create table of content

console.log( '\n\n\n # Table of contents\n\n' + Array.from(document.querySelectorAll('h1 > a, h2 > a, h3 > a')).map((a) => ( {'H1':' * ','H2':' * ','H3':' - '}[a.parentNode.tagName] + `[${a.parentNode.innerText.trim()}](${a.hash})` )).join('\n') + '\n\n\n' );

calculate secondary struture percent for each residue

> secstruct :69-91 out ss_per_res_prod.dat sumout dssp_prod.agr  #type this command in cpptraj windo after loading parm and traj

gnuplot in the terminal

set terminal dumb size 120, 30
set autoscale
plot 'file.dat' u 1:2

adding something to each numbers of a column

awk -v s=23 '{print $1+s, $2, $3, $4, $5}' csp_satisfied_in_medoid_TP_0.dat >csp_satisfied_in_medoid_TP_0_fixed.dat

add chain code in a pdb

sed 's/^\(ATOM.\{17\}\) /\1A/' x.pdb

upload something on remote github

fork the base directory from github. by that i will have a forked repo in my github
then upload the files to relevant directory in the forked repo(or we can do git push to forked one)
then go the original repo and do pull request ---base should be the original one and head should be the forked one with new files

to paste two file with their alternate line

paste -d \\n file2 file1

to put comma after each letter in a string

sed 's/\(.\{1\}\)/\1,/g' sequence.dat >a.dat

using sublime text

ctrl +a to select all
ctrl +shift +l to take curser to end of each line
shift + 'arrow' to move curser together

replace username@hostname with some shortcut for ssh login

go to you local .ssh directory (/home/name/.ssh for ubuntu and /User/name/.ssh for mac)
create a file names 'config' and inside it write --
------
Host x (whatever you want to use for ss login)
HostName hpg2.rc.ufl.edu
User yourusername
Port 2222
UseKeychain yes
------
now you can log in using 'ssh x' instead of 'ssh yourusername@hpg2.rc.ufl.edu'

setting up passphrase for ssh login

Step1...go to local .ssh directory and then type "ssh-keygen"
it will print a line saying 'enter file in which to save the key--just hit 'enter'
then it will ask for passphrase..type it hit enter and retype it.
Step2..cp id_rsa.pub to your authorized_keys in .ssh directory
Step3.. ssh-copy-id username@hostname
then it will ask for the password for log in..
Then it is all set..from next time it will ask to put the passphrase

set up serial/line number in a vi file

%s/^/\=printf('%-3d ', line('.'))

convert multiple blank line to single blank line

cat -s

put pending job on hold and then release them

scontrol hold job_id                  ##it will make priority 0 and will not run until we release it
scontrol release job_id               ##it will release the the job

how to transfter data between two remote server

1. log in to a server where you want to copy the data
2. scp -r arup.mondal@hpg2.rc.ufl.edu:/ufrc/alberto.perezant/arup.mondal/move.sh chemistry/
use -r for for another remote server, then use the server name and path for the file and then in the end the 
desitination in the currect logged in server

unmount

fusermount -u orange/

convert a color pdf to b/w pdf

gs \
 -sOutputFile=output.pdf \
 -sDEVICE=pdfwrite \
 -sColorConversionStrategy=Gray \
 -dProcessColorModel=/DeviceGray \
 -dCompatibilityLevel=1.4 \
 -dNOPAUSE \
 -dBATCH \
 input.pdf

extracting energy values from post analysed file in amber

awk -f get_energy.awk file

##file is

BEGIN{
    s = 0
}
{
    if ($0 ~ /^ BOND/) {
        s += $3 + $6 + $9
    }
    if ($0 ~ /^ VDWAALS/) {
        s += $3 + $6 + $9
    }
    if ($0 ~ /^ 1-4 VDW/) {
        s += $4 + $8 + $11
        printf "%f \n", s
        s = 0 
    }
}

blank line after each line(alternate blank line)

sed -e 'G' a.dat

swap two columns

%s/\v^(\S+)\s+(\S+).*$/\2 \1/

delete all blank lines

:g/^$/d

gnuplot

module load gnuplot
gnuplot
plot "trial_4_res_87_300K/topten.dat" ,  "trial_4_res_87_350K/topten.dat" , "trial_4_res_87_400K/topten.dat" , "trial_4_res_350_300K/topten.dat" , "trial_4_res_350_350K/topten.dat" , "trial_4_res_350_400K/topten.dat" , "trial_4_res_700_300K/topten.dat" , "trial_4_res_700_350K/topten.dat" , "trial_4_res_700_400K/topten.dat"

I do not know what this command was for

cut -d ' ' --complement -f -10 paste.dat

deleting some space separated column

cut -d" " -f1,2 T0968s2_ECs.txt >contacts.dat

appending files columnwise

paste rmsd.txt p.dat | column -s $'\t' -t

visualizing replica exchange

analyze_remd visualize_trace
analyze_remd visualize_fup

extracting the last pdb from traj


extract_trajectory extract_last last  #it will save pdbs as last.00.pdb.........last.30.pdb

meld with NMR data

getting rmsd using cpptraj

trajin step4_1.nc 1 500 1
parm clean_update.pdb
reference clean_update.pdb parm clean_update.pdb
autoimage :1-170
rms reference :3-165.CA :3-165.CA out rmsd_test.plo
rms reference :100.CA :100.CA nofit out rmsd_test2.plo
trajout testrmsd.pdb onlyframes 500
run
quit

deleteing any common thing from a vi file globally

:%s/_[A-Z]//g

checking resoures available for group

sacctmgr show qos alberto.perezant format="Name%-16,GrpSubmit,MaxWall,GrpTres%-45"

space separated to tab

sed 's/ /\t/g' test.log

deleting some tab separated columns

cut -f1,2 tab_ec.txt   #it will keep column 1 and 2 and will dlt everything else

tab separated to space separated

sed 's/\t/ /g' test_ec.txt

adding prefix and suffix

sed 's/^/I am a /; s/$/ 128... [}/' file.txt

add multiple linux account

go to users and then allow it to be chane by hitting unlock button then click on add user.

checking the priority of submitted job

squeue -o "%.18i %.9P %.8j %.8u %.2t %.10M %.6D %R %p %Q" |egrep "lijun|arup|alberto"
squeue -o "%.18i %.9P %.8j %.8u %.2t %.10M %.6D %R %p %Q" |egrep "lijun|arup|alberto" |grep " R "  |wc -l

deleting blank space in the begining of lines in a vi file

:%s/^ \+//g        # space after ^ is important. depneding on number of space you need to dlt, in command oyu should use that many space, and for selected area say line m to n....:m,ns/^ \+//

login to desktop from mac

ssh arup@am.yyrcd.com

installing sshfs in mac

xcode-select --install
ruby -e "$(curl -fsSL https://raw.githubusercontent.com/Homebrew/install/master/install)" < /dev/null 2> /dev/null ; brew install caskroom/cask/brew-cask 2> /dev/null
brew cask install osxfuse
brew install sshfs

removing space from .png and adding multiple png file

convert input.png -trim output.png

convert +append 1st.png 2nd.png final.png

making a column from a string and number them

for a in `cat binary.txt `
do echo $a
done                    #for numberig just do nl myfile

adding a constant integer to all number of a vi file

ctrl-v to and drag mouse to select all the numbers(those numbers you want to add integer to)
shift+colon
#some <> sign will show there and it s=hould be erased
then add :%s/\d\+/\=submatch(0)+1/g   #1 because I wanted to add 1

jnb in hipergator

ssh -L 2018:localhost:2018 arup.mondal@hpg2.rc.ufl.edu

installing vmd in ubuntu

#download vmd file from official site
cd Downloads
tar xvf ......tar.gz #eventhouth it's .gz, it is not a zip file
cd vmd-1.9.3
./configure LINUXAMD64  #before this sometime we might need to do $install_bin_dir and $install_library_dir
cd src
sudo apt-get update #for 1st time, other wise 'make' can not be installed
sudo apt-get install make 
sudo make install

space after one character in vi file

:%s/\(.\)/\1 /g      #apace after 1 is important and one . is for one spacing after 1 character

search and replace a string

:s/[A-Z]/new/g   # for replacing all character not number

regular expression with python

import re 
text="MNQSRRILRTVYLSLFLIGLFMLINDIFSSNILSSKSSDKEVQFDLNKSFDDNEMSSVKSNSFNLINKSQDIIVETGIYVATFSTFKGNLVSLKLKNHLNLEKNPTDLINIDRKNETFFDISFDYFVDDLFLYKKIDDFNHEFKAYFKNNGKTYEYVKKYTFSKKDEYLMQFKVTVNGLEDYNLFDFDSYKIIFSSEIERLSDKAKLQYNNYLSQIIYYDNKLKYGKDGLRINNPRWIGSSTKYFGVLVSKENMEVEFKKERGTLKSFIINNVRNKKNISDEFFIYAGPKDNRYLDVFDKRDDNTFGLFDIFFGMSVEKSFWYLIQVPMQMVMQVFYDVIPNWGLSIIFLTIVVRILIFPLTFKGFRATAELSKLQPKMKELQAKFKHDPKKLNEEMGRLYKEEGVNPLGGCLPVILQLPIFFALYSLVNNLFLLRGASFIPGWIDDLSIGDSVYHFGYKLYFVSWTDIRILPFIMMFTQLGSTIVSSNMDLKNLGAQQKFLYFGMPIMFFFILYNMPSGLLIYWITTNIFTILQQYYIKMHLS"
result = re.findall(r"L[A-Z]{1,5}Q[A-Z]{1,5}K$", text)
print(result)

Search a motif:: regular expression

K[A-Z]{1,5}X[A-Z]{1,5}P  #crtl+f then select regex then type this command
[K/R][A-Z]{1,5}[Y/F][A-Z]{1,5}[V/L] #CARC domain
[V/L][A-Z]{1,5}Y[A-Z]{1,5}[K/R] #CRAC domain

reverse the order of all caharcter in all line

sed '/\n/!G;s/\(.\)\(.*\n\)/&\2\1/;//D;s/.//' filename

appending file

cat file.out >> CRAC_CARC.dat

replace a character in a certain range of a vi file

:n-line/m-lines/old/new/g

meld restart after time out

prepare_restart --prepare-run (#then submit the jobscript again)

meld adding frame

import pickle
import shutil
from meld.system import restraints

# backup old files
shutil.copy("remd_runner.dat", "remd_runner.dat.before_extend")
shutil.copy("system.dat", "system.dat.before_extend")

# add an extra 500 ns
runner = pickle.load(open("remd_runner.dat", "rb"))
runner._max_steps += 10000
pickle.dump(runner, open("remd_runner.dat", "wb"))
#this script should be run in Data/Backup directory

meld extract last trajectory

extract_trajectory extract_last last (#will be saved last.00.pdb , last.01.pdb..)

Using Rosetta

#minimization

relax.static.linuxgccrelease -database /ufrc/alberto.perezant/arup.mondal/Source/Rosetta/rosetta_bin_linux_2019.14.60699_bundle/main/database -s S_00000937.pdb -relax:fast

#fargment picking

fragment_picker.static.linuxgccrelease -in::file::vall /ufrc/alberto.perezant/arup.mondal/Source/Rosetta/rosetta_bin_linux_2019.14.60699_bundle/main/database/sampling/filtered.vall.dat.2006-05-05.gz -in::file::fasta seq.fa -frags::ss_pred seq.ss2 psipred

#Extracting pdb from silent file

extract_pdbs.static.linuxgccrelease -in::file::silent default.out -in::file::tags S_00000025

2d scatter plot

import numpy as np
import os
import pandas
import matplotlib
matplotlib.use('Agg')
from matplotlib import pyplot
aa = np.loadtxt('trimer_matrix.txt')
num = np.loadtxt('trimer_modified_clean.txt')
pyplot.figure()
pyplot.imshow(aa,cmap='Greys',alpha=0.8,vmin=0)
pyplot.scatter(num[0],num[1],c=num[2],cmap='cool',s=num[2])
pyplot.savefig('trimer.png')

list to matrix

import numpy as np
from pandas import DataFrame as df
import sys
aa = np.loadtxt('pdb_modified_clean.txt')
aa.shape
out_matrix = np.zeros( (443,443) )
for i in aa[:,:3]:
    if float(i[2]) > 0:
        out_matrix[int(i[0]),int(i[1])] = i[2]
        out_matrix[int(i[1]),int(i[0])] = i[2]
np.savetxt('out_matrix.txt',out_matrix)

ignoring nearby contacts

import numpy as np
from pandas import DataFrame as df
import sys
num = np.loadtxt('pdb_modified.txt')
sys.stdout=open("pdb_modified_clean.txt","w")
for i in num[:,:3]:
    if abs(i[0]-i[1]) > 3:
        print(int(i[0]),int(i[1]),float(i[2]))
sys.stdout.close()

add a constant integer

import numpy as np
import sys
aa = np.loadtxt('out.txt')
sys.stdout=open("1stcolumn.txt","w")
for i in aa[:,:3]:
    if int(i[0]) > 33:
        i[0] = i[0]+18
        
        print(int(i[0]),int(i[1]),float(i[2]))
        
    else:
              
        i[0]=i[0]
        
        print(int(i[0]),int(i[1]),float(i[2]))
        
sys.stdout.close()
bb = np.loadtxt('1stcolumn.txt')
sys.stdout=open("2ndcolumn.txt","w")
for i in bb[:,:3]:
    if int(i[1]) > 33:
        i[1] = i[1]+18
        
        print(int(i[0]),int(i[1]),float(i[2]))
        
    else:
              
        i[1]=i[1]
        
        print(int(i[0]),int(i[1]),float(i[2]))
        
sys.stdout.close()
cc = np.loadtxt('2ndcolumn.txt')
sys.stdout=open("1stcolumn1.txt","w")
for i in cc[:,:3]:
    if int(i[0]) > 360:
        i[0] = i[0]+22
        
        print(int(i[0]),int(i[1]),float(i[2]))
        
    else:
              
        i[0]=i[0]
        
        print(int(i[0]),int(i[1]),float(i[2]))
        
sys.stdout.close()
dd = np.loadtxt('1stcolumn1.txt')
sys.stdout=open("2ndcolumn1.txt","w")
for i in dd[:,:3]:
    if int(i[1]) > 360:
        i[1] = i[1]+22
        
        print(int(i[0]),int(i[1]),float(i[2]))
        
    else:
              
        i[1]=i[1]
        
        print(int(i[0]),int(i[1]),float(i[2]))
        
sys.stdout.close()

change datashape from matrix to list

import numpy
aa = numpy.loadtxt('contact.dat')
aa
aa.shape
for i in range(464):
    for j in range(464):
        print(i,j,aa[i,j])

using rosetta

#exporting path

export PATH="$PATH:/ufrc/alberto.perezant/arup.mondal/Source/Rosetta/rosetta_bin_linux_2019.14.60699_bundle/main/source/bin"

#to get score of a pdb

score.static.linuxgccrelease -in:file:s *****.pdb -in:file:fullatom

#to replace HIE with HIS

for a in unique.c*.pdb;
do
sed 's/HIE/HIS/g' $a >TEMP/$a;
done

#to get 2nd column

awk '{print $NF,$2}' default.sc > my_score.txt

#to cut some line from below after a xxxx line

head -xxxx unique.c0.pdb |tail

#to cut some lines in starting upto a certain line YYYY (as well as from below)

head -xxxx unique.c0.pdb |tail -(xxxx-yyyy) |head

#to do that in a script

for a in unique.c*.pdb ;
do 
head -2757 $a |tail -2613 > TEMP2/$a;
done

open a .tgz file

tar xvzf file.tgz

vmd

resid number means whatever written in the pdb file next to the amino acid
residue number means it will count the 1st amino acid in pdb as zeroth amino acid and it will count continuously no matter what is written next to each amino acid.

space after 3 characters

sed 's/.\{3\}/& /g' originalfile >newfile

removing column

awk 'NF{NF-=1};1' <ec.txt >ec.dat

restart to pdb

$AMBERHOME/bin/ambpdb -p cram.prmtop -c min_qmmm.rst > min_qmmm.rst.pdb

sshfs

sshfs arup.mondal@hpg2.rc.ufl.edu:/ufrc/alberto.perezant/arup.mondal Mountpoint

float to int

from __future__ import division
import matplotlib.pyplot as plt
import numpy as np
import sys
#import pandas as pd
from pylab import plot, ylim, xlim, show, xlabel, ylabel, grid
from numpy import linspace, loadtxt, ones, convolve
filename= 'contacts.dat'

f = open(filename, "r")
lines = f.readlines()
time=[]
energy =[]
#running_std=[]
for line in lines:
	line = line.strip()
	line = line.split(" ")
	line = [float(i) for i in line if i!=""]
	time.append(int(line[0]))
	energy.append(int(line[1]))
#	running_std.append(np.std(energy))
print(time)
print(energy)

file = open("testfile.dat","w") 

for i in range(len(time)):
    file.write('%d %d\n'%(time[i], energy[i]))

file.close()