stjames 0.0.93__py3-none-any.whl → 0.0.94__py3-none-any.whl

stjames/__init__.py

@@ -7,12 +7,9 @@ from .molecule import *
 from .workflows import *
 
 from .scf_settings import *
-from .int_settings import *
 from .opt_settings import *
 from .compute_settings import *
-from .diis_settings import *
 from .thermochem_settings import *
-from .grid_settings import *
 from .settings import *
 
 from .method import *

stjames/scf_settings.py

@@ -1,77 +1,7 @@
-from typing import Any, Optional
+from pydantic import BaseModel
 
-import pydantic
-from pydantic import PositiveFloat, PositiveInt
 
-from .base import Base, LowercaseStrEnum
-from .diis_settings import DIISSettings
-from .grid_settings import GridSettings
-from .int_settings import IntSettings
+class SCFSettings(BaseModel):
+    max_iters: int = 250
 
-
-class SCFInitMethod(LowercaseStrEnum):
-    # (See https://manual.q-chem.com/5.2/Ch4.S4.SS2.html for a nice overview here.)
-    SAD = "sad"
-    CORE = "core"
-    #    GWH = "gwh"
-    READ = "read"
-
-
-class OrthonormalizationMethod(LowercaseStrEnum):
-    SYMMETRIC = "symmetric"
-    CANONICAL = "canonical"
-    # Cholesky, in future?
-
-
-class SCFSettings(Base):
-    max_iters: int = 100
-    init_method: SCFInitMethod = SCFInitMethod.SAD
-
-    int_settings: IntSettings = IntSettings()
-    grid_settings: GridSettings = GridSettings()
-    diis_settings: DIISSettings = DIISSettings()
-
-    #### orthonormalization
-    orthonormalization: OrthonormalizationMethod = OrthonormalizationMethod.CANONICAL
-
-    #### damping
-    do_damping: bool = True
-    # when should we stop damping?
-    end_damping_error: PositiveFloat = 0.1
-    # what damping factor should we use?
-    damping_factor: float = pydantic.Field(ge=0, le=1, default=0.7)
-
-    #### level shifting
-    do_level_shift: bool = True
-    # how much? (Eh)
-    level_shift_magnitude: PositiveFloat = 0.25
-    # when should we stop?
-    end_level_shift_error: PositiveFloat = 0.1
-
-    #### incremental
-    # do incremental fock build?
-    do_incremental: bool = True
-    # reset incremental fock build
-    rebuild_frequency: PositiveInt = 20
-
-    #### when are we converged?
-    energy_threshold: PositiveFloat = 1e-6
-    rms_error_threshold: PositiveFloat = 1e-8
-    max_error_threshold: PositiveFloat = 1e-5
-
-    #### DIIS
-    do_diis: bool = True
-    # error below which we'll start DIIS
-    start_diis_max_error: pydantic.PositiveFloat = 0.2
-    # first iteration we'll consider starting DIIS
-    start_diis_iter: PositiveInt = 3
-    # iteration past which we'll start DIIS even if error is high
-    start_diis_anyway: PositiveInt = 7
-
-    # if ``read`` initialization is selected
-    initial_density_matrix_guess: Optional[list[list[float]]] = None
-
-    def model_post_init(self, __context: Any) -> None:
-        # disable incremental Fock for RI
-        if self.int_settings.resolution_of_the_identity:
-            self.do_incremental = False
+    soscf: bool = False

stjames/settings.py

@@ -68,7 +68,6 @@ class Settings(Base):
         if self.mode == Mode.AUTO:
             self.mode = Mode.RAPID
 
-        self.scf_settings = _assign_scf_settings_by_mode(self.mode, self.scf_settings)
         self.opt_settings = _assign_opt_settings_by_mode(self.mode, self.opt_settings)
 
         return self
@@ -115,74 +114,6 @@ class Settings(Base):
         return [c for c in v if c] if v is not None else v
 
 
-def _assign_scf_settings_by_mode(mode: Mode, scf_settings: SCFSettings) -> SCFSettings:
-    """
-    Assign SCF settings based on the mode.
-
-    Values based off of the following sources:
-    QChem:
-        - https://manual.q-chem.com/5.2/Ch4.S3.SS2.html
-        - https://manual.q-chem.com/5.2/Ch4.S5.SS2.html
-
-    Gaussian:
-        - https://gaussian.com/integral/
-        - https://gaussian.com/overlay5/
-
-    Orca:
-        - manual 4.2.1, §9.6.1 and §9.7.3
-
-    Psi4:
-        - https://psicode.org/psi4manual/master/autodir_options_c/module__scf.html
-        - https://psicode.org/psi4manual/master/autodoc_glossary_options_c.html
-
-    TeraChem:
-        - Manual, it's easy to locate everything.
-
-    The below values are my best attempt at homogenizing various sources.
-    In general, eri_threshold should be 3 OOM lower than SCF convergence.
-    """
-    if mode == Mode.MANUAL:
-        return scf_settings
-
-    match mode:
-        case Mode.RECKLESS:
-            scf_settings.energy_threshold = 1e-5
-            scf_settings.rms_error_threshold = 1e-7
-            scf_settings.max_error_threshold = 1e-5
-            scf_settings.rebuild_frequency = 100
-            scf_settings.int_settings.eri_threshold = 1e-8
-            scf_settings.int_settings.csam_multiplier = 3.0
-            scf_settings.int_settings.pair_overlap_threshold = 1e-8
-        case Mode.RAPID | Mode.CAREFUL:
-            scf_settings.energy_threshold = 1e-6
-            scf_settings.rms_error_threshold = 1e-9
-            scf_settings.max_error_threshold = 1e-7
-            scf_settings.rebuild_frequency = 10
-            scf_settings.int_settings.eri_threshold = 1e-10
-            scf_settings.int_settings.csam_multiplier = 1.0
-            scf_settings.int_settings.pair_overlap_threshold = 1e-10
-        case Mode.METICULOUS:
-            scf_settings.energy_threshold = 1e-8
-            scf_settings.rms_error_threshold = 1e-9
-            scf_settings.max_error_threshold = 1e-7
-            scf_settings.rebuild_frequency = 5
-            scf_settings.int_settings.eri_threshold = 1e-12
-            scf_settings.int_settings.csam_multiplier = 1.0
-            scf_settings.int_settings.pair_overlap_threshold = 1e-12
-        case Mode.DEBUG:
-            scf_settings.energy_threshold = 1e-9
-            scf_settings.rms_error_threshold = 1e-10
-            scf_settings.max_error_threshold = 1e-9
-            scf_settings.rebuild_frequency = 1
-            scf_settings.int_settings.eri_threshold = 1e-14
-            scf_settings.int_settings.csam_multiplier = 1e10  # in other words, disable CSAM
-            scf_settings.int_settings.pair_overlap_threshold = 1e-14
-        case _:
-            raise ValueError(f"Unknown mode ``{mode.value}``!")
-
-    return scf_settings
-
-
 def _assign_opt_settings_by_mode(mode: Mode, opt_settings: OptimizationSettings) -> OptimizationSettings:
     """
     Assign optimization settings based on the mode.

stjames/status.py

@@ -19,3 +19,6 @@ class Status(int, Enum):
 
     # Status if a user has exceeded their allowed max_concurrency
     AWAITING_QUEUE = 5
+
+    # Job is not yet submitted
+    DRAFT = 6

stjames/workflows/protein_cofolding.py

@@ -1,6 +1,6 @@
 """Protein Cofolding Workflow."""
 
-from typing import Annotated
+from typing import Annotated, Literal
 
 from pydantic import AfterValidator, BaseModel, ConfigDict
 
@@ -17,6 +17,33 @@ class CofoldingModel(LowercaseStrEnum):
     BOLTZ_2 = "boltz_2"
 
 
+class Token(BaseModel):
+    """Either a atom in a ligand or a residue in a protein."""
+
+    input_type: Literal["ligand", "protein"]
+    input_index: int
+    token_index: int
+
+
+class ContactConstraint(BaseModel):
+    """Contact constraint to be used for prediction."""
+
+    token_1: Token
+    token_2: Token
+    max_distance: float  # Angstroms
+    force: bool = False  # Whether to use potentials to enforce the constraint
+
+
+class PocketConstraint(BaseModel):
+    """Pocket constraint to be used for prediction."""
+
+    input_type: Literal["ligand", "protein"]
+    input_index: int
+    contacts: list[Token]
+    max_distance: float  # Angstroms
+    force: bool = False  # Whether to use potentials to enforce the constraint
+
+
 class CofoldingScores(BaseModel):
     confidence_score: Annotated[float, AfterValidator(round_float(3))]
     ptm: Annotated[float, AfterValidator(round_float(3))]  # predicted template modeling score
@@ -52,6 +79,9 @@ class ProteinCofoldingWorkflow(FASTAWorkflow):
     use_msa_server: bool = False
     use_templates_server: bool = False
     use_potentials: bool = False
+    contact_constraints: list[ContactConstraint] = []
+    pocket_constraints: list[PocketConstraint] = []
+
     predicted_structure_uuid: UUID | None = None
     scores: CofoldingScores | None = None
     model: CofoldingModel = CofoldingModel.BOLTZ_2

{stjames-0.0.93.dist-info → stjames-0.0.94.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: stjames
-Version: 0.0.93
+Version: 0.0.94
 Summary: standardized JSON atom/molecule encoding scheme
 Author-email: Corin Wagen <corin@rowansci.com>
 Project-URL: Homepage, https://github.com/rowansci/stjames

{stjames-0.0.93.dist-info → stjames-0.0.94.dist-info}/RECORD

@@ -1,4 +1,4 @@
-stjames/__init__.py,sha256=8kqGRUcrOQY07DHp6VJN7GEttPPTHw49QpieMeQqkwE,608
+stjames/__init__.py,sha256=i_vqziEdoBNXhD7Gjb2_1zLkSx0Ko1N8BnCk6No_T6A,522
 stjames/_deprecated_solvent_settings.py,sha256=gj5j9p3zakIwSTK5_ndqBXJx--IzjZNxZ75z-wipLOo,450
 stjames/atom.py,sha256=hQCTMu3y30dvqjyCInnSs47DkUEnwhm_M2qB2jTD4Ik,2153
 stjames/base.py,sha256=YhmNZqFdWYD_lCw8rD2fZtt17nh8g7lUFBnGMezB-u8,1837
@@ -7,10 +7,7 @@ stjames/calculation.py,sha256=O2LwwQ_cOLmDOGXTHA9J71YbUZXigUSbvbLA-fSVm3w,915
 stjames/compute_settings.py,sha256=wuYE6W4WqP3oFHwAeEp7XQ0oMz_MNLucWgrsuJ4kEFQ,268
 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=8Cj0JYGMEaS_Cetfz8Wcu6-BZAv1SejRSagMgkKaXs0,4469
 stjames/mode.py,sha256=xw46Cc7f3eTS8i35qECi-8DocAlANhayK3w4akD4HBU,496
@@ -19,10 +16,10 @@ stjames/opt_settings.py,sha256=LEwGXUEKq5TfU5rr60Z4QQBhCqiw1Ch5w0M_lXawWo8,642
 stjames/pdb.py,sha256=6ayVUUdTufkXs_nfpRQuT1yGvymuyICB4L5Wh55OsaA,26507
 stjames/periodic_cell.py,sha256=eV_mArsY_MPEFSrFEsTC-CyCc6V8ITAXdk7yhjjNI7M,1080
 stjames/py.typed,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
-stjames/scf_settings.py,sha256=WotVgVrayQ_8PUHP39zVtG7iLT9PV41lpzruttFACP8,2356
-stjames/settings.py,sha256=NrNtHq-78BNp4RMP0tsABv4BjS5EscANakCyRdImI-A,8967
+stjames/scf_settings.py,sha256=Wx_Op5k4renAd-kUV1Utstb7iLxc5OHMQpOHJaAMAHA,113
+stjames/settings.py,sha256=qZ3yhuMIQNiLs8Z-uEyVReSg2IQAjnDzQ6euHHqE6xI,6128
 stjames/solvent.py,sha256=u037tmu-9oa21s-WEDZ7VC7nuNVjkqR2ML4JWjWSME4,1158
-stjames/status.py,sha256=0mOeF9CoW2gGMfOkAlxTOL32jXNdJ0cU1-Xwo9DCxUc,455
+stjames/status.py,sha256=KQHDqWSd4kBLow23YLcfOkFdtqN61RFZI-jf2zANWRY,501
 stjames/task.py,sha256=OLINRqe66o7t8arffilwmggrF_7TH0L79u6DhGruxV8,329
 stjames/thermochem_settings.py,sha256=ZTLz31v8Ltutde5Nfm0vH5YahWjcfFWfr_R856KffxE,517
 stjames/types.py,sha256=Fco-Lw8DYvUhbSvOjYZHaE_AaMyFNdWLUjNvb5aTAzw,4498
@@ -56,15 +53,15 @@ stjames/workflows/molecular_dynamics.py,sha256=kxugE73Ntzpj-xpJSoQ1EwGzXXdvi_NTy
 stjames/workflows/multistage_opt.py,sha256=SpbA8hNvktnlLS7C-9mBNGluBSrdVS8ygHl1C4TzWcI,16499
 stjames/workflows/pka.py,sha256=j3vBh2YM3nJzJ1XJKPsmYahRCeaU9n3P-G-u9_moaFw,2065
 stjames/workflows/pose_analysis_md.py,sha256=ES0XlzaLpTjhLrNvcB0zFZa1b1ZHXekN72EbLsx0Skw,4723
-stjames/workflows/protein_cofolding.py,sha256=_05DCzzKGZFtns9HARAMjcWxVrJU9DPb3VNVWSgwWR8,2173
+stjames/workflows/protein_cofolding.py,sha256=6WWbVOGzFjIRgQLMmMVODfIxo1jYFmRS1xnJmN0kOBw,3016
 stjames/workflows/redox_potential.py,sha256=7S18t9Y3eynSnA3lZbRlvLfdbgeBopdiigLzt1zxg5c,3871
 stjames/workflows/scan.py,sha256=DXQBpa2t2PowAtOwmdgpxaSLq--fEShljzAGSb8Nf5U,2993
 stjames/workflows/solubility.py,sha256=kGfVyPPGDLRpf2j6dSY7woCkfsoXSbUzdSImA4mcMpw,1898
 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-0.0.93.dist-info/licenses/LICENSE,sha256=i7ehYBS-6gGmbTcgU4mgk28pyOx2kScJ0kcx8n7bWLM,1084
-stjames-0.0.93.dist-info/METADATA,sha256=45Vdq_ji_cnZN3uRObImOTBgOsc9lcVCJOTWVms8xjY,1724
-stjames-0.0.93.dist-info/WHEEL,sha256=_zCd3N1l69ArxyTb8rzEoP9TpbYXkqRFSNOD5OuxnTs,91
-stjames-0.0.93.dist-info/top_level.txt,sha256=FYCwxl6quhYOAgG-mnPQcCK8vsVM7B8rIUrO-WrQ_PI,8
-stjames-0.0.93.dist-info/RECORD,,
+stjames-0.0.94.dist-info/licenses/LICENSE,sha256=i7ehYBS-6gGmbTcgU4mgk28pyOx2kScJ0kcx8n7bWLM,1084
+stjames-0.0.94.dist-info/METADATA,sha256=WjfSeqw_fW_J-9vstRKCwTHyJ5TVi0ZYO2BujRC2ucw,1724
+stjames-0.0.94.dist-info/WHEEL,sha256=_zCd3N1l69ArxyTb8rzEoP9TpbYXkqRFSNOD5OuxnTs,91
+stjames-0.0.94.dist-info/top_level.txt,sha256=FYCwxl6quhYOAgG-mnPQcCK8vsVM7B8rIUrO-WrQ_PI,8
+stjames-0.0.94.dist-info/RECORD,,

stjames/diis_settings.py

@@ -1,23 +0,0 @@
-import pydantic
-
-from .base import Base, LowercaseStrEnum
-
-
-class DIISStrategy(LowercaseStrEnum):
-    # regular Pulay DIIS
-    DIIS = "diis"
-
-    # Hu/Yang JCP 2010 - ADIIS
-    ADIIS = "adiis"
-
-    # first ADIIS, then DIIS
-    ADIIS_DIIS = "adiis_diis"
-
-
-class DIISSettings(Base):
-    strategy: DIISStrategy = DIISStrategy.ADIIS_DIIS
-    subspace_size: pydantic.PositiveInt = 12
-
-    # if it's a hybrid strategy, where do we transition?
-    adiis_diis_blend_start: pydantic.PositiveFloat = 1e-1
-    adiis_diis_blend_stop: pydantic.PositiveFloat = 1e-4

stjames/grid_settings.py

@@ -1,27 +0,0 @@
-import pydantic
-
-from .base import Base, LowercaseStrEnum
-
-
-class RadialGridType(LowercaseStrEnum):
-    """What sort of radial grid (only one option for now)"""
-
-    KRACK_KOSTER = "krack_koster"
-    LMG = "lmg"
-
-
-class GridSettings(Base):
-    radial_grid_type: RadialGridType = RadialGridType.LMG
-    angular_num_points: pydantic.PositiveInt = 434
-
-    weight_cutoff: pydantic.PositiveFloat = 1e-11
-
-    # for LMG
-    radial_precision: pydantic.PositiveFloat = 1e-11
-
-    # for other schemes, like KK
-    radial_num_points: pydantic.PositiveInt = 75
-
-    # pruning?
-    prune: bool = True
-    min_angular_points: pydantic.PositiveInt = 50

stjames/int_settings.py

@@ -1,31 +0,0 @@
-import pydantic
-
-from .base import Base, LowercaseStrEnum
-
-
-class ERIStrategy(LowercaseStrEnum):
-    # direct SCF, as per Almlof/Faegri/Korsell
-    DIRECT = "direct"
-
-    # Raffinetti-style supermatrix
-    SUPERMATRIX = "supermatrix"
-
-    # let the software choose between direct and supermatrix based on size
-    AUTO = "auto"
-
-    # resolution of the identity for J and K
-    RIJK = "rijk"
-
-
-class IntSettings(Base):
-    strategy: ERIStrategy = ERIStrategy.AUTO
-
-    # these will get overwritten by ``mode`` anyway, for the most part
-    eri_threshold: pydantic.PositiveFloat = 1e-9
-    csam_multiplier: pydantic.PositiveFloat = pydantic.Field(default=1, ge=1)
-    pair_overlap_threshold: pydantic.PositiveFloat = 1e-10
-
-    @property
-    def resolution_of_the_identity(self) -> bool:
-        """Abstracting in case we add RIJCOSX, etc later"""
-        return self.strategy == ERIStrategy.RIJK