Skip to content
Snippets Groups Projects
Commit 7ceffb45 authored by samuel hanot's avatar samuel hanot
Browse files

docuementation

parent 4ab1e431
No related branches found
No related tags found
No related merge requests found
...@@ -39,11 +39,13 @@ ${SRC_DIR}/recursive_gmconvert.sh -f map_filename -t threshold -n num_gaussians ...@@ -39,11 +39,13 @@ ${SRC_DIR}/recursive_gmconvert.sh -f map_filename -t threshold -n num_gaussians
`-h`: display this message `-h`: display this message
Unless you enable serial mode (`-s` flag), all the scripts assume that you are running a cluster with the `slurm` queuing system.
### Output:
The script creates a sub-directory (called `i`) for each recursion level `i`, and the output files are called `i/i.gmm` and `i_imp.gmm`. The script creates a sub-directory (called `i`) for each recursion level `i`, and the output files are called `i/i.gmm` and `i_imp.gmm`.
`i/i.gmm` contains the gmm in `gmconvert` format, and `i_imp.gmm` contains the gmm in `IMP` format (the conversion is handeld by `gmconvert2imp.sh`), which can be read in IMP using `IMP.isd.gmm_tools.decorate_gmm_from_text` function. `i/i.gmm` contains the gmm in `gmconvert` format, and `i_imp.gmm` contains the gmm in `IMP` format (the conversion is handeld by `gmconvert2imp.sh`), which can be read in IMP using `IMP.isd.gmm_tools.decorate_gmm_from_text` function.
Unless you enable serial mode (`-s` flag), all the scripts assume that you are running a cluster with the `slurm` queuing system.
## other scripts: ## other scripts:
......
#!/bin/bash
while read -a l
do
emd=${l[0]}
w=$(grep molWtTheo ${emd}/header/emd-${emd}.xml | head -n1 | cut -d '>' -f 2 | cut -d '<' -f 1)
res=$(grep resolutionByAuthor ${emd}/header/emd-${emd}.xml | head -n1 | cut -d '>' -f 2 | cut -d '<' -f 1)
res_method=$(grep resolutionMethod ${emd}/header/emd-${emd}.xml | head -n1 | cut -d '>' -f 2 | cut -d '<' -f 1)
#here we get the minimum in the plot of resolution vs #Gaussian
gmm_data=$(awk -v r=${res} 'function abs(x){return x<0?-x:x} BEGIN{m=1000} abs($3-r)<m && abs(abs($3-r)-m)/r>0.1{m=abs($3-r); b=$0} END{print b}' < ${emd}/tmp.txt | tr -d '"' | awk '{print $1,$2,$3}' | sed -e 's/ */ ; /g')
iteration=$(cut -d ';' -f1 <<< ${gmm_data} | tr -d ' ')
CC=$(awk '/^CC /{print $2}' ${emd}/${iteration}/gmmscore_threshold)
echo "${emd} ; ${w} ; ${res} ; ${res_method} ; ${gmm_data} ; ${CC}"
done
0% Loading or .
You are about to add 0 people to the discussion. Proceed with caution.
Finish editing this message first!
Please register or to comment