aromatools 0.1.0__tar.gz

aromatools-0.1.0/LICENSE

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+MIT License
+
+Copyright (c) 2025 Fernando Martínez Villarino
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights  
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell      
+copies of the Software, and to permit persons to whom the Software is          
+furnished to do so, subject to the following conditions:                        
+
+The above copyright notice and this permission notice shall be included in all 
+copies or substantial portions of the Software.                                 
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR     
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,       
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE    
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER         
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,  
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE  
+SOFTWARE.

aromatools-0.1.0/PKG-INFO

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+Metadata-Version: 2.4
+Name: aromatools
+Version: 0.1.0
+Summary: Herramientas para el análisis de aromaticidad
+Author: Fernando Martínez Villarino
+Author-email: fernandomv5897@gmail.com
+Classifier: Programming Language :: Python :: 3
+Classifier: License :: OSI Approved :: MIT License
+Classifier: Operating System :: OS Independent
+Requires-Python: >=3.12
+License-File: LICENSE
+Requires-Dist: numpy
+Requires-Dist: networkx
+Requires-Dist: matplotlib
+Requires-Dist: art
+Requires-Dist: ase
+Dynamic: author
+Dynamic: author-email
+Dynamic: classifier
+Dynamic: license-file
+Dynamic: requires-dist
+Dynamic: requires-python
+Dynamic: summary

aromatools-0.1.0/README.md

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+# AromaTools
+
+Paquete para el análisis de la aromaticidad.
+
+Este código incluye los 3 principales formas de diagnosticar la aromaticidad:
+* Criterios Magnéticos
+	Calcular el campo magnético inducido en direcciones x, y o z
+	Calcular NICS SP, NICS-XY-Scan (1D y 2D) y NICS 3D
+	Calcular la intensidad de corriente anular mediante integración numérica
+*Criterios Geométricos
+	Analisis de alternación de longuitudes de enlaces (BLA, por sus siglas en inglés)
+	Índice HOMA, HOMER y HOMAc
+*Criterios energéticos
+	Muy pronto...

aromatools-0.1.0/aromatools/arogeometric/__main__.py

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+#!/usr/bin/python3
+# -*- coding: utf-8 -*-
+
+import sys
+import math
+import numpy as np
+import networkx as nx
+import contextlib
+import glob
+import os
+import time
+import getpass
+from ase.data import covalent_radii, atomic_numbers
+from art import text2art
+
+# Diccionarios de parámetros
+R_opt = {'HOMA': {'CC': 1.388, 'CN': 1.334, 'NN': 1.309, 'CO': 1.265},
+         'HOMER': {'CC': 1.437, 'CN': 1.39, 'NN': 1.375, 'CO': 1.379},
+         'HOMAC': {'CC': 1.392, 'CN': 1.333, 'NN': 1.318, 'CO': 1.315, 'SiSi': 2.163, 'CSi': 1.752}}
+
+alpha = {'HOMA': {'CC': 257.7, 'CN': 93.52, 'NN': 130.33, 'CO': 157.38},
+         'HOMER': {'CC': 950.74, 'CN': 506.43, 'NN': 187.36, 'CO': 164.96},
+         'HOMAC': {'CC': 153.37, 'CN': 111.83, 'NN': 98.99, 'CO': 335.16, 'SiSi': 325.6, 'CSi': 115.41}}
+
+def arogeometric():
+    text_ascci = text2art("AROGEOMETRIC 1.0", font='old banner')
+    print("\n" + text_ascci)
+    welcome = """
+    Welcome to AroGeometric — Geometric Aromaticity Index Calculator
+    Authors: Fernando Martinez-Villarino and Gabriel Merino
+    Cinvestav Mérida, 2024
+
+    This tool allows you to compute geometric-based aromaticity indices for a set of molecules in .xyz files.
+    You can choose among three different indices:
+
+    • HOMA (HOMA93): 0 = non-aromatic, 1 = aromatic.
+    • HOMAc:       -1 = antiaromatic, 0 = non-aromatic, 1 = aromatic.
+    • HOMER:       Excited-state version of HOMAc.
+
+    Use as: aroegeometric.py [HOMA|HOMER|HOMAc]
+    """
+    print(welcome)
+
+def parse_xyz(file_xyz):
+    with open(file_xyz, 'r') as f:
+        lines = [line.strip() for line in f if line.strip()]
+    natoms = int(lines[0])
+    atoms = []
+    for i in range(2, 2 + natoms):
+        parts = lines[i].split()
+        if len(parts) < 4:
+            continue
+        symbol = parts[0].capitalize()
+        if symbol == 'H':
+            continue
+        try:
+            x, y, z = map(float, parts[1:4])
+            atoms.append((symbol, x, y, z))
+        except ValueError:
+            print(f"Error: Invalid coordinates at line {i+1}.")
+            sys.exit(1)
+    return atoms
+
+def build_graph(atoms, tol=0.45):
+    G = nx.Graph()
+    for idx, (sym, _, _, _) in enumerate(atoms):
+        G.add_node(idx, element=sym)
+    for i in range(len(atoms)):
+        sym1, x1, y1, z1 = atoms[i]
+        r1 = covalent_radii[atomic_numbers[sym1]]
+        for j in range(i + 1, len(atoms)):
+            sym2, x2, y2, z2 = atoms[j]
+            r2 = covalent_radii[atomic_numbers[sym2]]
+            dist = math.sqrt((x1 - x2)**2 + (y1 - y2)**2 + (z1 - z2)**2)
+            if dist <= r1 + r2 + tol:
+                bond_type = ''.join(sorted(sym1 + sym2))
+                G.add_edge(i, j, length=dist, bond_type=bond_type)
+    return G
+
+def compute_index(G, atoms, index_type, filename):
+    print(f"\nProcessing: {filename}")
+    rings = nx.minimum_cycle_basis(G)
+    print(f"Number of rings detected: {len(rings)}")
+    for idx, ring in enumerate(rings, start=1):
+        ring_atoms = ring + [ring[0]]
+        ring_bonds = []
+        bond_types_in_ring = []
+
+        for i in range(len(ring)):
+            a1, a2 = ring_atoms[i], ring_atoms[i+1]
+            if G.has_edge(a1, a2):
+                data = G[a1][a2]
+                bond_type = data['bond_type']
+                dist = data['length']
+
+                print(f"Ring {idx}: bond {bond_type} with distance {dist:.4f} Å")
+
+                if bond_type == 'SiSi':
+                    print(f"Ring {idx} contains Si-Si bond: distance = {dist:.4f} Å")
+
+                if bond_type not in R_opt[index_type]:
+                    continue
+
+                Ropt = R_opt[index_type][bond_type]
+                a = alpha[index_type][bond_type]
+                bond_types_in_ring.append(bond_type)
+                ring_bonds.append((bond_type, dist, Ropt, a))
+
+        if not ring_bonds:
+            print(f"Ring {idx}: No valid bonds for index {index_type}.")
+            continue
+
+        n = len(ring_bonds)
+        total = sum(a * (dist - Ropt)**2 for _, dist, Ropt, a in ring_bonds)
+        index_value = 1.0 - (1.0 / n) * total
+        print(f"{index_type} index for ring {idx}: {index_value:.4f}")
+
+def get_session_info():
+    init_time = time.strftime("%H:%M:%S", time.localtime())
+    work_direc = os.getcwd()
+    user = getpass.getuser()
+
+    session_info = f"""
+    Initiation time:      {init_time}
+    Working directory:    {work_direc}
+    User:                 {user}
+    """
+    return session_info
+
+def main():
+    if len(sys.argv) != 2:
+        arogeometric()
+        sys.exit(1)
+
+    index_type = sys.argv[1].upper()
+    if index_type not in R_opt:
+        print("Error: Invalid index type. Choose from HOMA, HOMER, HOMAC.")
+        sys.exit(1)
+
+    xyz_files = sorted(glob.glob("*.xyz"))
+    if not xyz_files:
+        print("No .xyz files found in the current directory.")
+        sys.exit(1)
+
+    ascci_title = text2art("AROGEOMETRIC", font='big')
+    session_info = get_session_info()
+    
+    with open("index.dat", "w") as log_file:
+        with contextlib.redirect_stdout(log_file):
+            print()
+            print(f"AroGeometric 2025, output file — {index_type}")
+            print(ascci_title)
+            print("Theoretical and Computational Chemistry Group")
+            print("Centro de Investigacion y de Estudios Avanzados — Unidad Merida")
+            print("Merida, Yucatan, Mexico\n")
+
+            print("---------------------------------Cite this work as---------------------------------")
+            print("AroGeometric 2025, Fernando Martinez-Villarino and G. Merino, Cinvestav, Merida, YUC, Mexico, 2025")
+            print("-----------------------------------------------------------------------------------\n")
+
+            print("Copyright (C) 1943, Cinvestav. All Rights Reserved")
+            print("Session information:")
+            print(session_info + "\n")
+
+            print(f"Total XYZ files found: {len(xyz_files)}\n")
+
+            for file_xyz in xyz_files:
+                atoms = parse_xyz(file_xyz)
+                G = build_graph(atoms)
+                compute_index(G, atoms, index_type, file_xyz)
+                
+            print("\n")
+            print("************************************ AroGeometric terminated normally! ************************************\n")
+
+    print("All calculations completed and saved to 'index.dat'")
+

aromatools-0.1.0/aromatools/aromatools.egg-info/PKG-INFO

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+Metadata-Version: 2.4
+Name: aromatools
+Version: 0.1.0
+Summary: Herramientas para el análisis de aromaticidad
+Author: Fernando Martínez Villarino
+Author-email: fernandomv5897@gmail.com
+Classifier: Programming Language :: Python :: 3
+Classifier: License :: OSI Approved :: MIT License
+Classifier: Operating System :: OS Independent
+Requires-Python: >=3.12
+License-File: LICENSE
+Requires-Dist: numpy
+Requires-Dist: networkx
+Requires-Dist: matplotlib
+Requires-Dist: art
+Requires-Dist: ase
+Dynamic: author
+Dynamic: author-email
+Dynamic: classifier
+Dynamic: license-file
+Dynamic: requires-dist
+Dynamic: requires-python
+Dynamic: summary

aromatools-0.1.0/aromatools/aromatools.egg-info/SOURCES.txt

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+LICENSE
+README.md
+pyproject.toml
+setup.py
+aromatools/aroenergetic/__init__.py
+aromatools/arogeometric/__init__.py
+aromatools/arogeometric/__main__.py
+aromatools/aromagnetic/__init__.py
+aromatools/aromatools.egg-info/PKG-INFO
+aromatools/aromatools.egg-info/SOURCES.txt
+aromatools/aromatools.egg-info/dependency_links.txt
+aromatools/aromatools.egg-info/entry_points.txt
+aromatools/aromatools.egg-info/requires.txt
+aromatools/aromatools.egg-info/top_level.txt

aromatools-0.1.0/aromatools/aromatools.egg-info/dependency_links.txt

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+

aromatools-0.1.0/aromatools/aromatools.egg-info/entry_points.txt

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+[console_scripts]
+arogeometric = aromatools.arogeometric.__main__:main

aromatools-0.1.0/aromatools/aromatools.egg-info/requires.txt

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+numpy
+networkx
+matplotlib
+art
+ase

aromatools-0.1.0/aromatools/aromatools.egg-info/top_level.txt

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+aroenergetic
+arogeometric
+aromagnetic

aromatools-0.1.0/pyproject.toml

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+[build-system]
+requires = ["setuptools", "wheel"]
+build-backend = "setuptools.build_meta"

aromatools-0.1.0/setup.cfg

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+[egg_info]
+tag_build = 
+tag_date = 0
+

aromatools-0.1.0/setup.py

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+from setuptools import setup, find_packages
+
+setup(
+    name="aromatools",
+    version="0.1.0",
+    packages=find_packages(where="aromatools"),
+    package_dir={"": "aromatools"},
+    description="Herramientas para el análisis de aromaticidad",
+    author="Fernando Martínez Villarino",
+    author_email="fernandomv5897@gmail.com",
+    classifiers=[
+        "Programming Language :: Python :: 3",
+        "License :: OSI Approved :: MIT License",
+        "Operating System :: OS Independent",
+    ],
+    entry_points={
+        "console_scripts": [
+            "arogeometric = aromatools.arogeometric.__main__:main"
+        ]
+    },
+    python_requires=">=3.12",
+    install_requires=[
+        "numpy",
+        "networkx",
+        "matplotlib",
+        "art",
+        "ase"
+    ],
+)