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MDAnalysis · Oct 5, 2023 · 273eb7d · 273eb7d
2 parents 4993a78 + 37c5d86
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diff --git a/.readthedocs.yaml b/.readthedocs.yaml
@@ -0,0 +1,14 @@
+version: 2
+
+build:
+  os: ubuntu-22.04
+  tools:
+    python: "mambaforge-4.10"
+
+python:
+  install:
+    - method: pip
+      path: .
+
+conda:
+  environment: docs/requirements.yaml
diff --git a/docs/requirements.yaml b/docs/requirements.yaml
@@ -9,5 +9,6 @@ dependencies:
   - pip
 
   - mdanalysis-sphinx-theme >=1.0.1
+  - sphinxcontrib-bibtex
     # Pip-only installs
   #- pip:
diff --git a/docs/source/api.rst b/docs/source/api.rst
@@ -1,8 +1,4 @@
 API Documentation
 =================
 
-.. autosummary::
-   :toctree: autosummary
-   :recursive:
-
-   pathsimanalysis
+.. automodule:: pathsimanalysis.psa
diff --git a/docs/source/conf.py b/docs/source/conf.py
@@ -53,9 +53,12 @@
     "sphinx.ext.napoleon",
     "sphinx.ext.intersphinx",
     "sphinx.ext.extlinks",
+    'sphinxcontrib.bibtex',
     "mdanalysis_sphinx_theme",
 ]
 
+bibtex_bibfiles = ['references.bib']
+
 autosummary_generate = True
 # This skips generating an autodoc of the test module
 # when using the autosummary directive that is included

diff --git a/docs/source/getting_started.rst b/docs/source/getting_started.rst
@@ -2,3 +2,14 @@ Getting Started
 ===============
 
 This page details how to get started with PathSimAnalysis. 
+
+Installation
+------------
+
+PathSimAnalysis is currently only installable from source.
+
+.. code-block:: bash
+
+	git clone --depth=1 https://github.com/MDAnalysis/PathSimAnalysis
+	cd PathSimAnalysis
+	pip install .
diff --git a/docs/source/index.rst b/docs/source/index.rst
@@ -6,6 +6,8 @@
 Welcome to PathSimAnalysis's documentation!
 =========================================================
 
+PathSimAnalysis is an MDAnalysis based analysis package for calculating the similarity between molecular dynamics trajectories.
+
 .. toctree::
    :maxdepth: 2
    :caption: Contents:

diff --git a/docs/source/references.bib b/docs/source/references.bib
@@ -0,0 +1,64 @@
+@article{Seyler2015,
+    doi = {10.1371/journal.pcbi.1004568},
+    author = {Seyler, Sean L. AND Kumar, Avishek AND Thorpe, M. F. AND Beckstein, Oliver},
+    journal = {PLOS Computational Biology},
+    publisher = {Public Library of Science},
+    title = {Path Similarity Analysis: A Method for Quantifying Macromolecular Pathways},
+    year = {2015},
+    month = {10},
+    volume = {11},
+    pages = {1-37},
+    number = {10}
+}
+
+@article{Taha2015,
+    author={Taha, Abdel Aziz and Hanbury, Allan},
+    journal={IEEE Transactions on Pattern Analysis and Machine Intelligence}, 
+    title={An Efficient Algorithm for Calculating the Exact Hausdorff Distance}, 
+    year={2015},
+    volume={37},
+    number={11},
+    pages={2153-2163},
+    doi={10.1109/TPAMI.2015.2408351}
+}
+
+@article{Alt1995,
+	author = {Alt, Helmut and Godau, Michael},
+	title = {Computing the Frechet distance between two polygonal curves},
+	journal = {International Journal of Computational Geometry \& Applications},
+	volume = {05},
+	number = {01n02},
+	pages = {75-91},
+	year = {1995},
+	doi = {10.1142/S0218195995000064}
+}
+
+@article{EiterMannila1994,
+	author = {Eiter, Thomas and Mannila, Heikki},
+	year = {1994},
+	month = {05},
+    journal = {},
+	title = {Computing Discrete Frechet Distance}
+}
+
+@article{EiterMannila1997,
+	author = {Eiter, Thomas and Mannila, Heikki},
+	doi = {10.1007/s002360050075},
+	journal = {Acta Informatica},
+	Number = {2},
+	Pages = {109--133},
+	Title = {Distance measures for point sets and their computation},
+	Volume = {34},
+	year = {1997}
+}
+
+@article{Frechet1906,
+	author = {Frèchet, M. Maurice},
+	doi = {10.1007/BF03018603},
+	journal = {Rendiconti del Circolo Matematico di Palermo (1884-1940)},
+	Number = {1},
+	Pages = {1--72},
+	Title = {Sur quelques points du calcul fonctionnel},
+	Volume = {22},
+	year = {1906}
+}
diff --git a/pathsimanalysis/data/README.md b/pathsimanalysis/data/README.md
diff --git a/pathsimanalysis/data/__init__.py b/pathsimanalysis/data/__init__.py
diff --git a/pathsimanalysis/data/files.py b/pathsimanalysis/data/files.py
diff --git a/pathsimanalysis/data/mda.txt b/pathsimanalysis/data/mda.txt
diff --git a/pathsimanalysis/psa.py b/pathsimanalysis/psa.py
@@ -25,10 +25,6 @@
 Calculating path similarity --- :mod:`pathsimanalysis.psa`
 ==========================================================================
 
-:Author: Sean Seyler
-:Year: 2015
-:Copyright: GNU Public License v3
-
 .. versionadded:: 0.10.0
 
 The module contains code to calculate the geometric similarity of trajectories
@@ -88,11 +84,11 @@
 
    .. attribute:: u_original
 
-      :class:`MDAnalysis.Universe` object with a trajectory
+      :class:`~MDAnalysis.Universe` object with a trajectory
 
    .. attribute:: u_reference
 
-      :class:`MDAnalysis.Universe` object containing a reference structure
+      :class:`~MDAnalysis.Universe` object containing a reference structure
 
    .. attribute:: select
 
@@ -112,7 +108,7 @@
 
    .. attribute:: u_fitted
 
-      :class:`MDAnalysis.Universe` object with the fitted trajectory
+      :class:`~MDAnalysis.Universe` object with the fitted trajectory
 
    .. attribute:: path
 
@@ -386,7 +382,7 @@ def hausdorff(P, Q):
      >>> import MDAnalysis as mda
      >>> import numpy
      >>> from MDAnalysis.tests.datafiles import PSF, DCD
-     >>> from MDAnalysis.analysis import psa
+     >>> import pathsimanalysis as psa
      >>> u = mda.Universe(PSF,DCD)
      >>> mid = int(len(u.trajectory)/2)
      >>> ca = u.select_atoms('name CA')
@@ -453,7 +449,7 @@ def hausdorff_wavg(P, Q):
      >>> import MDAnalysis as mda
      >>> from MDAnalysis import Universe
      >>> from MDAnalysis.tests.datafiles import PSF, DCD
-     >>> from MDAnalysis.analysis import psa
+     >>> import pathsimanalysis as psa
      >>> u = mda.Universe(PSF,DCD)
      >>> mid = int(len(u.trajectory)/2)
      >>> ca = u.select_atoms('name CA')
@@ -511,7 +507,7 @@ def hausdorff_avg(P, Q):
 
      >>> import MDAnalysis as mda
      >>> from MDAnalysis.tests.datafiles import PSF, DCD
-     >>> from MDAnalysis.analysis import psa
+     >>> import pathsimanalysis as psa
      >>> u = mda.Universe(PSF,DCD)
      >>> mid = int(len(u.trajectory)/2)
      >>> ca = u.select_atoms('name CA')
@@ -610,7 +606,7 @@ def discrete_frechet(P, Q):
      >>> import MDAnalysis as mda
      >>> import numpy as np
      >>> from MDAnalysis.tests.datafiles import PSF, DCD
-     >>> from MDAnalysis.analysis import psa
+     >>> import pathsimanalysis as psa
      >>> u = mda.Universe(PSF,DCD)
      >>> mid = int(len(u.trajectory)/2)
      >>> ca = u.select_atoms('name CA')
@@ -1494,7 +1490,7 @@ def run_pairs_analysis(self, **kwargs):
         indexed according to distance vector convention (i.e., element *(i,j)*
         in distance matrix representation corresponds to element
         :math:`s=N*i+j-(i+1)*(i+2)` in distance vector representation, which is
-        the :math:`s^\text{th}` comparison). For each unique pair of paths, the
+        the :math:`s`:sup:`th` comparison). For each unique pair of paths, the
         nearest neighbors for that pair can be stored in :attr:`NN` and the
         Hausdorff pair in :attr:`HP`. :attr:`PP` stores the full information
         of Hausdorff pairs analysis that is available for each pair of path,

diff --git a/pathsimanalysis/tests/conftest.py b/pathsimanalysis/tests/conftest.py
diff --git a/pathsimanalysis/tests/utils.py b/pathsimanalysis/tests/utils.py