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Documentation for alphaPredict

File Path: /home/nicai_zht/.local/share/mamba/envs/idr_llm/lib/python3.13/site-packages/alphaPredict/__init__.py

Module Docstring

short description of alphaPredict.

Predict confidence scores of alphaFold2

🚦 Navigator: How to Drive

This section helps you understand how to run this library from the command line or entry points.

  • ℹ️ No Direct Entry Point: This module seems to be a library intended for import, not direct execution.

🐍 Python API Usage (Inferred)

Since no CLI entry point was found, here are the likely Python API entry points for your script:

🚀 Top 20 Recommended Entry Points

Type API Description
ƒ alphaPredict.predict(sequence) Function to return confidence scores from
ƒ alphaPredict.graph(sequence, title, confidence_threshold, shaded_regions, shaded_region_color, confidence_line_color, threshold_line_color, DPI, output_file) No description.

Note: Bold parameters are required. Others are optional.

🧩 Code Snippets (Auto-Generated)

import alphaPredict

# --- Top 20 Ranked Functions ---
# 1. predict
result_1 = alphaPredict.predict(sequence=...)

# 2. graph
result_2 = alphaPredict.graph(sequence=...)

No explicit argparse configuration detected in the main module.

📊 Network & Architecture Analysis

🌍 Top 20 External Dependencies

Library Usage Count
_frozen_importlib_external 4
_frozen_importlib 4

🕸️ Network Metrics (Advanced)

👑 Top 20 Modules by PageRank (Authority)

Rank Module Score Type Role
1 _frozen_importlib_external 0.2067 External External Lib
2 _frozen_importlib 0.2067 External External Lib
3 alpha 0.1085 Internal Utility / Core
4 alpha_exceptions 0.1030 Internal Utility / Core
5 backend.parrot_alpha 0.1030 Internal External Lib
6 backend.alpha_graph 0.1030 Internal External Lib
7 alphaPredict 0.0846 Internal Utility / Core
8 _version 0.0846 Internal Utility / Core

🗺️ Dependency & Architecture Map

graph TD
    classDef core fill:#f96,stroke:#333,stroke-width:2px;
    classDef external fill:#9cf,stroke:#333,stroke-width:1px;
    id_6["alphaPredict"] -.-> id_1["_frozen_importlib_external"]
    class id_6 core;
    class id_1 external;
    id_6["alphaPredict"] -.-> id_4["_frozen_importlib"]
    class id_6 core;
    class id_4 external;
    id_6["alphaPredict"] --> id_7["alpha"]
    class id_6 core;
    class id_7 core;
    id_7["alpha"] --> id_10["alpha_exceptions"]
    class id_7 core;
    class id_10 core;
    id_7["alpha"] -.-> id_1["_frozen_importlib_external"]
    class id_7 core;
    class id_1 external;
    id_7["alpha"] -.-> id_4["_frozen_importlib"]
    class id_7 core;
    class id_4 external;
    id_7["alpha"] --> id_5["parrot_alpha"]
    class id_7 core;
    class id_5 core;
    id_7["alpha"] --> id_9["alpha_graph"]
    class id_7 core;
    class id_9 core;
    id_2["_version"] -.-> id_1["_frozen_importlib_external"]
    class id_2 core;
    class id_1 external;
    id_2["_version"] -.-> id_4["_frozen_importlib"]
    class id_2 core;
    class id_4 external;
    id_10["alpha_exceptions"] -.-> id_1["_frozen_importlib_external"]
    class id_10 core;
    class id_1 external;
    id_10["alpha_exceptions"] -.-> id_4["_frozen_importlib"]
    class id_10 core;
    class id_4 external;
    id_8["AlphaError"] ==> id_0["Exception"]
    class id_8 core;
    class id_0 external;
    id_8["AlphaError"] ==> id_0["Exception"]
    class id_8 core;
    class id_0 external;
    id_3["DomainError"] ==> id_0["Exception"]
    class id_3 core;
    class id_0 external;
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🚀 Global Execution Flow & Extraction Guide

This graph visualizes how data flows between functions across the entire project.

graph TD
    classDef main fill:#f9f,stroke:#333,stroke-width:2px;
    classDef func fill:#fff,stroke:#333,stroke-width:1px;
    f_3["predict"] -->|sequence| f_0["_alpha_predict"]
    class f_3 func;
    class f_0 func;
    f_2["graph"] -->|sequence<br>title<br>confidence_threshold<br>shaded_regions<br>shaded_region_color<br>confidence_line_color<br>threshold_line_color<br>DPI<br>output_file| f_1["_graph"]
    class f_2 func;
    class f_1 func;
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✂️ Navigator: Snippet Extractor

Want to use a specific function without the whole library? Here is the Dependency Closure for Top 20 key functions.

To extract predict:

You need these 2 components: _alpha_predict, predict

To extract graph:

You need these 2 components: _graph, graph

📑 Top-Level API Contents & Logic Flow

🔧 Functions

graph(sequence, title='Predicted Confidence Score', confidence_threshold=50, shaded_regions=None, shaded_region_color='red', confidence_line_color='blue', threshold_line_color='black', DPI=150, output_file=None)

No documentation available.

Full Docstring 
No documentation available.

predict(sequence)

Function to return confidence scores from

Full Docstring 
Function to return confidence scores from
Alpha fold 2 of a single input sequence. Returns the
predicted values as a float.

Parameters
------------

sequence : str 
    Input amino acid sequence (as string) to be predicted.

Returns
--------

Float
    Returns a float of the confidence score value (predicted)