<img src="docs/README_pics/logo_fingernat.png" width="500" class="center" />

Welcome to fingeRNAt's README

fingeRNAt is a software tool for detecting non-covalent interactions formed within complexes of nucleic acids with ligands.

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• Overview
  • What is the Structural Interaction Fingerprint (SIFt)?
• Installation
  • Conda environment (the recommended method)
  • Using apt-get
  • Using pip and apt-get
  • Singularity image
  • Manual installation
• Usage
  • Quick start :zap:
  • fingeRNAt in action
  • Parameters description
  • Inputs
  • Structural Interaction Fingerprint (SIFt) types
  • Interactions with inorganic ions
  • User-defined interactions
    • Point-point interactions, distance only
    • Point-point interactions, distance and angle
      • Variant 1
      • Variant 2
    • Point-point interactions, distance and two angles
  • User-defined thresholds
  • Outputs
    • FULL
    • SIMPLE
    • PBS
  • Wrappers
    • ACUG
    • PuPy
    • Counter
  • Detail mode
  • PyMOL visualization
  • Usage examples
  • Graphical User Interface
  • Debugging mode
  • Warnings/Errors
• Frequently Asked Questions (FAQ)
• fingerDISt :straight_ruler:
  • Installation
  • Usage
    • Quick start :zap:
    • Parameters description
    • Inputs
    • Distance Metrics
    • Outputs
    • Usage examples
• Singularity image
• Running fingeRNAt in parallel
• Documentation
• Unit test
• Implementation details
• Contributors
• Feedback, issues, and questions
• Acknowledgments
• How to cite
• License

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Overview

fingeRNAt is a Python 3 software tool for detecting non-covalent interactions formed within complexes of nucleic acids with ligands.

Interactions are encoded and saved, i.e., in the form of bioinformatic-friendly Structural Interaction Fingerprint (SIFt) - a binary string, where the respective bit in the fingerprint is set to 1 in case of a presence of a particular interaction and to 0 otherwise. This enables high-throughput analysis of the interaction data using data analysis techniques.

Interactions can be calculated for the following complexes:

<p align="center"> <img src="docs/README_pics/detected_interactions.png" width="900" /> </p>

fingeRNAt runs under Python 3.5 - 3.9 on Linux and macOS.

Supplementary code and data regarding the manuscript can be found here.

What is the Structural Interaction Fingerprint (SIFt)?

Structural Interaction Fingerprint (SIFt) is a binary string describing the existence (1/0) of specified molecular interactions between all receptor's residues and the ligand (Deng et al., 2004).

<p align="center"> <img src="docs/README_pics/SIFs.png" width="800" /> </p> <br/> <br/> <p align="center"> <img src="docs/README_pics/SIFs_merging.png" width="500" /> </p> <br/>

SIFt translates information about 3D interactions in the receptor-ligand complex into a string, where the respective bit in the fingerprint is set to 1 in case of detecting particular interaction and to 0 otherwise.

Therefore, the interactions are represented in a unified fashion, thus allowing for easy high-throughput computational analysis, as they provide a full picture of all interactions within the complex.

Installation

Recommended fingeRNAt usage is in a conda environment.

Conda environment (the recommended method)

Tested under Debian (11 stable), Ubuntu (18.04, 20.04, and 21.10), and macOS (10.15 and 11).

1. Install conda

   Please refer to the conda manual and install the conda version with Python 3.x according to your operating system.

2. Download fingeRNAt

   Clone the repository

   git clone --depth=1 https://github.com/n-szulc/fingernat.git

   Or

   Download the latest stable release from the releases page.

3. Create conda environment

   conda env create -f fingeRNAt/env/fingeRNAt_env.yml

Using apt-get

To install fingeRNAt at Debian and Debian-like systems using repository packages (tested under Debian 11 stable and Ubuntu 20.04):

# install packages
sudo apt-get update && sudo apt-get --no-install-recommends -y install openbabel python3.9-minimal python3-openbabel python3-pip python-is-python3 \
python3-pandas python3-numpy python3-rdkit python3-tqdm python3-yaml

# clone the fingeRNAt repository:
git clone --depth=1 https://github.com/n-szulc/fingernat.git

Using pip and apt-get

To install fingeRNAt at Debian and Debian-like systems using repository packages and pip-installed packages (tested under Debian 11 stable and Ubuntu 20.04):

# install a minimal python and openbabel tool box:
apt-get update && apt-get --no-install-recommends -y install openbabel python3.9-minimal python3-openbabel python3-pip python-is-python3

# install python packages:
pip install -r env/fingeRNAt_pip.txt

# clone the fingeRNAt repository:
git clone --depth=1 https://github.com/n-szulc/fingernat.git

Singularity image

Singularity image with the fineRNAt suite is available in the sylabs cloud: cloud.sylabs.io.

To fetch the latest image directly, run:

singularity pull library://filips/default/fingernat:latest

For usage examples of the image, see section below.

Manual installation

Required dependencies are:

• python 3 (tested on versions 3.5, 3.6, 3.7, 3.8, 3.9)
• openbabel 3.1.1
• numpy
• pandas
• rdkit
• pyyaml
• tk
• tqdm
• sphinx

Usage

Quick start :zap:

To call fingeRNAt with example inputs:

conda activate fingernat

cd fingeRNAt

python code/fingeRNAt.py -r example_inputs/1aju_model1.pdb -l example_inputs/ligands.sdf

See the output file with SIFts in the outputs/ directory.

fingeRNAt in action

See the basic usage of the fingeRNAt

Parameters description

fingeRNAt accepts the following parameters:

| Parameter | Description | |---|---| | -r | path to RNA/DNA structure; see -> Inputs | | [-l] | path to ligands' file; see -> Inputs | | [-f] | optional Structural Interactions Fingerprint (SIFt) type; see -> SIFt types; <br />available types are: FULL [default],   SIMPLE,   PBS| | `