X-Git-Url: http://mmka.chem.univ.gda.pl/gitweb/?a=blobdiff_plain;f=files%2Fcluster2allatom.sh;fp=files%2Fcluster2allatom.sh;h=639ac2a0100ea65ad0bb2ae07660b5f0e499bffa;hb=e7ce5a8738d19336986d61d52a8080fe7cb3eefb;hp=54a4dfbb57eaaa4e858a9dc81e7f32691232d35a;hpb=79b5efa813414f99e23a4fefa0b360be6b5c17a6;p=django_unres.git

diff --git a/files/cluster2allatom.sh b/files/cluster2allatom.sh
index 54a4dfb..639ac2a 100755
--- 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
-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*//'`
@@ -11,13 +11,26 @@ echo $i $onestruc
 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
-/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 $i/2|bc`
-#mv act.rebuilt.pdb  MODEL${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
 
+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
-rm tmp.pdb act.pdb act.rebuilt.pdb 
+rm tmp.pdb tmp1.pdb tmp2.pdb act.pdb act.rebuilt.pdb  act_file*