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Add some trajectory analysis scripts

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cryobry
2018-06-10 23:07:04 -04:00
parent dbb3bcb3ce
commit d28cafc5b6
11 changed files with 1221 additions and 0 deletions
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53
trajectory_analysis/3-cluster.sh Executable file
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#!/usr/bin/env bash
#######################################################################################
## ADJUSTABLE PARAMETERS ##
#######################################################################################
# set folder name that contains the jobs
job_folder="4-new_jobs"
#######################################################################################
## CLUSTER ANALYSIS ##
#######################################################################################
out_dir="$(basename ${0})"
out_dir="${out_dir%%.*}"
# create array of systems
function get_systems() {
systems=()
all_systems=()
_jobs=( $(ls -d ../${job_folder}/*/*/) )
for _job in ${_jobs[@]}; do
all_systems+=( $(basename ${_job}) )
done
systems+=( $(for _system in ${all_systems[@]}; do echo ${_system}; done | sort -u) )
}
get_systems
for system in ${systems[@]}; do
mkdir -p ${out_dir}/median/${system}
mkdir -p ${out_dir}/average/${system}
# median clusters
# on SrtA
( echo 'chA_&_CA_&_r_66-205' 'System' | gmx cluster -f 1-concat/combined/${system}-*.trr -s 1-concat/combined/${system}-*.pdb -n 2-ndx/${system}.ndx -g ${out_dir}/median/${system}/${system}.log -cutoff 0.2 -fit -method gromos -o ${out_dir}/median/${system}/${system}.xpm -dist ${out_dir}/median/${system}/${system}.xvg -cl ${out_dir}/median/${system}/${system}.pdb ) &
# on ligand
( echo 'chB' 'System' | gmx cluster -f 1-concat/combined/${system}-*.trr -s 1-concat/combined/${system}-*.pdb -n 2-ndx/${system}.ndx -g ${out_dir}/median/${system}/${system}_ligand.log -cutoff 0.2 -fit -method gromos -o ${out_dir}/median/${system}/${system}_ligand.xpm -dist ${out_dir}/median/${system}/${system}_ligand.xvg -cl ${out_dir}/median/${system}/${system}_ligand.pdb ) &
# average clusters
# on SrtA
( echo 'chA_&_CA_&_r_66-205' 'System' | gmx cluster -f 1-concat/combined/${system}-*.trr -s 1-concat/combined/${system}-*.pdb -n 2-ndx/${system}.ndx -g ${out_dir}/average/${system}/${system}_av.log -cutoff 0.2 -fit -method gromos -o ${out_dir}/average/${system}/${system}_av.xpm -dist ${out_dir}/average/${system}/${system}_av.xvg -av -cl ${out_dir}/average/${system}/${system}_av.pdb ) &
# on ligand
( echo 'chB' 'System' | gmx cluster -f 1-concat/combined/${system}-*.trr -s 1-concat/combined/${system}-*.pdb -n 2-ndx/${system}.ndx -g ${out_dir}/average/${system}/${system}_ligand_av.log -cutoff 0.2 -fit -method gromos -o ${out_dir}/average/${system}/${system}_ligand_av.xpm -dist ${out_dir}/average/${system}/${system}_ligand_av.xvg -av -cl ${out_dir}/average/${system}/${system}_ligand_av.pdb ) &
wait
done