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Installation Guide

Requirements

  • Python: 3.8 or higher
  • Operating System: macOS, Linux, or Windows
  • Dependencies: NumPy, Biotite, OpenMM (optional), Numba (optional)

Installation Methods

The easiest way to install synth-pdb is via PyPI:

pip install synth-pdb

This installs: - The synth-pdb command-line tool - The synth_pdb Python library - All required dependencies

From Source

For development or to get the latest features:

git clone https://github.com/elkins/synth-pdb.git
cd synth-pdb
pip install -e .

The -e flag installs in "editable" mode, so changes to the source code are immediately reflected.

Development Installation

To install with development dependencies (testing, linting, etc.):

git clone https://github.com/elkins/synth-pdb.git
cd synth-pdb
pip install -e ".[dev]"

Optional Dependencies

OpenMM (Physics Engine)

For energy minimization and MD equilibration:

pip install openmm

Or via conda (recommended for Apple Silicon):

conda install -c conda-forge openmm

Apple Silicon Users

OpenMM on M1/M2/M3/M4 Macs supports GPU acceleration via OpenCL/Metal, providing 5x speedup over CPU.

Numba (JIT Compilation)

For 50-100x speedup on geometry and NMR calculations:

pip install numba

Verification

Verify your installation:

synth-pdb --version

Expected output: 

synth-pdb version 1.24.0

Test basic functionality:

synth-pdb --length 5 --output test.pdb

This should create a test.pdb file in the current directory.

Troubleshooting

ImportError: No module named 'openmm'

If you see this error when using --minimize:

pip install openmm

Or skip minimization:

synth-pdb --length 10  # Works without OpenMM

Apple Silicon: OpenMM Not Found

Use conda instead of pip:

conda install -c conda-forge openmm

Windows: Long Path Issues

Enable long paths in Windows:

# Run as Administrator
New-ItemProperty -Path "HKLM:\SYSTEM\CurrentControlSet\Control\FileSystem" -Name "LongPathsEnabled" -Value 1 -PropertyType DWORD -Force

Next Steps