JonasR

## calc.py
#!/usr/bin/env python

from __future__ import division
import pymongo as pym
import datetime as dt
import codecs
import re
import sys
import matplotlib.pyplot as plt
import numpy as np

## README.md

      
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                JonasR
                / README.md
            
            
              Last active
              August 29, 2015 14:14
            
              
                ANN OP<->ED swaps: https://anime.stackexchange.com/questions/17003/has-there-been-a-anime-that-used-its-op-as-ed-and-or-vice-versa
              
          
    Requires database set up with maintaindb.py.

  
## gist:2919934
#!/bim/bash

echo "This even allows versioning and forking!"

## gist:2944226
>P06865
MTSSRLWFSLLLAAAFAGRATALWPWPQNFQTSDQRYVLYPNNFQFQYDVSSAAQPGCSV
LDEAFQRYRDLLFGSGSWPRPYLTGKRHTLEKNVLVVSVVTPGCNQLPTLESVENYTLTI
NDDQCLLLSETVWGALRGLETFSQLVWKSAEGTFFINKTEIEDFPRFPHRGLLLDTSRHY
LPLSSILDTLDVMAYNKLNVFHWHLVDDPSFPYESFTFPELMRKGSYNPVTHIYTAQDVK
EVIEYARLRGIRVLAEFDTPGHTLSWGPGIPGLLTPCYSGSEPSGTFGPVNPSLNNTYEF
MSTFFLEVSSVFPDFYLHLGGDEVDFTCWKSNPEIQDFMRKKGFGEDFKQLESFYIQTLL
DIVSSYGKGYVVWQEVFDNKVKIQPDTIIQVWREDIPVNYMKELELVTKAGFRALLSAPW
YLNRISYGPDWKDFYIVEPLAFEGTPEQKALVIGGEACMWGEYVDNTNLVPRLWPRAGAV
AERLWSNKLTSDLTFAYERLSHFRCELLRRGVQAQPLNVGFCEQEFEQT

## gist:2944236
M1V
L39R
C58Y
L127R
R170W
R178H
S210F
D258H
L451V
E482K

## gist:2944224
P06865 1 M V
P06865 39 L R
P06865 58 C Y
P06865 127 L R
P06865 170 R W
P06865 178 R H
P06865 210 S F
P06865 258 D H
P06865 451 L V
P06865 482 E K

## prepareFiles.pml
###Create base file
fetch 2gjx
select chainA, chain A
select rest, not chainA
remove rest

select firstDomain, resi 1-166
select secondDomain, not firstDomain
remove firstDomain
zoom secondDomain

## allmuts_*.sh
#!/bin/bash

for i in R178H R178C P183L D207E S293I F434L L451V E482K L484Q E506D; do
        perl prepForSQRWL2.pl -i 2gjxA_sequence -mut $i > SCWRL_$i.sequence
done

for i in R178H R178C P183L D207E S293I F434L L451V E482K L484Q E506D; do
        /opt/SS12-Practical/scwrl4/Scwrl4 -s SCWRL_$i.sequence -i ../2gjxA_secondD.pdb -o SCWRL_$i.pdb &>> SCWRL.log
done

## prepForSQRWL2.pl
#!/usr/bin/perl


use Getopt::Long;
our $opt_f = ();

sub usage {
        printf "Usage: $0 [flags] file...\n";
        printf "flags:\n";

## run.txt
<TITLE>FOLDX_runscript;
<JOBSTART>#;
<PDBS>#;
<BATCH>list.txt;
<COMMANDS>FOLDX_commandfile;
<BuildModel>#,individual_list.txt;
<END>#;
<OPTIONS>FOLDX_optionfile;
<Temperature>298;
<R>#;
	#!/usr/bin/env python

	from __future__ import division
	import pymongo as pym
	import datetime as dt
	import codecs
	import re
	import sys
	import matplotlib.pyplot as plt
	import numpy as np
	>P06865
	MTSSRLWFSLLLAAAFAGRATALWPWPQNFQTSDQRYVLYPNNFQFQYDVSSAAQPGCSV
	LDEAFQRYRDLLFGSGSWPRPYLTGKRHTLEKNVLVVSVVTPGCNQLPTLESVENYTLTI
	NDDQCLLLSETVWGALRGLETFSQLVWKSAEGTFFINKTEIEDFPRFPHRGLLLDTSRHY
	LPLSSILDTLDVMAYNKLNVFHWHLVDDPSFPYESFTFPELMRKGSYNPVTHIYTAQDVK
	EVIEYARLRGIRVLAEFDTPGHTLSWGPGIPGLLTPCYSGSEPSGTFGPVNPSLNNTYEF
	MSTFFLEVSSVFPDFYLHLGGDEVDFTCWKSNPEIQDFMRKKGFGEDFKQLESFYIQTLL
	DIVSSYGKGYVVWQEVFDNKVKIQPDTIIQVWREDIPVNYMKELELVTKAGFRALLSAPW
	YLNRISYGPDWKDFYIVEPLAFEGTPEQKALVIGGEACMWGEYVDNTNLVPRLWPRAGAV
	AERLWSNKLTSDLTFAYERLSHFRCELLRRGVQAQPLNVGFCEQEFEQT
	P06865 1 M V
	P06865 39 L R
	P06865 58 C Y
	P06865 127 L R
	P06865 170 R W
	P06865 178 R H
	P06865 210 S F
	P06865 258 D H
	P06865 451 L V
	P06865 482 E K
	###Create base file
	fetch 2gjx
	select chainA, chain A
	select rest, not chainA
	remove rest

	select firstDomain, resi 1-166
	select secondDomain, not firstDomain
	remove firstDomain
	zoom secondDomain
	#!/bin/bash

	for i in R178H R178C P183L D207E S293I F434L L451V E482K L484Q E506D; do
	perl prepForSQRWL2.pl -i 2gjxA_sequence -mut $i > SCWRL_$i.sequence
	done

	for i in R178H R178C P183L D207E S293I F434L L451V E482K L484Q E506D; do
	/opt/SS12-Practical/scwrl4/Scwrl4 -s SCWRL_$i.sequence -i ../2gjxA_secondD.pdb -o SCWRL_$i.pdb &>> SCWRL.log
	done
	#!/usr/bin/perl


	use Getopt::Long;
	our $opt_f = ();

	sub usage {
	printf "Usage: $0 [flags] file...\n";
	printf "flags:\n";
	<TITLE>FOLDX_runscript;
	<JOBSTART>#;
	<PDBS>#;
	<BATCH>list.txt;
	<COMMANDS>FOLDX_commandfile;
	<BuildModel>#,individual_list.txt;
	<END>#;
	<OPTIONS>FOLDX_optionfile;
	<Temperature>298;
	<R>#;