formatting

docs/index.md

@@ -5,4 +5,7 @@ The project consists of several modules which can be used like this:
 ```julia
 using BiomolecularStructures.<ModuleName>
 ```
-e.g. ```julia using BiomolecularStructures.Kabsch```
+e.g. 
+```julia
+using BiomolecularStructures.Kabsch
+```

docs/kabsch.md

@@ -24,24 +24,32 @@ julia> kabsch_rmsd(P, Q)
 
 ## Exported functions
 
-```julia rmsd(A::Array{Float64,2}, B::Array{Float64,2}) ```
+```julia
+rmsd(A::Array{Float64,2}, B::Array{Float64,2})
+```
 
 Calculates the root mean square deviation of two matrices A and B in using the following formula:
 
 ![RMSD formula](assets/kabsch/rmsd.png)
 
-### `calc_centroid(m::Array{Float64,2})`
+```julia
+calc_centroid(m::Array{Float64,2})
+```
 
 Returns the centroid of a matrix m as a [x y z] vector (An ```Array{Float54,2}```).
 
-### `translate_points(P::Array{Float64,2}, Q::Array{Float64,2})`
+```julia
+translate_points(P::Array{Float64,2}, Q::Array{Float64,2})
+```
 
 Translates two matrices P, Q so that their centroids are equal to the origin of the coordinate system.
 
-### `kabsch(reference::Array{Float64,2},coords::Array{Float64,2})`
+```julia
+kabsch(reference::Array{Float64,2},coords::Array{Float64,2})
+```
 
 Calculates the optimal rotation matrix of two matrices P, Q.
-Using `translate_points` it shifts the matrices' centroids to the origin of the coordinate system, then computes the covariance matrix A:
+Using ```translate_points``` it shifts the matrices' centroids to the origin of the coordinate system, then computes the covariance matrix A:
 
 ![Covariance Formula](assets/kabsch/cov.png)
 
@@ -61,7 +69,9 @@ The last two steps are translating U so that the superimposed matrix will "fit"
 
 The function returns the superimposed matrix.
 
-### `kabsch_rmsd(P::Array{Float64,2}, Q::Array{Float64,2})`
+```julia
+kabsch_rmsd(P::Array{Float64,2}, Q::Array{Float64,2})
+```
 Directly returns the RMSD after rotation for convenience.
 
 ## Background

docs/pdb.md

@@ -4,14 +4,20 @@ The PDB module provides utility functions to deal with [PDB (Protein Data Bank)]
 
 ## Exported functions
 
-```julia get_structure(filename::String)```
+```julia
+get_structure(filename::String)
+```
 
 Parses a PDB file and returns a structure PyObject.
 
-```get_chains(structure::PyObject)```
+```julia
+get_chains(structure::PyObject)
+```
 
 Gets the chains of protein structure from a BioPython PyObject and returns an Array of Array{Float64,2} matrices.
 
-```structure_to_matrix(structure::PyObject)```
+```julia
+structure_to_matrix(structure::PyObject)
+```
 
 Converts a BioPython structure to a Array{Float64,2} matrix.

docs/plot.md

@@ -4,7 +4,9 @@ Provides a utility function to plot two matrices P, Q
 
 ## Exported functions
 
-```julia matrices_plot(P::Array{Float64,2},Q::Array{Float64,2})```
+```julia
+matrices_plot(P::Array{Float64,2},Q::Array{Float64,2})
+```
 
 Plots two matrices P, Q. Example output: