xtclib 0.1.3

Fast, standalone reader/writer for GROMACS XTC trajectory files

xtclib

A fast, standalone Python library for reading and writing GROMACS XTC trajectory files. The coordinate compression and decompression are implemented in C and wrapped with Cython, giving performance close to the native GROMACS routines while requiring only NumPy at runtime.

Why make this?

This package was written so we have a simple, stand-alone and low-dependency reference implementation of the XTC library for reading/writing XTC files. In many cases, we work with XTC files and do not need the dependency overhead of large packages which themselves often come with large dependency overheads, so having a reference and lightweight implementation felt like a good idea for improved modularity across our ecosystem. The use case here is specifically where reading/writing XTC files is necessary, but we want to avoid installing mdtraj, mdanalysis, gromacs etc. YMMC in terms of how often this is an issue, of course.

This also removes the need for any kind of topology file to read/write an XTC file - we may in the future OPTIONALLY add this in as a .pdb file to provide a simple objective oriented interface but having separate and independent XTC read/write power is a core basal interface we want access to directly.

Features

• Read XTC files frame-by-frame (iterator) or all-at-once into NumPy arrays.
• Write XTC files with full compression, producing output that is bit-identical to GROMACS.
• Zero runtime dependencies beyond NumPy — no GROMACS installation, no MDTraj, no MDAnalysis required.
• Handles both small systems (intrinsically disordered proteins) and large solvated systems (50 k+ atoms) correctly.
• Pure-C compression core with Cython bindings — no external shared libraries to manage.

Installation

From PyPI (stable release)

pip install xtclib

From GitHub (latest development version)

pip install git+https://github.com/holehouse-lab/xtclib.git

From source (for local development)

git clone https://github.com/holehouse-lab/xtclib.git
cd xtclib
pip install -e .

Build requirements (setuptools, Cython, numpy) are declared in pyproject.toml and installed automatically during the build.

Quick start

Reading a trajectory

from xtclib import read_xtc

data = read_xtc("trajectory.xtc")

data["coords"]   # ndarray, shape (nframes, natoms, 3), float32, in nm
data["time"]     # ndarray, shape (nframes,), float32
data["step"]     # ndarray, shape (nframes,), int32
data["box"]      # ndarray, shape (nframes, 3, 3), float32
data["natoms"]   # int

Writing a trajectory

from xtclib import write_xtc

write_xtc(
    "output.xtc",
    coords,                # (nframes, natoms, 3) array in nm
    time=times,            # optional, defaults to [0, 1, 2, ...]
    step=steps,            # optional, defaults to [0, 1, 2, ...]
    box=boxes,             # optional, defaults to zeros
    precision=1000.0,      # optional, default 1000.0
)

Frame-by-frame iteration

For large trajectories where loading everything into memory at once is impractical, use the XTCReader iterator:

from xtclib import XTCReader

with XTCReader("large_trajectory.xtc") as reader:
    for frame in reader:
        print(frame.step, frame.time, frame.coords.shape)
        # frame.coords is (natoms, 3) float32
        # frame.box    is (3, 3)      float32

Round-tripping a file

from xtclib import read_xtc, write_xtc

data = read_xtc("input.xtc")
write_xtc("copy.xtc", data["coords"],
          time=data["time"], step=data["step"], box=data["box"])

The output file will be byte-identical to the input.

API reference

read_xtc(filename)

Read an entire XTC file and return a dict of NumPy arrays.

Key	Type	Description
"coords"	ndarray (nframes, natoms, 3) float32	Atom coordinates in nm
"time"	ndarray (nframes,) float32	Simulation time (usually ps)
"step"	ndarray (nframes,) int32	Integration step number
"box"	ndarray (nframes, 3, 3) float32	Unit-cell box vectors in nm
"natoms"	int	Number of atoms per frame

write_xtc(filename, coords, time=None, step=None, box=None, precision=1000.0)

Write coordinates to an XTC file with compression.

Parameter	Type	Default	Description
filename	str	—	Output file path
coords	array-like (nframes, natoms, 3)	—	Coordinates in nm
time	array-like (nframes,)	[0, 1, 2, ...]	Frame times
step	array-like (nframes,)	[0, 1, 2, ...]	Step numbers
box	array-like (nframes, 3, 3) or (3, 3)	zeros	Box vectors
precision	float	1000.0	Precision factor

XTCReader(filename)

Iterator-based reader. Yields XTCFrame objects with attributes step, time, box, coords, and natoms. Can be used as a context manager. Also provides a read_all() method that returns the same dict as read_xtc().

How XTC compression works

The XTC format uses a lossy compression scheme for 3-D coordinates:

1. Float → integer: each coordinate is multiplied by a precision factor (default 1000) and rounded to the nearest integer. This gives ~0.001 nm (1 pm) resolution.

2. Full-range encoding: each atom's integer coordinates are encoded relative to the bounding box (minint/maxint) using a mixed-radix bit-packing scheme.

3. Run-length delta encoding: consecutive atoms whose inter-atom distances are "small" are encoded as differences from the previous atom, using a smaller bit range. The small range adapts up or down across the trajectory to track typical bond lengths.

4. Water optimisation: within small-delta runs, the first two atoms are swapped (O-H → H-O order) to make the deltas even smaller for water molecules. This is reversed transparently on reading.

The result is typically 10–20× smaller than raw float arrays for solvated biomolecular systems.

Precision and lossy encoding

XTC is a lossy format. The maximum per-coordinate rounding error is 0.5 / precision nm:

Precision	Max error (nm)	Max error (Å)
1000 (default)	0.0005	0.005
10000	0.00005	0.0005
100	0.005	0.05

When reading a file that was written with a given precision, read_xtc returns the exact integer-reconstructed values — there is no additional loss on read. A read → write → read round-trip with the same precision produces bit-identical coordinate arrays.

Compatibility

Files written by xtclib are fully compatible with:

• GROMACS (gmx trjconv, gmx trajcat, etc.)
• MDTraj (mdtraj.load_xtc)
• MDAnalysis (MDAnalysis.coordinates.XTC)
• Any tool that reads standard XTC (magic number 1995)

This has been validated by round-trip testing: files written by xtclib produce byte-identical coordinate arrays when read back by MDTraj.

System size limits

xtclib uses the classic XTC format (magic number 1995) with 32-bit frame sizes, which imposes the following limits:

Quantity	Limit
Atoms per frame	~300 million (limited by 32-bit integer range)
Frames per file	Unlimited (sequential frames, no index)
Coordinate range	±2,147,483 nm at precision 1000
Compressed frame size	~2 GB per frame

Project structure

xtclib/
├── xtclib/
│   ├── __init__.py        # Package entry point
│   ├── reader.py          # XTCReader, read_xtc()
│   ├── writer.py          # write_xtc()
│   ├── _xtc_core.pyx      # Cython wrapper
│   ├── xdr_xtc.c          # C compression/decompression
│   └── xdr_xtc.h          # C header
├── tests/
│   └── test_xtclib.py     # 21 tests (pytest)
├── example/
│   ├── synuclein_STARLING.xtc   # 140-atom IDP, 400 frames
│   ├── synuclein_STARLING.pdb   # Reference structure
│   └── lysozyme_md.xtc          # 50,949-atom solvated system, 101 frames
├── setup.py
└── pyproject.toml

Running tests

python -m pytest tests/ -v

The test suite validates:

• Reading both example files (shapes, metadata)
• Exact round-trip (read → write → read) for coords, time, step, box
• Byte-identical file sizes after round-trip
• PDB cross-validation (atom count, first-frame coordinates)
• MDTraj compatibility (our written files read back identically)
• Compression of synthetic/random coordinate data

License

The C compression algorithm is based on the XTC specification as implemented in GROMACS (LGPL-2.1+).