nathanmlim

// Use Gists to store code you would like to remember later on
console.log(window); // log the "window" object to the console

nathanmlim

############################################################################
# DESCRIPTION:
#
# VMD startup script.  The commands here are executed as soon as VMD starts up
############################################################################

# turn on lights 0 and 1
light 0 on
light 1 on
light 2 off

nathanmlim

#!/bin/bash
input="prep"
for fname in *-${input}.oeb.gz; do
    molid="${fname%%-${input}.oeb.gz}"
    echo Submitting molecule $molid
    sbatch -J "$molid" gpu_floe.slurm
    sleep 2
done

nathanmlim

find . -maxdepth 1 -type d -exec bash -c "echo -ne '{}\t'; ls '{}' | wc -l" \; |   awk -F"\t" '$NF<=2{print $1}' >> cleanup.txt
while read p; do echo $p; rm -rf $p ; done <cleanup.txt

nathanmlim

for i in *-prod01-truncated.oeb.gz; do 
    suffix=${i%-prod01-truncated.oeb.gz}
    qsub -N ${suffix} gpu_floe-blues.pbs
done

nathanmlim

import mdtraj as md

def centerTrajectory(traj,outfname):
    nosolv = traj.remove_solvent()
    anchor = nosolv.top.guess_anchor_molecules()[0]
    imgd = nosolv.image_molecules(anchor_molecules=[anchor])
    prt_idx = imgd.top.select('protein')
    superposed = imgd.superpose(reference=imgd,frame=0,atom_indices=prt_idx)
    superposed.save_dcd(outfname+'-centered.dcd')
    superposed[0].save_pdb(outfname+'-centered.pdb')

nathanmlim

#!/bin/sh

for fn in *-centered.dcd; do
    molid=${fn%*-107*-blues00*}
    echo $molid
    mkdir "$molid" && cp $fn $molid
done

nathanmlim

#!/bin/bash
for fn in *.local/*.log; do 
    file=$( basename $fn )
    pjobid=${fn%.tscc-mgr.local/*}
    molid=${file%*-blues00*}
    outfname="$molid-$pjobid-blues00.log"
    cp $fn centered/$outfname
done

nathanmlim

setfacl -m u:username:rwx myfolder

nathanmlim

import subprocess, os, glob

cwd = os.getcwd()
nc_files = glob.glob('nc_traj/*.nc')

for nc in nc_files:
    l = nc.split('/')
	fn = l[1].strip('pEH_l').split('-')
	molid = fn[0]
	suffix = fn[1].strip('.nc')