polyphys 1.0.0__py3-none-any.whl

polyphys/__init__.py

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+"""Top-level package for polyphys."""
+from .__version__ import __version__
+from polyphys import analyze
+from polyphys import manage
+from polyphys import simulate
+
+__all__ = ['__version__', 'analyze', 'manage', 'simulate']

polyphys/__version__.py

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+"""
+Version information for PolyPhys, :mod:`polyphys.__version__`.
+
+:data:`__version__` is the release of PolyPhys, a `semantic versioning`_
+string, ``MAJOR.MINOR.PATCH`` with optional pre-release and build labels.
+Which names the versioning promise covers, which modules are stable or
+provisional, and how a name is deprecated are stated once, on the
+documentation's "API stability" page (``docs/source/stability.md``).
+
+.. _`semantic versioning`: https://semver.org/spec/v2.0.0.html
+
+Data
+----
+
+.. autodata:: __version__
+
+"""
+
+# keep __version__ in separate file to avoid circular imports
+
+#: Release of PolyPhys as a string, using `semantic versioning`_.
+__version__ = "1.0.0"

polyphys/analyze/__init__.py

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+"""
+Analyze Module --- :mod:`polyphys.analyze`
+==========================================
+
+
+The `polyphys.analyze` module provides tools for analyzing molecular simulation
+data: geometric and structural measurements of a particle group, simple
+statistics, and the binning and histogram machinery used to build spatial
+distributions.
+
+Submodules
+==========
+- `measurer`: Geometric and structural measurements, summary statistics, and
+  fixed-size binning with radial, axial, azimuthal, and planar histograms.
+- `stats`: Autocorrelation-aware uncertainty of a time average over
+  correlated frames, by Flyvbjerg-Petersen block averaging.
+- `clusters`: Contact and cluster statistics of a particle group, pair
+  separation densities, the binding statistics of two-patch binders, and
+  the binding-threshold sweep on saved distance matrices.
+- `correlations`: The autocorrelation function of a time series with
+  Bartlett's band, decay-model fits, and the bond cosine correlation of a
+  chain.
+- `sumrule`: The density sum rule on a space's ensemble-averaged density
+  profiles: scaled, normalized, folded, and summed over species.
+- `density`: The local number density and volume fraction of a species
+  from a histogram of its bead centers, with the share of a finite bead
+  spread over the bins it reaches.
+- `pipeline`: The reducer of one space's probe artifacts down the lineage,
+  driven by a study's analysis tables, with the post-hooks that derive time
+  averages, autocorrelations, density profiles, and foci pair distances.
+"""
+
+from polyphys.analyze import (
+    clusters,
+    correlations,
+    density,
+    measurer,
+    pipeline,
+    stats,
+    sumrule,
+)
+
+__all__ = [
+    'clusters',
+    'correlations',
+    'density',
+    'measurer',
+    'pipeline',
+    'stats',
+    'sumrule',
+]