,sha256=l4S6prH1xflnZtbwidSF2THsiHaSJtRiy1rmUbH366Q,20631
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  stjames/opt_settings.py,sha256=LEwGXUEKq5TfU5rr60Z4QQBhCqiw1Ch5w0M_lXawWo8,642
@@ -54,7 +54,7 @@ stjames/workflows/macropka.py,sha256=KRIyk4gsSYL3eqyzCDndStGLwjWSo60cgCAzvAoD1Nk
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  stjames/workflows/molecular_dynamics.py,sha256=kxugE73Ntzpj-xpJSoQ1EwGzXXdvi_NTyeP4913EVwE,3173
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  stjames/workflows/multistage_opt.py,sha256=P8rxMUhKXMmDi7Id95IOTEmM0xN1ErsKcDJfgY08vjc,16538
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  stjames/workflows/pka.py,sha256=j3vBh2YM3nJzJ1XJKPsmYahRCeaU9n3P-G-u9_moaFw,2065
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- stjames/workflows/pose_analysis_md.py,sha256=LAn6IXcQIUCt9M54kDzwWkmoCH0r1H99_APFu55skQc,4619
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+ stjames/workflows/pose_analysis_md.py,sha256=hRObMVt4VlL3TMo9yb6SxcpVhjiuPX0tUyaQwbe7qxc,4657
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  stjames/workflows/protein_cofolding.py,sha256=_05DCzzKGZFtns9HARAMjcWxVrJU9DPb3VNVWSgwWR8,2173
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  stjames/workflows/redox_potential.py,sha256=7S18t9Y3eynSnA3lZbRlvLfdbgeBopdiigLzt1zxg5c,3871
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  stjames/workflows/scan.py,sha256=DXQBpa2t2PowAtOwmdgpxaSLq--fEShljzAGSb8Nf5U,2993
@@ -62,8 +62,8 @@ stjames/workflows/solubility.py,sha256=kGfVyPPGDLRpf2j6dSY7woCkfsoXSbUzdSImA4mcM
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  stjames/workflows/spin_states.py,sha256=0degmE-frovgoXweshZyjfjqL7nkbaFoO9YoJhvQnaI,4748
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  stjames/workflows/tautomer.py,sha256=7eYKziGPg8Km6lfowTzSkgJfJ4SHUPrAmnTf8Bi-SB0,1164
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  stjames/workflows/workflow.py,sha256=OE05pt2ZOd8TzTOlBngXCVg9wv_553ZR60VNRPlq0f8,1953
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- stjames-0.0.84.dist-info/licenses/LICENSE,sha256=i7ehYBS-6gGmbTcgU4mgk28pyOx2kScJ0kcx8n7bWLM,1084
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- stjames-0.0.84.dist-info/METADATA,sha256=dEb-WmFhVPEDv3AlXVG9gy-t5Pj8Gnz_pY7ZrmEIL4g,1724
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- stjames-0.0.84.dist-info/WHEEL,sha256=_zCd3N1l69ArxyTb8rzEoP9TpbYXkqRFSNOD5OuxnTs,91
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- stjames-0.0.84.dist-info/top_level.txt,sha256=FYCwxl6quhYOAgG-mnPQcCK8vsVM7B8rIUrO-WrQ_PI,8
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- stjames-0.0.84.dist-info/RECORD,,
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+ stjames-0.0.87.dist-info/licenses/LICENSE,sha256=i7ehYBS-6gGmbTcgU4mgk28pyOx2kScJ0kcx8n7bWLM,1084
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+ stjames-0.0.87.dist-info/METADATA,sha256=SovSL3LRuwiQBWTIHGaRsZJg84aNAG1LUz_2CRxM4FU,1724
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+ stjames-0.0.87.dist-info/WHEEL,sha256=_zCd3N1l69ArxyTb8rzEoP9TpbYXkqRFSNOD5OuxnTs,91
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+ stjames-0.0.87.dist-info/top_level.txt,sha256=FYCwxl6quhYOAgG-mnPQcCK8vsVM7B8rIUrO-WrQ_PI,8
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+ stjames-0.0.87.dist-info/RECORD,,