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🧩 Software Ecosystem & Tools

The ProteinDF suite consists of several modular repositories designed to work together, covering everything from core all-electron quantum chemical calculations to automated SCF convergence, data post-processing, and cross-platform bridging.

graph TD
    A[Structure Input / PDB] --> B[QCLObot]
    B -->|Generates QCLO Initial Orbitals| C[ProteinDF Engine]
    C -->|Wavefunction & Density Matrix| D[ProteinDF_pytools]
    C <-->|Interoperability| E[ProteinDF_bridge]
    D --> F[Orbital Visualization & Analysis]

⚛️ ProteinDF

Core All-Electron Density Functional Calculation Program

ProteinDF is the main quantum chemistry calculation engine. It is specialized in performing all-electron Kohn-Sham DFT calculations on massive biological systems such as proteins, nucleic acids, and enzyme active centers.

🤖 QCLObot

Automated SCF Convergence Assistant based on the QCLO Method

In large biomolecular DFT calculations, standard SCF iterations frequently suffer from convergence difficulties. QCLObot automates the preparation, calculation, and generation of Quasi-Canonical Localized Orbitals (QCLO), providing superior initial guesses for ProteinDF and ensuring robust SCF convergence.

🐍 ProteinDF_pytools

Python Utilities for Analysis and Visualization

A collection of Python scripts and libraries designed to parse ProteinDF output files, compute electrostatic potentials, analyze molecular orbital compositions, and interface with 3D visualization packages.

  • Key Capabilities:
  • Density of states (DOS) and canonical orbital energy analysis
  • Electrostatic potential (ESP) mapping
  • Batch job management
  • Links:
  • GitHub Repository

🌉 ProteinDF_bridge

Interoperability Interface for External Software

ProteinDF_bridge provides converters and interfaces allowing ProteinDF to exchange molecular geometries, basis sets, and wavefunction data with other quantum chemistry packages and molecular modeling environments.

  • Key Capabilities:
  • File format conversion and preprocessing
  • Interfacing with third-party chemical modeling workflows
  • Links:
  • GitHub Repository