From e7ce5a8738d19336986d61d52a8080fe7cb3eefb Mon Sep 17 00:00:00 2001
From: Cezary Czaplewski <czarek@chem.univ.gda.pl>
Date: Sun, 17 Sep 2017 23:48:57 +0200
Subject: [PATCH] multichain refine ssbond

---
 django_simple/todo/jobfiles.py |   13 ++++++++-----
 files/cluster2allatom.sh       |   23 ++++++++++++++++++-----
 2 files changed, 26 insertions(+), 10 deletions(-)

diff --git a/django_simple/todo/jobfiles.py b/django_simple/todo/jobfiles.py
index be88312..a569298 100644
--- a/django_simple/todo/jobfiles.py
+++ b/django_simple/todo/jobfiles.py
@@ -255,15 +255,18 @@ CUTOFF=7.00000 WCORR4=0.00000
         pbs = '#PBS -l nodes='+str(nodes)+':ppn=4+1:ppn='+str(reszta)
         
       tmp_ss=''
-      ix=0
-      if seq[0]=='X':
-       ix=1
       if instance.ssbond!='':
+        ix=[]
+        ii=0
+        for i in range(0,len(seq)):
+           if seq[i]=='X':
+              ii=ii+1
+           ix.append(ii)
         l=[]
         ss=json.loads(instance.ssbond)
         for e in ss:
-           l.append(e[0]-ix)
-           l.append(e[1]-ix)
+           l.append(e[0]-ix[e[0]])
+           l.append(e[1]-ix[e[1]])
         tmp_ss=' '.join(map(str,l))
 
       os.chdir(instance.jobdirname)
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*
-- 
1.7.9.5