molmdtools 0.1.0

Tools for molecular dynamics trajectory analysis, hydrogen bond characterization and quantum chemistry workflows.

MolMDTools

MolMDTools is a Python package for molecular structure analysis, molecular dynamics trajectory processing, hydrogen bond characterization, and preparation of quantum chemical calculations.

The package provides a unified object-oriented framework for working with molecular geometries, molecular dynamics trajectories, hydrogen-bonded systems, and computational chemistry workflows.

It was originally developed for the analysis of proton-transfer systems and hydrogen-bond networks obtained from quantum chemistry calculations and molecular dynamics simulations.

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Key Features

Molecular Structures

• Atomic and molecular object representations
• Distance matrix generation
• Geometrical analysis:
  • interatomic distances
  • bond angles
  • torsion angles
• Center of mass calculations

Molecular Dynamics Trajectories

• Reading and writing XYZ trajectories
• Trajectory manipulation and filtering
• Random frame selection
• Subsystem extraction
• Trajectory concatenation
• Center-of-mass alignment
• Periodic boundary condition handling

Hydrogen Bond Analysis

• Hydrogen bond representation
• Automatic hydrogen bond detection
• Hydrogen bond trajectory analysis
• Collective variable calculations
• Distribution analysis of proton-transfer coordinates

Quantum Chemistry Utilities

• Generation of Gaussian input files
• Support for geometry optimization jobs
• Frequency calculations
• NMR calculations

Data Conversion

• LAMMPS dump → XYZ trajectory conversion

Visualization

• Distance evolution plots
• Angle evolution plots
• Torsion angle evolution plots
• Collective variable analysis
• Publication-ready scientific figures

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Installation

pip install molmdtools

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Example: Reading an XYZ trajectory

from molmdtools import XYZ_Trajectory

traj = XYZ_Trajectory.extr_from_xyz("trajectory.xyz")

print(f"Number of frames: {traj.steps_number}")

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Example: Center-of-Mass Alignment

aligned_traj = traj.static_center_of_mass()

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Example: Hydrogen Bond Analysis

from molmdtools import HB_Analyzer

frames_with_hbond = HB_Analyzer.hb_in_traj(
    traj,
    atoms_nums=[0, 1, 2]
)

print(frames_with_hbond)

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Example: Gaussian Input Generation

from molmdtools import Calc_Data_Inp

calc = Calc_Data_Inp(
    molecule=molecule,
    method="B3LYP",
    basis="def2-TZVPD",
    opt=True,
    freq=True
)

calc.generate_gaussian_inp(
    path="inputs",
    filename="calculation.inp"
)

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Supported Formats

Input

• XYZ trajectories
• XYZ molecular structures
• LAMMPS dump trajectories

Output

• XYZ trajectories
• Gaussian input files

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Scientific Applications

MolMDTools is intended for:

• molecular dynamics trajectory analysis;
• hydrogen-bond characterization;
• proton-transfer studies;
• collective variable analysis;
• preparation of quantum chemistry calculations;
• post-processing of computational chemistry results.

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Author

Vladimir Rogachevskii

Computational Chemistry Researcher

Email: [e-mail]

GitHub: https://github.com/NCI-laboratory-SPb

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License

Distributed under the MIT License.