stjames 0.0.93__tar.gz → 0.0.95__tar.gz

{stjames-0.0.93/stjames.egg-info → stjames-0.0.95}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: stjames
-Version: 0.0.93
+Version: 0.0.95
 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 → stjames-0.0.95}/pyproject.toml

@@ -1,6 +1,6 @@
 [project]
 name = "stjames"
-version = "0.0.93"
+version = "0.0.95"
 description = "standardized JSON atom/molecule encoding scheme"
 readme = "README.md"
 requires-python = ">=3.11"

{stjames-0.0.93 → stjames-0.0.95}/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-0.0.95/stjames/scf_settings.py

@@ -0,0 +1,19 @@
+from .base import Base, LowercaseStrEnum
+
+
+class UseSOSCF(LowercaseStrEnum):
+    ALWAYS = "always"
+    UPON_FAILURE = "upon_failure"
+    NEVER = "never"
+
+
+class SCFSettings(Base):
+    """
+    Settings for SCF convergence.
+
+    :param max_iters: the maximum number of SCF iterations to permit
+    :param soscf: whether or not to use SOSCF (second-order SCF).
+    """
+
+    max_iters: int = 250
+    soscf: UseSOSCF = UseSOSCF.UPON_FAILURE

{stjames-0.0.93 → stjames-0.0.95}/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-0.0.93 → stjames-0.0.95}/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-0.0.93 → stjames-0.0.95}/stjames/workflows/__init__.py

@@ -17,6 +17,7 @@ from .irc import *
 from .macropka import *
 from .molecular_dynamics import *
 from .multistage_opt import *
+from .nmr import *
 from .pka import *
 from .pose_analysis_md import *
 from .protein_cofolding import *
@@ -43,6 +44,7 @@ WORKFLOW_NAME = Literal[
     "macropka",
     "molecular_dynamics",
     "multistage_opt",
+    "nmr",
     "pka",
     "pose_analysis_md",
     "protein_cofolding",
@@ -69,6 +71,7 @@ WORKFLOW_MAPPING: dict[WORKFLOW_NAME, Workflow] = {
     "macropka": MacropKaWorkflow,  # type: ignore [dict-item]
     "molecular_dynamics": MolecularDynamicsWorkflow,  # type: ignore [dict-item]
     "multistage_opt": MultiStageOptWorkflow,  # type: ignore [dict-item]
+    "nmr": NMRSpectroscopyWorkflow,  # type: ignore [dict-item]
     "pka": pKaWorkflow,  # type: ignore [dict-item]
     "pose_analysis_md": PoseAnalysisMolecularDynamicsWorkflow,  # type: ignore [dict-item]
     "protein_cofolding": ProteinCofoldingWorkflow,  # type: ignore [dict-item]

{stjames-0.0.93 → stjames-0.0.95}/stjames/workflows/ion_mobility.py

@@ -1,6 +1,11 @@
 """Ion mobility workflow."""
 
-from ..types import UUID
+from typing import Annotated
+
+from pydantic import AfterValidator
+
+from ..base import round_optional_float
+from ..types import UUID, round_list
 from .workflow import MoleculeWorkflow
 
 
@@ -34,9 +39,9 @@ class IonMobilityWorkflow(MoleculeWorkflow):
 
     conformers: list[UUID] = []
 
-    conformer_ccs: list[float] = []
-    conformer_ccs_stdev: list[float] = []
-    boltzmann_weights: list[float] = []
+    conformer_ccs: Annotated[list[float], AfterValidator(round_list(3))] = []
+    conformer_ccs_stdev: Annotated[list[float], AfterValidator(round_list(3))] = []
+    boltzmann_weights: Annotated[list[float], AfterValidator(round_list(3))] = []
 
-    average_ccs: float | None = None
-    average_ccs_stdev: float | None = None
+    average_ccs: Annotated[float | None, AfterValidator(round_optional_float(3))] = None
+    average_ccs_stdev: Annotated[float | None, AfterValidator(round_optional_float(3))] = None

stjames-0.0.95/stjames/workflows/nmr.py

@@ -0,0 +1,54 @@
+"""Nuclear-magnetic-resonance spectroscopy workflow."""
+
+from typing import Annotated
+
+from pydantic import AfterValidator
+
+from ..base import LowercaseStrEnum
+from ..mode import Mode
+from ..settings import Settings
+from ..solvent import Solvent
+from ..types import UUID, round_list
+from .conformer_search import ConformerGenSettings, iMTDSettings
+from .multistage_opt import MultiStageOptSettings
+from .workflow import MoleculeWorkflow
+
+
+class NMRMethod(LowercaseStrEnum):
+    MAGNETZERO = "magnet-zero"
+
+
+class NMRSpectroscopyWorkflow(MoleculeWorkflow):
+    """
+    Workflow for calculating NMR spectra.
+
+    Inherited:
+    :param initial_molecule: Molecule of interest
+    :param mode: Mode for workflow (currently unused)
+
+    New:
+    :param nmr_method: how to run the NMR calculations
+    :param solvent: the solvent in which to run the calculations
+    :param conf_gen_settings : the conformer-search settings. if `None`, no conformer search will be performed
+    :param multistage_opt_settings: the optimization settings. if `None`, no optimization will be performed
+
+    Results:
+    :param conformers: list of conformer UUIDs
+    :param boltzmann_weights: the boltzmann weights for each conformer
+    :param per_conformer_isotopic_shieldings: the per-atom shieldings for each conformer
+    :param isotopic_shieldings: the per-atom shieldings
+    """
+
+    nmr_method: NMRMethod = NMRMethod.MAGNETZERO
+    solvent: Solvent = Solvent.CHLOROFORM
+
+    conf_gen_settings: ConformerGenSettings | None = iMTDSettings(mode="careful")
+    multistage_opt_settings: MultiStageOptSettings | None = MultiStageOptSettings(
+        mode=Mode.MANUAL,
+        optimization_settings=[Settings(method="aimnet2_wb97md3")],
+    )
+
+    conformers: list[UUID] = []
+    boltzmann_weights: Annotated[list[float], AfterValidator(round_list(3))] = []
+    per_conformer_isotropic_shieldings: list[Annotated[list[float], AfterValidator(round_list(3))]] = []
+    isotropic_shieldings: Annotated[list[float], AfterValidator(round_list(3))] = []

{stjames-0.0.93 → stjames-0.0.95}/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 → stjames-0.0.95/stjames.egg-info}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: stjames
-Version: 0.0.93
+Version: 0.0.95
 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 → stjames-0.0.95}/stjames.egg-info/SOURCES.txt

@@ -10,10 +10,7 @@ stjames/calculation.py
 stjames/compute_settings.py
 stjames/constraint.py
 stjames/correction.py
-stjames/diis_settings.py
 stjames/engine.py
-stjames/grid_settings.py
-stjames/int_settings.py
 stjames/message.py
 stjames/method.py
 stjames/mode.py
@@ -62,6 +59,7 @@ stjames/workflows/irc.py
 stjames/workflows/macropka.py
 stjames/workflows/molecular_dynamics.py
 stjames/workflows/multistage_opt.py
+stjames/workflows/nmr.py
 stjames/workflows/pka.py
 stjames/workflows/pose_analysis_md.py
 stjames/workflows/protein_cofolding.py

stjames-0.0.93/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-0.0.93/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-0.0.93/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

stjames-0.0.93/stjames/scf_settings.py

@@ -1,77 +0,0 @@
-from typing import Any, Optional
-
-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 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