projects
/
django_unres.git
/ blobdiff
commit
grep
author
committer
pickaxe
?
search:
re
summary
|
shortlog
|
log
|
commit
|
commitdiff
|
tree
raw
|
inline
| side by side
multichain refine ssbond
[django_unres.git]
/
files
/
cluster2allatom.sh
diff --git
a/files/cluster2allatom.sh
b/files/cluster2allatom.sh
index
54a4dfb
..
639ac2a
100755
(executable)
--- a/
files/cluster2allatom.sh
+++ b/
files/cluster2allatom.sh
@@
-1,7
+1,7
@@
#!/bin/bash
# to use you need syntax ./cluster2allatom.sh YOUR_CLUSTER_FILENAME
file=$1
#!/bin/bash
# to use you need syntax ./cluster2allatom.sh YOUR_CLUSTER_FILENAME
file=$1
-sed -n '/ENERGY/,/TER/p' $file |sed 's/CB /SC /' >tmp.pdb
+sed -n '/ENERGY/,/ENDMDL/p' $file |sed 's/CB /SC /' >tmp.pdb
numstruc=`grep ENERGY tmp.pdb|wc -l`
allline=`cat tmp.pdb|wc -l`
onestruc=`echo $allline "/" $numstruc| bc -l|sed 's/\.0*//'`
numstruc=`grep ENERGY tmp.pdb|wc -l`
allline=`cat tmp.pdb|wc -l`
onestruc=`echo $allline "/" $numstruc| bc -l|sed 's/\.0*//'`
@@
-11,13
+11,26
@@
echo $i $onestruc
headval=`echo $i "*" $onestruc|bc -l`
head -n $headval tmp.pdb | tail -n $onestruc >act.pdb
headval=`echo $i "*" $onestruc|bc -l`
head -n $headval tmp.pdb | tail -n $onestruc >act.pdb
+rm -f act_file*
+cat act.pdb | tr '\n' '\r' | sed -e 's/TER\rTER/TERTER/' | tr '\r' '\n' \
+ | awk 'BEGIN{f=1}/TERTER/{close("act_file"f);f++}{ if ($0!="TERTER") print $0 > "act_file"f}'
+
+ for f in act_file*
+ do
#change the pulchra directory for each server acordingly
#change the pulchra directory for each server acordingly
-/users2/local/pulchra306/pulchra -q -g act.pdb
+ /users2/local/pulchra306/pulchra -q -g $f
+ done
+
+cat act_file*.rebuilt.pdb |grep -v TER |grep -v END > tmp1.pdb
+
+/users2/local/mmtsb/perl/convpdb.pl -renumber 1 -out generic tmp1.pdb > act.rebuilt.pdb
+
halfi=`echo $i/2|bc`
halfi=`echo $i/2|bc`
-#mv act.rebuilt.pdb MODEL${halfi}_pulchra.pdb
-/users2/local/scwrl4/Scwrl4 -h -i act.rebuilt.pdb -o MODEL${halfi}.pdb
+#mv act.rebuilt.pdb MODEL${halfi}_pulchra.pdba
+/users2/local/scwrl4/Scwrl4 -h -i act.rebuilt.pdb -o tmp2.pdb
#tmscore MODEL${i}a.pdb ../template_1.pdb > tmscore${i}a.txt
#tmscore MODEL${i}a.pdb ../template_1.pdb > tmscore${i}a.txt
+awk 'BEGIN{oxt=0}{if (substr($0,14,3)=="OXT") oxt=int(substr($0,24,3)); if (int(substr($0,24,3))>oxt && oxt>0) {print "TER";print $0;oxt=0} else print $0}' tmp2.pdb > MODEL${halfi}.pdb
done
done
-rm tmp.pdb act.pdb act.rebuilt.pdb
+rm tmp.pdb tmp1.pdb tmp2.pdb act.pdb act.rebuilt.pdb act_file*