pydseams#

Read

Load a LAMMPS dump, XYZ, PDB, GRO, DCD, or eOn .con as a Frame.

Quickstart
Classify

CHILL+ labels and HC / DDC cage scores on one frame.

Tutorial: Classify ice
Bind

Round-trip ASE Atoms. Optional solvis view of the same cloud.

Classify ASE Atoms

About#

pydseams is the Python package for the d-SEAMS engine. The compiled module is yoda. Helpers (Frame, read, ASE, solvis) sit on that surface. import pydseamslib still works.

Primary author: Ruhila S. The project started as PSF GSoC 2023 (pyseams; the PyPI name is pydseamslib). Helpers stay in Python so the C++ ABI does not grow a second I/O layer.

The engine and the seams CLI live in seams-core. Lua is dseams in yodaStruct. This site documents the Python Frame API. The header Ecosystem menu jumps to the engine docs, the Lua front end, and the neighbour backends (vesin cutoff lists, linkcell k-NN).

import pydseams as ds

frame = ds.read("water.lammpstrj")
print(frame.chill_plus())
print(frame.cages())

Suite stack#

Python helpers sit on the compiled yoda module. The same libyodaLib engine backs the seams CLI and the Lua dseams module.

        flowchart TB
  subgraph engine["seams-core"]
    LIB[libyodaLib]
  end
  subgraph compiled["pydseams.yoda"]
    YODA[yoda]
    ALIAS["_core / cyoda"]
  end
  subgraph helpers["Python helpers"]
    READ[ds.read]
    FRAME[Frame]
    ASE[from_ase / to_ase]
    SOL[to_solvis]
  end
  CLI["seams CLI"]
  LUA["yodaStruct / dseams"]
  LC["linkcell k-NN"]
  VE["vesin cutoff"]
  LC --> LIB
  VE --> LIB
  LIB --> YODA
  YODA --- ALIAS
  LIB --> CLI
  LIB --> LUA
  YODA --> READ
  YODA --> FRAME
  FRAME --> ASE
  FRAME --> SOL

Documentation structure#

This documentation follows the Diataxis framework.

Getting Started

Tutorials

How-to

Explanation

Reference

Development

License#

MIT. Cite the 2020 d-SEAMS paper (DOI 10.1021/acs.jcim.0c00031). See How to cite.

#+begin_export rst Indices and tables ================

:ref:`genindex`#

:ref:`modindex`#