Welcome to npfc’s documentation!

This Python 3 package is designed for analyzing Natural-Product Fragment Combination (npfc).

It is mostly based on the RDKit, Pandas and NetworkX.

On top of the existing modules, a set of scripts are included as well. The execution of scripts is orchestrated via Snakemake workflows.

Getting Started

• Introduction
• Installation
  • Conda environment setup
  • Install the NPFC package
• Package Architecture
  • Module interactions
  • Class hierarchy
  • Code from other sources

Concepts and Examples

• Preparation
  • Load
  • Standardize
  • Deduplicate
  • Depict
• Fragment Search
  • Usage
• Fragment Combination Classification
  • Fusions
  • Connections
  • False Positives
  • Usage
• Fragment Combination Graphs
  • Alternative Fragment Combinations
  • Usage
• Pseudo-NP Annotation
  • Usage

Workflows

• Command Line Interface
• Fragments
  • The workflow
  • Running the workflow
  • Folder tree
• Natural Products
  • The workflow
  • Running the workflow
  • Folder tree
• Synthetic Compounds
  • The workflow
  • Running the workflow
  • Folder tree

API

• deduplicate
• draw
  • Module draw
• filter
  • Module filter
• fragment_search
  • Module fragment_search
• fragment_combination
  • Module fragment_combination
• fragment_combination_graph
  • Module fragment_combination_graph
• fragment_combination_point
  • Usage
• load
  • Module load
• notebook
  • Module notebook
• save
  • Module save
• standardize
  • Module standardize
• utils
  • Module utils

Indices and tables

• Index

• Module Index

• Search Page