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Sdg23 add getting started page md (#443)
* FIX broken links * add mamba instructions and refine installation quick start * add mamba instructions and refine installation quick start * address PR review comments * Add 'Getting Started' page with installation, basic example, and learning resources * Update basic_example.md slight changes to improve readability of the code example comments for new users * address PR review comments * Address PR review comments * address PR review comments and restyle code block * restyle code block in basic example page --------- Co-authored-by: Micaela Matta <31009265+micaela-matta@users.noreply.github.com>
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‎pages/basic_example.md‎

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---
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layout: page
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layout: otherpage
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title: Basic example
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order: 1
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---
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A typical usage pattern is to iterate through a trajectory and analyze
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coordinates for every frame. In the following example the end-to-end
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distance of a protein and the radius of gyration of the backbone atoms
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are calculated:
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{% highlight python %}
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import MDAnalysis
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from MDAnalysis.tests.datafiles import PSF, DCD # test trajectory
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import numpy.linalg
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<div class="wide-code">
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{% highlight python %}
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import MDAnalysis
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from MDAnalysis.tests.datafiles import PSF, DCD # test trajectory
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import numpy.linalg
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u = MDAnalysis.Universe(PSF,DCD) # always start with a Universe
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# can access via segid (4AKE) and atom name
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# we take the first atom named N and the last atom named C
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nterm = u.select_atoms('segid 4AKE and name N')[0]
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cterm = u.select_atoms('segid 4AKE and name C')[-1]
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# load trajectory and topology into a Universe
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u = MDAnalysis.Universe(PSF,DCD)
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# from the 4AKE segid, select
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# the first atom named N and the last atom named C
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nterm = u.select_atoms('segid 4AKE and name N')[0]
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cterm = u.select_atoms('segid 4AKE and name C')[-1]
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# select the backbone atoms (AtomGroup)
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bb = u.select_atoms('protein and backbone')
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bb = u.select_atoms('protein and backbone') # a selection (AtomGroup)
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for ts in u.trajectory: # iterate through all frames
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r = cterm.position - nterm.position # end-to-end vector from atom positions
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d = numpy.linalg.norm(r) # end-to-end distance
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rgyr = bb.radius_of_gyration() # method of AtomGroup
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print("frame = {0}: d = {1} A, Rgyr = {2} A".format(
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ts.frame, d, rgyr))
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{% endhighlight %}
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for ts in u.trajectory: # iterate through all frames
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r = cterm.position - nterm.position # end-to-end vector from atom positions
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d = numpy.linalg.norm(r) # end-to-end distance
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rgyr = bb.radius_of_gyration() # method of AtomGroup
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print("frame = {0}: d = {1} A, Rgyr = {2} A".format(
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ts.frame, d, rgyr))
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{% endhighlight %}
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</div>
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To find out what else you can do, head over to [learning
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MDAnalysis]({{ site.baseurl }}/pages/learning_MDAnalysis) to have a look

‎pages/getting_started.md‎

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---
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layout: page
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title: Getting Started
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order: 1
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---
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MDAnalysis is a Python library for analyzing molecular dynamics (MD) simulations. This page will guide you through quickly installing MDAnalysis, exploring a basic example, and accessing learning resources to get started.
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## Installation Instructions
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Our [Installation Quick Start]({{ site.baseurl }}/pages/installation_quick_start) guide contains instructions to get MDAnalysis up and running in a few minutes. Try this guide first.
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For a more thorough installation with advanced options, including dependencies and environment configurations, see the [installation instructions in the User Guide]({{ site.docs.userguide.url }}/stable/installation.html).
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## Basic Example
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Once MDAnalysis is installed, you can load a trajectory and perform a simple analysis. A typical usage pattern is to iterate through a trajectory and analyze
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coordinates for every frame.
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In the following example, the end-to-end distance of a protein and the radius of gyration of the backbone atoms are calculated:
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<div class="wide-code">
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{% highlight python %}
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import MDAnalysis
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from MDAnalysis.tests.datafiles import PSF, DCD # test trajectory
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import numpy.linalg
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# load trajectory and topology into a Universe
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u = MDAnalysis.Universe(PSF,DCD)
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# from the 4AKE segid, select
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# the first atom named N and the last atom named C
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nterm = u.select_atoms('segid 4AKE and name N')[0]
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cterm = u.select_atoms('segid 4AKE and name C')[-1]
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# select the backbone atoms (AtomGroup)
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bb = u.select_atoms('protein and backbone')
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for ts in u.trajectory: # iterate through all frames
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r = cterm.position - nterm.position # end-to-end vector from atom positions
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d = numpy.linalg.norm(r) # end-to-end distance
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rgyr = bb.radius_of_gyration() # method of AtomGroup
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print("frame = {0}: d = {1} A, Rgyr = {2} A".format(
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ts.frame, d, rgyr))
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{% endhighlight %}
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</div>
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## Learning Resources
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To find out what else you can do, head over to [Learning
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MDAnalysis]({{ site.baseurl }}/pages/learning_MDAnalysis) to explore
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tutorials and documentation.
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If you have questions, visit our [Community]({{ site.baseurl }}/pages/community) page to learn about available discussion channels. Happy coding!
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‎pages/installation_quick_start.md‎

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---
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layout: page
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layout: otherpage
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title: Installation Quick Start
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order: 2
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---
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MDAnalysis can be installed using [mamba][], a faster drop-in replacement for [conda][], or [pip][].

‎public/css/local.css‎

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position: absolute;
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.wide-code pre {
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white-space: pre;
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overflow-x: auto;
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display: block;
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width: 100%;
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}
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