TiledCompound accepts tuple instead of 3 different params; house clea…

…ning: cleaned up readme.md, removing unused rst files, updated tutorials
sallai · Mar 2, 2015 · 790b2d5 · 790b2d5
1 parent 8e0972d
commit 790b2d5
Show file tree

Hide file tree

Showing 126 changed files with 4,422 additions and 2,048 deletions.
diff --git a/AUTHORS.rst b/AUTHORS.rst
diff --git a/CONTRIBUTING.rst b/CONTRIBUTING.rst
diff --git a/HISTORY.rst b/HISTORY.rst
diff --git a/INSTALLATION.rst b/INSTALLATION.rst
diff --git a/MANIFEST.in b/MANIFEST.in
@@ -1,6 +0,0 @@
-include AUTHORS.rst
-include CONTRIBUTING.rst
-include HISTORY.rst
-include LICENSE.rst
-include README.rst
-include requirements.txt

diff --git a/Makefile b/Makefile
diff --git a/README.md b/README.md
@@ -0,0 +1,44 @@
+## mBuild: a hierarchical, component based molecule builder
+
+[![Linux Build Status](https://travis-ci.org/sallai/mbuild.png?branch=master)](https://travis-ci.org/sallai/mbuild)
+[![Test Coverage](https://coveralls.io/repos/sallai/mbuild/badge.png?branch=master)](https://coveralls.io/r/sallai/mbuild)
+[![PyPI Version](https://badge.fury.io/py/mbuild.png)](https://pypi.python.org/pypi/mbuild)
+
+With just a few lines of mBuild code, you can assemble reusable components into
+complex molecular systems for molecular dynamics simulations.
+
+mBuild
+* is designed to minimize or even eliminate the need to explicitly translate and
+  orient components when building systems: you simply tell it to connect two
+  pieces!
+* keeps track of the system's topology so you don't have to
+  worry about keeping track of bonds when constructing chemically bonded
+  structures from smaller components.
+
+To learn more, get started or contribute, check out our [website](http://mbuild.rtfd.org/en/master/).
+
+#### Example system
+
+Components in dashed boxes are drawn by hand using, e.g.,
+[Avogadro](http://avogadro.cc/wiki/Main_Page) or generated elsewhere. Each
+component is wrapped as a simple python class with user defined attachment
+sites, or ports. That's the hard part! Now mBuild can do the rest. Each component
+further down the hierarchy is, again, a simple python class that describes
+which piece should connect to which piece.
+
+Ultimately, complex systems structures can be created with just a line or two
+of code. Additionally, this approach easily exposes tunable parameters within
+the hierarchy so you can actually create whole families of structures simply
+by adjusting a variable:
+
+    mask = random_mask_2d(20)  # A random arrangement of 20 pieces on a 2D surface.
+    brush_layer = BrushLayer(chain_lenth=20, mask=mask, tile_x=3, tile_y=2)
+
+![Zwitterionic brushes on beta-cristobalite substrate](pmpc.png)
+
+
+#### http://img.shields.io/badge/license-LGPLv2.1-blue.svg
+
+GNU LGPL version 2.1, or at your option a later version of the license.
+Various sub-portions of this library may be independently distributed under
+different licenses. See those files for their specific terms.