schrodinger.application.transforms.prepwizard module¶

PrepWizard transforms for preparing protein structures.

class schrodinger.application.transforms.prepwizard.PrepWizardConfig(*, settings: schrodinger.application.prepwizard.PrepWizardSettings | None = None, force_field: ~typing.Literal['OPLS_2005', 'S-OPLS'] = 'OPLS_2005', preserve_st_titles: bool = False, max_states: int = 1, preprocess: bool = True, assign_bond_orders: bool = True, use_ccd: bool = True, skip_assigned_residues: bool = False, add_missing_inter_residue_bonds: bool = True, add_terminal_oxygens: bool = False, add_hydrogens: bool = False, readd_hydrogens: bool = True, idealize_hydrogen_tf: bool = True, preprocess_delete_far_waters: bool = False, preprocess_watdist: ~typing.Optional[float] = None, delete_far_waters: bool = True, watdist: float = 5.0, delete_nonbridging_waters: bool = False, delwater_hbond_cutoff: int = 0, treat_metals: bool = True, treat_disulfides: bool = True, treat_glycosylation: bool = True, treat_palmitoylation: bool = False, selenomethionines: bool = True, cap_termini: bool = False, cap_termini_min_atoms: int = 200, fillsidechains: bool = False, fillloops: bool = False, custom_fasta_file: ~typing.Optional[~pathlib.Path] = None, annotate_gpcr: bool = False, antibody_cdr_scheme: ~typing.Literal['Chothia', 'Kabat', 'IMGT', 'EnhancedChothia', 'AHo'] = 'Kabat', renumber_ab_residues: bool = False, tcr_cdr_scheme: ~typing.Optional[~typing.Literal['Chothia', 'Kabat', 'IMGT', 'EnhancedChothia', 'AHo']] = 'IMGT', renumber_tcr_residues: bool = False, run_epik: bool = True, include_epik_states: bool = True, epik_pH: float = 7.4, epik_pHt: float = 2.0, xtal: bool = False, run_protassign: bool = True, sample_water_orientation: bool = True, use_propka: bool = True, propka_pH: float = 7.4, pH: float = 7.4, simplified_pH: ~typing.Literal['very_low', 'low', 'neutral', 'high'] = 'neutral', label_pkas: bool = False, minimize_adj_h: bool = False, protassign_number_sequential_cycles: ~typing.Optional[int] = None, protassign_max_cluster_size: ~typing.Optional[int] = None, run_refine: bool = True, rmsd: float = 0.3, fixheavy: bool = False, reference_struct_path: ~typing.Optional[~pathlib.Path] = None, use_PDB_pH: bool = False, force_list: list[str] = <factory>, error_handling: schrodinger.seam.transforms.outcomes.ErrorHandling | None = None)¶

Bases: BaseModel

Configuration for PrepWizard transforms.

settings: Annotated[PrepWizardSettings | None, WithJsonSchema({})]¶

force_field: ForceFieldName¶

preserve_st_titles: bool¶

max_states: PositiveInt¶

preprocess: bool¶

assign_bond_orders: bool¶

use_ccd: bool¶

skip_assigned_residues: bool¶

add_missing_inter_residue_bonds: bool¶

add_terminal_oxygens: bool¶

add_hydrogens: bool¶

readd_hydrogens: bool¶

idealize_hydrogen_tf: bool¶

preprocess_delete_far_waters: bool¶

preprocess_watdist: NonNegativeFloat | None¶

delete_far_waters: bool¶

watdist: NonNegativeFloat¶

delete_nonbridging_waters: bool¶

delwater_hbond_cutoff: NonNegativeInt¶

treat_metals: bool¶

treat_disulfides: bool¶

treat_glycosylation: bool¶

treat_palmitoylation: bool¶

selenomethionines: bool¶

cap_termini: bool¶

cap_termini_min_atoms: NonNegativeInt¶

fillsidechains: bool¶

fillloops: bool¶

custom_fasta_file: FilePath | None¶

annotate_gpcr: bool¶

antibody_cdr_scheme: CDRSchemeName¶

renumber_ab_residues: bool¶

tcr_cdr_scheme: CDRSchemeName | None¶

renumber_tcr_residues: bool¶

run_epik: bool¶

include_epik_states: bool¶

epik_pH: PH_TYPE¶

epik_pHt: NonNegativeFloat¶

xtal: bool¶

run_protassign: bool¶

sample_water_orientation: bool¶

use_propka: bool¶

propka_pH: PH_TYPE¶

pH: PH_TYPE¶

simplified_pH: SimplifiedPH¶

label_pkas: bool¶

minimize_adj_h: bool¶

protassign_number_sequential_cycles: PositiveInt | None¶

protassign_max_cluster_size: PositiveInt | None¶

run_refine: bool¶

rmsd: PositiveFloat¶

fixheavy: bool¶

reference_struct_path: FilePath | None¶

use_PDB_pH: bool¶

force_list: list[str]¶

error_handling: ErrorHandling | None¶

model_config: ClassVar[ConfigDict] = {'arbitrary_types_allowed': True, 'frozen': True}¶: Configuration for the model, should be a dictionary conforming to [ConfigDict][pydantic.config.ConfigDict].

class schrodinger.application.transforms.prepwizard.PrepWizardResult(*, source_id: ~schrodinger.seam.io.sourceid.SourceID, output_structures: list[schrodinger.structure._structure.Structure] = <factory>)¶

Bases: BaseModel

Per-input result from RunPrepWizard.

source_id: SourceID¶

output_structures: list[Structure]¶

model_config: ClassVar[ConfigDict] = {'arbitrary_types_allowed': True, 'frozen': True}¶: Configuration for the model, should be a dictionary conforming to [ConfigDict][pydantic.config.ConfigDict].

class schrodinger.application.transforms.prepwizard.RunPrepWizard(settings: PrepWizardSettings | None = None, **kwargs)¶

Bases: PTransformWithConfig

Run PrepWizard and emit a PrepWizardResult per input structure.

config_class¶: alias of PrepWizardConfig

__init__(settings: PrepWizardSettings | None = None, **kwargs)¶

Initialize the transform with configuration.

All keyword arguments are passed to the config_class constructor to create a validated configuration instance stored as self.config.

Parameters:

_config – An existing configuration model
kwargs – Configuration parameters for the config_class

Raises:

AttributeError – If config_class is not defined on the subclass
ValueError – If _config is combined with kwargs
ValidationError – If the configuration parameters are invalid

class schrodinger.application.transforms.prepwizard.ProteinPrep(settings: PrepWizardSettings | None = None, **kwargs)¶