Coding denovo prediction from density maps in PyRosetta

I want to code the below scripts using PyRosetta. I’m totally new to Pyrosetta, only starting to read the tutorials today. However, I know Python very well. Anyway, all the scripts seem to be calling the denovo_density.linuxgccrelease binary so I’m guessing, if there’s a Pyrosetta class or module built on that, it shouldn’t be but a few lines of code.

My qustions are, can it be done? How? 

#!/bin/sh





mkdir round3_alpha_tubulin



$ROSETTA3/source/bin/denovo_density.linuxgccrelease

-in::file::fasta /home/labusr/Documents/tubulin_exercise/5ucy_alpha.fasta

-fragfile /home/labusr/Documents/tubulin_exercise/9mers_alpha

-startmodel /home/labusr/Documents/round2_alpha_tubulin.pdb 

-mapfile /home/labusr/Documents/tubulin_exercise/masked_map_center_alpha.mrc

-n_to_search 1000 -n_filtered 4500 -n_output 50 

-bw 16 

-atom_mask_min 2 

-atom_mask 3 

-clust_radius 3 

-clust_oversample 4 

-point_radius 3 

-movestep 1 

-delR 2 

-frag_dens 0.8 

-ncyc 3 

-min_bb false 

-pos $1 

-out:file:silent round3_alpha_tubulin/alpha_tubulin.$1.silent

#!/bin/sh



$ROSETTA3/source/bin/denovo_density.linuxgccrelease

-mode score 

-in::file::silent round3_alpha_tubulin/alpha_tubulin*silent 

-scorefile round3_alpha_tubulin/scores3 

-n_matches 50

#!/bin/sh



$ROSETTA3/source/bin/denovo_density.linuxgccrelease

-mode assemble 

-nstruct 5 

-in::file::silent round3_alpha_tubulin/alpha_tubulin*silent 

-scorefile round3_alpha_tubulin/scores3 

-assembly_weights 4 20 6 

-null_weight -150 

-out:file:silent round3_alpha_tubulin/assembled.$1 

-scale_cycles 1 

-mute core

#!/bin/sh



$ROSETTA3/source/bin/denovo_density.linuxgccrelease

-mode consensus 

-in::file::silent round3_alpha_tubulin/assembled.*silent 

-consensus_frac 0.8 -energy_cut 0.05 

-mute core



# use the old model as a starting point

cp S_0001.pdb round3_alpha_tubulin.pdb