more documentation for modeller module and some clean up

docs/modeller.md

@@ -1,4 +1,6 @@
 # Modeller
+This module provides simple Julia integration for [MODELLER](https://salilab.org/modeller/), a bioinformatics tool for comparative protein structure modelling.
+You need to [install](https://salilab.org/modeller/download_installation.html) MODELLER locally on your computer in order to use this module.
 
 ## Exported functions
 
@@ -8,7 +10,7 @@ gen_modeller_script(name::String)
 
 Generates Julia scripts for MODELLER.
 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 MODELLER website.
+These scripts are based on the basic example scripts from Tutorial 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`.
 
 **Example:**
@@ -17,10 +19,14 @@ Scripts are generated in the current working directory. You can find all scripts
 gen_modeller_script("build_profile")
 ```
 
+This module also provides a few simple functions that provide common MODELLER tasks. These are again adapted from the MODELLER basic example. The given examples calls should work inside the modeller-basic-example directory. 
+
 ```julia
 build_profile(;seq_database_file::String = "", seq_database_format::String="PIR", alignment_file::String = "", alignment_format::String = "PIR", output_name::String = "build_profile", output_profile_format::String="TEXT", output_alignment_format::String="PIR")
 ```
 
+Note: this function is using keyword arguments
+
 **Example:**
 
 ```julia
@@ -36,3 +42,35 @@ align2d(model_file::String, model_segment, model_align_codes::String, atom_files
 ```julia
 align2d("1bdm.pdb", ("FIRST:A","LAST:A"), "1bdmA", "1bdm.pdb", "TvLDH.ali", "TvLDH", "TvLDH-1bdmA")
 ```
+
+```julia
+model_single(alnf::String, known_structure::String, seq::String)
+```
+alnf: path to alignment file
+known_structure: path or name of known pdb structure
+seq: sequence  
+
+**Example:**
+
+```julia
+model_single("TvLDH-1bdmA.ali", "1bdmA", "TvLDH")
+```
+
+```julia
+evaluate_model(pdbfile::String, outputfile::String = "")
+```
+pdbfile: path to pdb file
+outputfile: optional path to output file. Defaults to pdbfile+".profile" 
+
+**Example:**
+
+```julia
+evaluate_model("TvLDH.B99990002.pdb", "TvLDH.profile")
+```
+
+##References
+
+  * N. Eswar, M. A. Marti-Renom, B. Webb, M. S. Madhusudhan, D. Eramian, M. Shen, U. Pieper, A. Sali. Comparative Protein Structure Modeling With MODELLER. Current Protocols in Bioinformatics, John Wiley & Sons, Inc., Supplement 15, 5.6.1-5.6.30, 2006.
+  * M.A. Marti-Renom, A. Stuart, A. Fiser, R. Sánchez, F. Melo, A. Sali. Comparative protein structure modeling of genes and genomes. Annu. Rev. Biophys. Biomol. Struct. 29, 291-325, 2000.
+  * A. Sali & T.L. Blundell. Comparative protein modelling by satisfaction of spatial restraints. J. Mol. Biol. 234, 779-815, 1993.
+  * A. Fiser, R.K. Do, & A. Sali. Modeling of loops in protein structures, Protein Science 9. 1753-1773, 2000.

src/MODELLER/modeller.jl

@@ -87,7 +87,7 @@ export  gen_modeller_script, build_profile, model_single, evaluate_model, align2
 
         # check for optional argument output and set it to the first part of the name of the PDB file
         if outputfile == ""
-            outputfile = string(split(pdbfile,".")[1], ".profile")
+            outputfile = string(pdbfile, ".profile")
         end
 
         @pyimport modeller