docs: removed duplicated text from modules

orbeckst · orbeckst · commit b024570103f4 · 2018-10-05T01:02:35.000-07:00
diff --git a/MDAnalysisData/adk_equilibrium.py b/MDAnalysisData/adk_equilibrium.py
@@ -1,35 +1,10 @@
 # -*- coding: utf-8 -*-
 
-"""AdK equilibrium trajectory without water
+"""AdK equilibrium trajectory without water.
 
-The original dataset is available from doi
-`10.6084/m9.figshare.5108170.v1
-<https://doi.org/10.6084/m9.figshare.5108170.v1>`_
-
-   https://figshare.com/articles/Molecular_dynamics_trajectory_for_benchmarking_MDAnalysis/5108170
-
-MD trajectory of apo adenylate kinase with CHARMM27 force field and
-simulated with explicit water and ions in NPT at 300 K and 1
-bar. Saved every 240 ps for a total of 1.004 µs. Produced on PSC
-Anton. The trajectory only contains the protein and all solvent
-stripped. Superimposed on the CORE domain of AdK by RMSD fitting.
-
-The topology is contained in the PSF file (CHARMM format). The
-trajectory is contained in the DCD file (CHARMM/NAMD format).
-
-
-References
-----------
-
-Seyler, Sean; Beckstein, Oliver (2017): Molecular dynamics trajectory for benchmarking MDAnalysis. figshare. Fileset. `10.6084/m9.figshare.5108170.v1
-<https://doi.org/10.6084/m9.figshare.5108170.v1>`_
+https://figshare.com/articles/Molecular_dynamics_trajectory_for_benchmarking_MDAnalysis/5108170/1
 """
 
-# TODO: generate docs from DESCR or link
-
-# Authors: Oliver Beckstein, Sean L. Seyler
-# License: CC-BY 4.0
-
 from os.path import dirname, exists, join
 from os import makedirs, remove
 import codecs
diff --git a/MDAnalysisData/adk_transitions.py b/MDAnalysisData/adk_transitions.py
@@ -1,45 +1,8 @@
 # -*- coding: utf-8 -*-
 
-"""Ensembles of AdK transitions
-
-The original dataset is available from doi
-`10.6084/m9.figshare.7165306
-<https://doi.org/10.6084/m9.figshare.7165306>`_
-
-The macromolecular conformational transition between the closed
-conformation of apo-adenylate kinase from E. coli (EcAdK) to the open
-conformation was sampled with two methods: (1) dynamic importance
-sampling molecular dynamics (DIMS MD), and (2) Framework Rigidity
-Optimized Dynamics Algorithm (FRODA). Each ensemble of independently
-generated paths contains 200 trajectories in the CHARMM DCD format.
-
-
-Data are from: [Seyler2015]_ (see there for more details).
-
-
-Each tar file contains a directory trajectories containing the DCD
-files and a directory topologies with files that include information
-about the atoms (CHARMM PSF format or PDB format).
-
-
-DIMS.tar.gz: DIMS AdK (implicit solvent) with dynamic importance
-sampling MD from closed (1AKE) to open (4AKE). CHARMM 22 force
-field. Topology file: adk4ake.psf
-
-
-FRODA.tar.gz: FRODA AdK with geometric targeting on a rigid
-decomposition (FRODA server); closed (1AKE) to open (4AKE). Topology
-file: 1ake.pdb
-
-
-References
-----------
-
-.. [Seyler2015] Seyler SL, Kumar A, Thorpe MF, Beckstein O (2015) Path
-   Similarity Analysis: A Method for Quantifying Macromolecular
-   Pathways. PLoS Comput Biol 11(10):
-   e1004568. https://doi.org/10.1371/journal.pcbi.1004568
+"""Ensembles of AdK transitions.
 
+https://figshare.com/articles/Simulated_trajectory_ensembles_for_the_closed-to-open_transition_of_adenylate_kinase_from_DIMS_MD_and_FRODA/7165306
 """
 
 
diff --git a/MDAnalysisData/base.py b/MDAnalysisData/base.py
@@ -1,4 +1,4 @@
-"""Base IO code for all datasets.
+"""Base I/O code for all datasets.
 
 Based on :mod:`sklearn.datasets.base` (used under BSD 3-clause license).
 
diff --git a/MDAnalysisData/datasets.py b/MDAnalysisData/datasets.py
@@ -1,3 +1,6 @@
+"""Access to all datasets via ``fetch_*()`` functions.
+
+"""
 # import load_* and fetch_* functions from modules
 
 from __future__ import absolute_import
diff --git a/MDAnalysisData/ifabp_water.py b/MDAnalysisData/ifabp_water.py
@@ -1,31 +1,8 @@
 # -*- coding: utf-8 -*-
 
-"""MD simulation of I-FABP with water
-
-The original dataset is available from doi
-`10.6084/m9.figshare.7058030.v1
-<https://doi.org/10.6084/m9.figshare.7058030.v1>`_
-
-   https://figshare.com/articles/Molecular_dynamics_trajectory_of_I-FABP_for_testing_and_benchmarking_solvent_dynamics_analysis/7058030
-
-The trajectory is a short MD run of I-FABP (intestinal fatty acid binding protein) in water.
-
-It was simulated in CHARMM for 500 ps with a 2 fs timestep. Frames
-were saved every 1 ps and the trajectory was RMSD-fitted to the
-protein.
-
-There are 500 frames in the trajectory.
-
-It is used as a test case for the hop package https://github.com/Becksteinlab/hop.
-
-References
-----------
-
-Beckstein, Oliver (2018): Molecular dynamics trajectory of I-FABP for
-testing and benchmarking solvent dynamics
-analysis. figshare. Fileset. DOI: `10.6084/m9.figshare.7058030.v1
-<https://doi.org/10.6084/m9.figshare.7058030.v1>`_
+"""MD simulation of I-FABP with water.
 
+https://figshare.com/articles/Molecular_dynamics_trajectory_of_I-FABP_for_testing_and_benchmarking_solvent_dynamics_analysis/7058030
 """
 
 from os.path import dirname, exists, join
diff --git a/MDAnalysisData/vesicles.py b/MDAnalysisData/vesicles.py
@@ -1,6 +1,6 @@
 # -*- coding: utf-8 -*-
 
-"""Large vesicles
+"""Large vesicles library (coarse grained).
 
 https://figshare.com/articles/Large_System_Vesicle_Benchmark_Library/3406708
 """
diff --git a/docs/vesicles.rst b/docs/vesicles.rst
@@ -1,9 +1,9 @@
 .. -*- coding: utf-8 -*-
 
 
-==========
- Vesicles
-==========
+===================
+ Vesicles datasets
+===================
 
 .. module:: MDAnalysisData.vesicles
 

Original file line number	Diff line number	Diff line change
`@@ -1,4 +1,4 @@`
`1`		`-"""Base IO code for all datasets.`
	`1`	`+"""Base I/O code for all datasets.`
`2`	`2`
`3`	`3`	Based on :mod:`sklearn.datasets.base` (used under BSD 3-clause license).
`4`	`4`