update documentation

docs/kabsch.md

@@ -24,6 +24,8 @@ julia> kabsch_rmsd(P, Q)
 
 ## Exported functions
 
+### rmsd
+
 ```julia
 rmsd(A::Array{Float64,2}, B::Array{Float64,2})
 ```
@@ -32,23 +34,44 @@ Calculates the root mean square deviation of two matrices A and B in using the f
 
 ![RMSD formula](assets/kabsch/rmsd.png)
 
+**A** a matrix
+
+**B** a matrix
+
+### calc_centroid
+
 ```julia
 calc_centroid(m::Array{Float64,2})
 ```
 
 Returns the centroid of a matrix m as a [x y z] vector (An ```Array{Float54,2}```).
 
+**m** a matrix
+
+
+### translate_points
 ```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.
 
+**P** a matrix
+
+**Q** a matrix
+
+### kabsch
+
 ```julia
 kabsch(reference::Array{Float64,2},coords::Array{Float64,2})
 ```
 
-Calculates the optimal rotation matrix of two matrices P, Q.
+Calculates the optimal rotation matrix of two matrices P, Q and superimposes the two matrices
+
+**reference** a matrix to superimpose on.
+
+**coords** the matrix to be rotated
+
 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)
@@ -69,10 +92,17 @@ The last two steps are translating U so that the superimposed matrix will "fit"
 
 The function returns the superimposed matrix.
 
+### kabsch_rmsd
+
 ```julia
 kabsch_rmsd(P::Array{Float64,2}, Q::Array{Float64,2})
 ```
-Directly returns the RMSD after rotation for convenience.
+Directly returns the RMSD after rotation for 
+convenience.
+
+**P** reference matrix 
+
+**Q** matrix to be rotated
 
 ## Background
 

docs/mafft.md

@@ -38,7 +38,7 @@ mafft(fasta_in::String, preconfiguration=:default)
 
 Runs mafft with the provided fasta file and returns the alignment in FastaIO dataformat. By default mafft is called with the `--auto` option.
 
-*fasta_in*: path to FASTA file
+**fasta_in**: path to FASTA file
 
 *preconfiguration*: optional commandline arguments for MAFFT (array of strings)
 
@@ -48,17 +48,17 @@ mafft_from_string(fasta_in::String, preconfiguration=:default)
 
 Calls MAFFT with the given FASTA string as input and returns aligned FASTA in the FastaIO dataformat. 
 
-*fasta_in*: FASTA string
+**fasta_in**: FASTA string
 
-*preconfiguration*: optional commandline arguments for MAFFT (array of strings) 
+**preconfiguration**: optional commandline arguments for MAFFT (array of strings) 
 
 ```julia
 mafft_from_fasta(fasta_in, preconfiguration=:default)
 ```
 
 Calls MAFFT with the given FASTA in FastaIO format
 
-*fasta_in*: FASTA in FastaIO format
+**fasta_in**: FASTA in FastaIO format
 
 *preconfiguration*: optional commandline arguments for MAFFT (array of strings)
 
@@ -67,22 +67,22 @@ mafft_profile(group1::String, group2::String)
 ```
 Group-to-group alignments
 
-*group1* and *group2* have to be files with alignments. Returns aligned FASTA in the FastaIO dataformat.
+**group1** and **group2** have to be files with alignments. Returns aligned FASTA in the FastaIO dataformat.
 
 ```julia
 mafft_profile_from_string(group1::String, group2::String)
 ```
 Group-to-group alignments with input strings in FASTA format.
 
- *group1* and *group2* have to be strings with alignments in FASTA format.
+ **group1** and **group2** have to be strings with alignments in FASTA format.
 
 ```julia
 mafft_profile_from_fasta(group1, group2)
 ```
 
 Group-to-group alignments with input in FastaIO format
 
-*group1* and *group2* have to be in FastaIO format and have to be alignments
+**group1** and **group2** have to be in FastaIO format and have to be alignments
 
 ### Helper functions for aligned FASTA
 This module also includes a few helper functions for the FastaIO dataformat (which is returned by the mafft functions of this module).
@@ -92,21 +92,21 @@ alignment_length(fasta)
 ```
 Returns the length of the alignment.
 
-*fasta*: A FastaIO dataformat object
+**fasta**: A FastaIO dataformat object
 
 ```julia
 to_aminoacids(fasta)
 ```
 Converts a FastaIO-formatted array into an array of BioSeq AminoAcid.
 
-*fasta*: A FastaIO dataformat object
+**fasta**: A FastaIO dataformat object
 
 ```julia
 print_fasta(fasta)
 ```
 Prints a FastaIO object in a nicely formatted way to the screen.
 
-*fasta*: A FastaIO dataformat object
+**fasta**: A FastaIO dataformat object
 
 
 ## Supported pre-configurations (strategies)

docs/modeller.md

@@ -19,7 +19,7 @@ gen_modeller_script(name::String)
 
 Generates Julia templates for MODELLER usage with Julia.
 
-*name:* The name of the script (minus the extension). Possible values: "align2d", "build_profile", "compare", "evaluate_model", "model-single", "plot_profiles".
+**name:** The name of the script (minus the extension). Possible values: "align2d", "build_profile", "compare", "evaluate_model", "model-single", "plot_profiles".
 
 These scripts are based on the basic example scripts from  the [tutorial](https://salilab.org/modeller/tutorial/basic.html) on the MODELLER website.
 Scripts are generated in the current working directory. You can find all scripts that can be generated in `src/MODELLER/modeller-basic-example-julia`.
@@ -51,7 +51,7 @@ compare(pdbs)
 ```
 Prints out a table with the similarities between the given structures and a dendrogram.
 
-*pdbs:* Array of pairs of pdb-files and chains that should be compared.
+**pdbs:** Array of pairs of pdb-files and chains that should be compared.
 
 #### align2d
 
@@ -61,39 +61,39 @@ align2d(model_file::String, model_segment, model_align_codes::String, atom_files
 
 Aligns a structure model (pdb) with a sequence. Writes the alignment to <outputname>.ali in PIR format and to <outputname>.pap in PAP format.
 
-*model_file:* the file of the structure model
+**model_file:** the file of the structure model
 
-*model_segment:* the segment of the model to be used, e.g. ``('FIRST:A','LAST:A')``
+**model_segment:** the segment of the model to be used, e.g. ``('FIRST:A','LAST:A')``
 
-*model_align_codes:* the code name of the structure. e.g. "1bdmA" for "1bdm:A"
+**model_align_codes:** the code name of the structure. e.g. "1bdmA" for "1bdm:A"
 
-*atom_files:* path to the model pdb file
+**atom_files:** path to the model pdb file
 
-*sequence_file:* path to the sequence file
+**sequence_file:** path to the sequence file
 
-*sequence_codes:* the code name of the structure, e.g. "TvLDH"
+**sequence_codes:** the code name of the structure, e.g. "TvLDH"
 
-*outputname:* name of the files that ``align2d()`` creates.
+**outputname:** name of the files that ``align2d()`` creates.
 
 #### model_single
 
 ```julia
 model_single(alnf::String, known_structure::String, seq::String)
 ```
-*alnf:* path to alignment file
+**alnf:** path to alignment file
 
-*known_structure:* path or name of known pdb structure
+**known_structure:** path or name of known pdb structure
 
-*seq:* sequence  
+**seq:** sequence  
 
 #### evaluate_model
 
 ```julia
 evaluate_model(pdbfile::String, outputfile::String = "")
 ```
-*pdbfile:* path to pdb file
+**pdbfile:** path to pdb file
 
-*outputfile:* optional path to output file. Defaults to pdbfile+".profile" 
+**outputfile:** optional path to output file. Defaults to pdbfile+".profile" 
 
 #### plot_profiles
 
@@ -103,17 +103,17 @@ plot_profiles(alignment_file::String, template_profile::String, template_sequenc
 
 Plots a two profiles with data from a corresponding alignment file (for both structures).
 
-*alignment_file:* path to alignment file
+**alignment_file:** path to alignment file
 
-*template_profile:* path to profile that was used as the template
+**template_profile:** path to profile that was used as the template
 
-*template_profile:* sequence name from *template_profile* that should be used
+**template_profile:** sequence name from *template_profile* that should be used
 
-*model_profile:* path to model profile 
+**model_profile:** path to model profile 
 
-*model_profile:* sequence name from *model_profile* that should be used
+**model_profile:** sequence name from *model_profile* that should be used
 
-*plot_file:* (optional) path where created plot should be saved. Default: dope_profile.png
+**plot_file:** (optional) path where created plot should be saved. Default: dope_profile.png
 
 ## Usage / Usecase
 This usecase is again based on the [tutorial](https://salilab.org/modeller/tutorial/basic.html) on the MOELLER website. You should download the corresponding files and call the julia functions with the julia interactive prompt inside the tutorial example folder.

docs/pdb.md

@@ -4,27 +4,53 @@ The PDB module provides utility functions to deal with [PDB (Protein Data Bank)]
 
 ## Exported functions
 
+### get_structure
 ```julia
 get_structure(filename::String)
 ```
-
 Parses a PDB file and returns a structure PyObject.
 
+*filename* Path/Filename of a PDB file.
+
+### get_chains
 ```julia
 get_chains(structure::PyObject)
 ```
 
-Gets the chains of protein structure from a BioPython PyObject and returns an Array of Array{Float64,2} matrices.
+Gets the chains of a protein structure from a BioPython PyObject and returns an Array of Array{Float64,2} matrices of C<sub>&alpha;</sub> atomic coordinates.
 
+**structure** A protein structure.
+
+### structure_to_matrix
 ```julia
 structure_to_matrix(structure::PyObject)
 ```
 
-Converts a BioPython structure to a Array{Float64,2} matrix.
+Converts a BioPython structure to a Array{Float64,2} matrix of C<sub>&alpha;</sub> atomic coordinates.
+
+**structure** A protein structure
+
+### export_pdb (experimental)
 
 ```julia
 export_to_pdb(residueName::String,chainID::String,matrix::Array{Float64,2}, filename::String)
 ```
 
 Exports a matrix of C<sub>&alpha;</sub> atomic coordinates to a PDB File. As of now, it produces files as defined in the [PDB specification](http://deposit.rcsb.org/adit/docs/pdb_atom_format.html) (Section ATOM) with one minor difference: The atom name is right-aligned, because Formatting.jl does not support center-aligning (yet). This isn't in the specification, but [some descriptions](http://cupnet.net/tag/pdb/) include it.
 
+**residueName** residue name to write to the file
+
+**chainID** chain ID (e.g. "A", "B", "C"..)
+
+**matrix** the matrix to export.
+
+**filename** Path/filename to export to.
+
+### get_remote_pdb
+```julia
+get_remote_pdb(id::String)
+```
+
+Downloads and caches a PDB from [rcsb.org](http://www.rcsb.org/)
+
+**id** a PDB ID

docs/plot.md

@@ -4,10 +4,16 @@ Provides a utility function to plot two matrices P, Q
 
 ## Exported functions
 
+### matrices_plot
+
 ```julia
 matrices_plot(P::Array{Float64,2},Q::Array{Float64,2})
 ```
 
 Plots two matrices P, Q. Example output:
 
-![Example output](assets/kabsch/alpha_init.png)
+![Example output](assets/kabsch/alpha_init.png)
+
+**P** A matrix
+
+**Q** A matrix

docs/webblast.md

@@ -1,33 +1,19 @@
 # WebBLAST
 
-An API for Julia to call the BLAST Web API of NCBI and EBI.
-## Usage
+API for Julia to call the BLAST Web API of NCBI and EBI.
 
-```
-usage: WebBLAST.jl [-f FASTA FASTA] [-s SEQUENCE] [-t THRESHOLD] [-h]
-                   fasta_out
-
-WebBLAST
+## Exported functions
 
-positional arguments:
-  fasta_out             FASTA output file
-
-optional arguments:
-  -f, --fasta FASTA FASTA
-                        Sequences in FASTA format, Sequence #
-  -s, --sequence SEQUENCE
-                        Sequence as string
-  -t, --threshold THRESHOLD
-                        E-Value threshold (type: Float64, default:
-                        0.0)
-  -h, --help            show this help message and exit
+#### webblast
 
+```julia
+webblast(provider::String, sequence::String, threshold::Float64, cached=false)
 ```
-## Examples
 
-Sequence:
-```julia WebBLAST/WebBLAST.jl -s MNQLQQLQNPGESPPVHPFVAPLSYLLGTWRGQGEGEYPTIPSFRYGEEIRFSHSGKPVIAY -t 0.000000000000000000000000000001 out.fasta```
+Calls the the API of the given provider to search for a protein sequence and returns all hits within a E-Value threshold.
+
+**provider** A provider for a BLAST REST API, e.g. NCBI/EBI BLAST. Default "ncbi" (EBI to be implemented), "ncbi" searches for the sequence in the PDB.
 
-FASTA:
+**sequence** The sequence to search for.
 
-```julia WebBLAST.jl -f fasta.txt 4```
+**cached** Default ```false```, results can be cached, for example during development.