docuementation

README.md

@@ -39,11 +39,13 @@ ${SRC_DIR}/recursive_gmconvert.sh -f map_filename -t threshold -n num_gaussians
 
 `-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`.
 `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:
 

make_benchmark_table.sh

-#!/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