schrodinger.application.jaguar.macro_pka.html_report.macro_pka_report module¶

Self-contained interactive HTML report for Jaguar Macro-pKa.

Interactive scientific calculations are performed by the embedded JavaScript port of the canonical Python numerical kernel. This module owns the typed report model, static Python-generated baseline, structure presentation, and HTML assembly.

class schrodinger.application.jaguar.macro_pka.html_report.macro_pka_report.ReportEntry(id: str, charge: int, label: str, member_ids: tuple[str, ...], mol: Mol, structure: Any)¶

Bases: object

One displayed row entry in a collapsed or split report view.

id: str¶

charge: int¶

label: str¶

member_ids: tuple[str, ...]¶

mol: Mol¶

structure: Any¶

__init__(id: str, charge: int, label: str, member_ids: tuple[str, ...], mol: Mol, structure: Any) → None¶

class schrodinger.application.jaguar.macro_pka.html_report.macro_pka_report.ReportSpecies(id: str, parent_id: str, charge: int, population: float)¶

Bases: object

One selectable stereoisomer and its static baseline population.

id: str¶

parent_id: str¶

charge: int¶

population: float¶

__init__(id: str, parent_id: str, charge: int, population: float) → None¶

class schrodinger.application.jaguar.macro_pka.html_report.macro_pka_report.InitialReportState(species_fractions: dict[str, float], populations: dict[str, float], pka_ordering_physical: bool)¶

Bases: object

Static all-enabled state rendered before JavaScript initialization.

species_fractions: dict[str, float]¶

populations: dict[str, float]¶

pka_ordering_physical: bool¶

__init__(species_fractions: dict[str, float], populations: dict[str, float], pka_ordering_physical: bool) → None¶

class schrodinger.application.jaguar.macro_pka.html_report.macro_pka_report.ReportView(name: str, entries: tuple[ReportEntry, ...])¶

Bases: object

Displayed entries for one stereochemistry presentation.

name: str¶

entries: tuple[ReportEntry, ...]¶

__init__(name: str, entries: tuple[ReportEntry, ...]) → None¶

class schrodinger.application.jaguar.macro_pka.html_report.macro_pka_report.ReportEvaluatorData(input: Input, species_ids: dict[tuple[int, int, int], int])¶

Bases: object

Numerical evaluator input and its report-species mapping.

input: Input¶

species_ids: dict[tuple[int, int, int], int]¶

__init__(input: Input, species_ids: dict[tuple[int, int, int], int]) → None¶

class schrodinger.application.jaguar.macro_pka.html_report.macro_pka_report.MacroPkaTautomerViews(collapsed: Any, split: Any, use_pka_populations: bool)¶

Bases: object

Prepared collapsed and stereoisomer-split tautomer collections.

collapsed: Any¶

split: Any¶

use_pka_populations: bool¶

__init__(collapsed: Any, split: Any, use_pka_populations: bool) → None¶

class schrodinger.application.jaguar.macro_pka.html_report.macro_pka_report.MacroPkaReportData(species: tuple[ReportSpecies, ...], macro_pkas: dict[tuple[int, int], float], collapsed: ReportView, split: ReportView | None, user_pH: float, initial_view: str, display_cutoff: float, use_pka_populations: bool, kernel_input: Input | None = None, kernel_species_ids: dict[str, int] | None = None)¶

Bases: object

Complete scientific and presentation model embedded in the report.

species: tuple[ReportSpecies, ...]¶

macro_pkas: dict[tuple[int, int], float]¶

collapsed: ReportView¶

split: ReportView | None¶

user_pH: float¶

initial_view: str¶

display_cutoff: float¶

use_pka_populations: bool¶

kernel_input: Input | None = None¶

kernel_species_ids: dict[str, int] | None = None¶

initial_state() → InitialReportState¶

as_json_data() → dict¶

__init__(species: tuple[ReportSpecies, ...], macro_pkas: dict[tuple[int, int], float], collapsed: ReportView, split: ReportView | None, user_pH: float, initial_view: str, display_cutoff: float, use_pka_populations: bool, kernel_input: Input | None = None, kernel_species_ids: dict[str, int] | None = None) → None¶

schrodinger.application.jaguar.macro_pka.html_report.macro_pka_report.write_populations_report(jobname: str, tautomer_views: MacroPkaTautomerViews, macro_pkas: dict[tuple[int, int], float], user_pH: float, evaluator: ReportEvaluatorData | None = None, cmdline: str | None = None, scaling: int = 30, cutoff: float = 0.0001, print_warning: bool = False, extra_html: str = '', job_date: str | None = None, build_info: str | None = None) → str¶: Write and register the standard self-contained populations report.

schrodinger.application.jaguar.macro_pka.html_report.macro_pka_report.write_population_curves(jobname: str, tautomers, macro_pkas: dict[tuple[int, int], float], user_pH: float, cutoff: float = 0.0001) → str¶

Write a standalone PNG of tautomer population curves vs pH.

Parameters:

jobname – job name for the output filename
tautomers – the tautomer view used for .out and .mae output — collapsed when split_stereoisomers is off, split when it is on
macro_pkas – macro-pKa values keyed by (prot_charge, deprot_charge)
user_pH – user-requested pH for the reference line
cutoff – population cutoff for including tautomers in the plot

Returns:

path to the output PNG file