OrganometallicStructureAnalyzer

A Python toolkit for analyzing organometallic structures, focusing on metallocenes and inverse sandwich complexes.

Overview

This repository provides two Python scripts to analyze organometallic compounds, calculating geometric properties such as distances, angles, and dihedral angles:

• ring_analyzer.py: A command-line tool for analyzing metallocenes (2 rings, 1 metal) and inverse sandwich complexes (3 rings, 2 metals).
• ring_analyzer_interactive.py: An interactive version that prompts users for input during execution.

Both scripts support structures with 5- or 6-membered rings (e.g., cyclopentadienyl, benzene) and handle inverse sandwich complexes (e.g., Ring1-Metal1-Ring2-Metal2-Ring3).

Features

• Places dummy atoms (X) at ring centroids.
• Calculates metal-centroid distances:
  • For 2 rings: Metal1 to Ring1 and Ring2 centroids.
  • For 3 rings: Metal1 to Ring1 and Ring2 centroids, Metal2 to Ring2 and Ring3 centroids, and Metal1 to Metal2 distance.
• Computes angles:
  • For 2 rings: CoM1-Metal1-CoM2.
  • For 3 rings: CoM1-Metal1-CoM2, CoM1-CoM2-CoM3, CoM2-Metal2-CoM3, Metal1-CoM2-Metal2.
• For 3-ring cases, calculates:
  • Bond distances in the middle ring (ring2, e.g., C3--C61: 1.4555 Å).
  • Dihedral angles in the middle ring (ring2).
• Outputs modified XYZ files with dummy atoms at centroids.
• For ring_analyzer.py (3-ring case): Dynamically assigns Metal1 to the metal closer to Ring1 and Metal2 to the metal closer to Ring3, ensuring consistent results regardless of input order.
• Supports 5- or 6-membered rings.

Requirements

• Python 3.x
• numpy (install with pip3 install numpy --user)

Installation

Clone the repository:

git clone https://github.com/Ahmad-Fermion/OrganometallicStructureAnalyzer.git
cd OrganometallicStructureAnalyzer

Example (2 rings):

python ring_analyzer.py ferrocene.xyz --ring1 1 2 3 4 5 --ring2 6 7 8 9 10 --metal1 11

Example (3 rings):

python ring_analyzer.py inverse_sandwich.xyz --ring1 2 4 5 7 9 --ring2 3 61 6 8 64 118 --ring3 62 63 65 66 67 --metal1 1 --metal2 60

ring_analyzer_interactive.py (Interactive):

python ring_analyzer_interactive.py